Contacts of the helix formed by residues 111 - 141 (chain A) in PDB entry 5X11
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 1.3 78.0 - - - +
112A GLU* 1.3 65.8 + - + +
114A SER* 3.2 8.8 + - - -
115A ASP* 3.0 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER 4.4 8.5 - - - +
110A ARG 3.3 4.9 + - - +
111A GLN* 1.3 80.4 - - + +
113A ALA* 1.3 55.8 + - - +
115A ASP* 3.5 6.7 + - - +
116A LEU* 3.1 29.2 + - - +
81B HIS* 3.4 36.7 + - - -
85B ILE* 3.8 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.9 32.3 - - + +
110A ARG* 3.6 9.6 + - - +
111A GLN 3.3 0.6 - - - -
112A GLU* 1.3 75.4 - - - +
114A SER* 1.3 65.7 + - - +
116A LEU* 3.6 6.5 + - - -
117A PHE* 2.9 34.2 + - + +
179A ILE* 5.9 4.5 - - + -
147B PHE* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG 3.2 13.7 + - - -
111A GLN* 3.2 12.7 + - - -
113A ALA* 1.3 74.7 - - - +
115A ASP* 1.3 54.2 + - - +
117A PHE* 3.3 2.1 + - - +
118A THR* 2.7 43.5 + - - -
176A LEU* 3.9 14.8 - - - +
179A ILE* 5.6 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN 3.0 15.4 + - - +
112A GLU* 3.8 7.2 - - - +
114A SER* 1.3 75.2 - - - +
116A LEU* 1.3 58.6 + - - +
118A THR* 3.2 6.3 + - - -
119A ASP* 2.9 32.8 + - - +
87B HIS* 4.2 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 4.0 18.5 - - + -
101A LYS* 4.3 25.1 - - + +
102A ALA* 6.2 0.2 - - - -
112A GLU 3.1 14.7 + - - +
113A ALA* 3.9 6.7 - - - +
115A ASP* 1.3 78.9 - - - +
117A PHE* 1.3 69.8 + - + +
119A ASP* 3.8 6.6 + - - +
120A GLN* 3.4 23.2 + - - +
84B LEU* 3.5 29.4 - - + +
85B ILE* 4.6 12.1 - - + +
86B ARG 4.1 16.2 - - - +
87B HIS* 4.9 11.0 + - + -
88B GLN 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.7 31.0 - + - -
102A ALA* 4.2 11.9 - - + -
105A ILE* 3.8 19.5 - - + -
113A ALA* 2.9 31.6 + - + +
114A SER 3.9 2.2 - - - +
116A LEU* 1.3 89.7 - - + +
118A THR* 1.3 55.1 + - - +
119A ASP 3.2 0.2 - - - -
120A GLN* 3.2 6.7 + - - +
121A LEU* 2.8 34.3 + - - +
171A TRP* 4.1 11.9 - + - -
172A LEU* 3.8 16.6 - - + +
175A ILE* 3.6 29.4 - - + -
176A LEU* 4.0 19.7 - - + +
156B LEU* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 2.7 30.6 + - - -
115A ASP* 3.7 6.7 - - - -
117A PHE* 1.3 71.7 - - - +
119A ASP* 1.3 57.8 + - - +
121A LEU* 3.2 4.5 + - + +
122A LEU* 3.0 29.6 + - + +
176A LEU* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP 2.9 10.4 + - - +
116A LEU* 3.9 5.8 - - - +
118A THR* 1.3 77.8 - - - +
120A GLN* 1.3 62.0 + - - +
122A LEU* 3.2 7.6 + - - +
123A LYS* 2.9 66.1 + - - +
87B HIS* 2.9 46.4 + - + +
88B GLN 4.8 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.5 42.5 - - + +
116A LEU* 3.4 13.9 + - - +
117A PHE 3.2 8.6 + - - +
119A ASP* 1.3 84.9 + - - +
121A LEU* 1.3 57.7 + - - +
123A LYS* 4.7 3.1 - - - +
124A ARG* 2.9 72.7 + - - +
172A LEU* 3.8 24.2 - - + -
88B GLN 4.9 7.7 + - - -
90B ILE* 4.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE 2.8 17.1 + - - +
118A THR* 3.4 11.0 - - + +
120A GLN* 1.3 72.7 - - - +
122A LEU* 1.3 51.7 + - - +
124A ARG* 3.7 1.0 - - - +
125A LYS* 2.8 43.7 + - + +
169A VAL* 4.9 5.0 - - + +
172A LEU* 3.9 19.4 - - + +
173A GLU* 5.8 6.1 - - + -
176A LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.0 14.5 + - + +
119A ASP* 3.2 10.5 + - - +
121A LEU* 1.3 76.8 - - - +
123A LYS* 1.3 63.0 + - + +
125A LYS* 3.4 9.5 + - - +
126A ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 2.9 48.3 + - - +
120A GLN* 4.0 4.7 - - - +
122A LEU* 1.3 76.7 - - + +
124A ARG* 1.3 58.8 + - - +
126A ALA* 3.3 8.1 + - - +
127A LYS* 3.0 26.9 + - - +
87B HIS* 4.0 12.1 - - - +
88B GLN 3.2 32.2 + - - +
89B PRO* 4.1 4.4 - - + +
90B ILE* 3.9 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASP* 4.4 7.9 + - - -
98A PHE* 5.3 0.4 - - - +
120A GLN* 2.9 49.0 + - - +
121A LEU 4.0 1.8 - - - +
123A LYS* 1.3 73.2 - - - +
125A LYS* 1.3 60.7 + - - +
127A LYS* 3.9 5.3 - - - +
128A LEU* 3.0 28.2 + - - +
164A ARG* 6.2 0.2 - - - +
165A GLU* 3.2 37.2 + - - +
168A TYR* 3.4 59.9 + - - -
169A VAL* 3.8 17.3 - - + +
172A LEU* 4.0 4.7 - - + -
90B ILE* 3.7 31.1 - - + +
91B PRO* 4.6 11.3 + - - +
94B VAL* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 2.8 23.5 + - + +
122A LEU* 3.6 9.0 - - - +
123A LYS 3.4 0.2 - - - -
124A ARG* 1.3 75.2 - - - +
126A ALA* 1.3 58.1 + - - +
128A LEU* 3.3 11.8 + - + +
129A SER* 3.0 26.9 + - - -
169A VAL* 4.0 23.3 - - + +
173A GLU* 5.3 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU 3.1 13.6 + - - +
123A LYS* 3.4 11.7 - - - +
124A ARG 3.3 0.2 - - - -
125A LYS* 1.3 74.2 - - - +
127A LYS* 1.3 64.9 + - - +
129A SER* 3.0 18.7 + - - -
130A ASP* 3.1 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 3.2 29.1 + - - +
123A LYS 3.0 15.9 + - - +
124A ARG* 3.9 4.9 - - - +
126A ALA* 1.3 75.8 - - - +
128A LEU* 1.3 57.0 + - - +
130A ASP* 3.6 7.7 + - + +
131A LEU* 3.1 33.1 + - + +
164A ARG* 4.3 4.0 - - - +
165A GLU* 3.5 28.8 + - + +
90B ILE* 3.0 27.6 - - + +
91B PRO 3.4 15.4 + - - -
92B GLU* 3.2 28.5 + - - +
94B VAL* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 3.0 18.1 + - - +
125A LYS* 3.4 9.4 - - + +
126A ALA 3.1 0.2 - - - -
127A LYS* 1.3 76.1 - - - +
129A SER* 1.3 59.9 + - - +
131A LEU* 3.1 4.6 + - + +
132A GLN* 2.9 40.0 + - - +
162A LEU* 3.7 28.5 - - + +
165A GLU* 3.9 11.4 - - + +
166A LYS* 3.8 37.0 - - + +
169A VAL* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS 3.0 12.9 + - - -
126A ALA* 3.0 12.3 + - - -
128A LEU* 1.3 76.4 - - - +
130A ASP* 1.3 61.3 + - - +
132A GLN* 3.5 6.5 + - - +
133A GLY* 3.1 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 3.1 11.2 + - - +
127A LYS* 3.8 11.2 - - + +
129A SER* 1.3 77.0 + - - +
131A LEU* 1.3 62.5 + - + +
133A GLY* 3.5 2.5 + - - +
134A SER* 3.2 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 4.4 17.3 - - + +
127A LYS* 3.1 30.5 + - + +
128A LEU 3.1 4.4 + - - +
130A ASP* 1.3 76.4 - - + +
132A GLN* 1.3 59.6 + - - +
134A SER* 3.4 6.4 + - - +
135A TYR* 3.0 27.7 + - - +
158A LEU* 4.1 25.5 - - + +
161A ALA* 3.7 30.3 - - + +
162A LEU* 4.2 14.9 - - + +
165A GLU* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 2.9 26.9 + - - +
129A SER* 3.7 7.4 - - - +
131A LEU* 1.3 73.7 - - - +
133A GLY* 1.3 65.2 + - - +
135A TYR* 3.1 15.5 + - + +
136A GLU* 3.0 43.2 + - + +
162A LEU* 4.0 26.9 - - - +
166A LYS* 4.4 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER 3.1 12.0 + - - -
130A ASP* 3.8 4.3 - - - -
131A LEU 3.3 0.2 - - - -
132A GLN* 1.3 78.8 - - - +
134A SER* 1.3 55.1 + - - +
136A GLU* 3.4 14.5 + - - +
137A LYS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP 3.2 16.7 + - - -
131A LEU* 3.7 8.7 - - - +
132A GLN 3.2 0.4 - - - -
133A GLY* 1.3 72.7 - - - +
135A TYR* 1.3 65.0 + - - +
137A LYS* 3.5 8.0 + - - +
138A LEU* 3.1 23.4 + - - +
154A HIS* 5.3 0.6 + - - -
158A LEU* 3.7 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 3.0 13.7 + - - +
132A GLN* 3.1 18.8 + - - +
134A SER* 1.3 77.2 - - - +
136A GLU* 1.3 65.9 + - + +
138A LEU* 3.5 4.6 + - + +
139A MET* 3.1 62.8 + - + +
155A TYR* 4.2 22.5 + + - -
158A LEU* 3.9 21.2 - - + +
159A THR* 4.3 14.3 - - + +
162A LEU* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLN* 3.0 33.9 + - + +
133A GLY* 3.7 12.0 - - - +
135A TYR* 1.3 85.1 - - + +
137A LYS* 1.3 63.2 + - - +
139A MET* 3.5 5.4 + - - +
140A ALA* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY 3.1 15.1 + - - +
134A SER* 3.6 12.1 - - - +
135A TYR 3.4 0.2 - - - -
136A GLU* 1.3 77.1 - - - +
138A LEU* 1.3 61.5 + - - +
140A ALA* 3.8 9.9 + - - +
141A SER* 3.8 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER 3.1 16.3 + - - +
135A TYR* 3.7 7.0 - - + +
136A GLU 3.3 0.2 - - - -
137A LYS* 1.3 76.7 - - - +
139A MET* 1.3 76.9 + - - +
141A SER* 3.2 24.5 + - - +
145A MET* 4.7 5.2 - - + +
151A ASP* 4.2 24.5 - - + +
154A HIS* 3.9 26.0 - - + +
155A TYR* 3.8 31.4 - - + -
158A LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 3.1 49.3 + - + +
136A GLU* 3.5 5.4 + - - +
137A LYS 3.4 0.2 - - - -
138A LEU* 1.3 79.3 - - - +
140A ALA* 1.3 66.0 + - - +
141A SER 3.5 4.3 + - - +
144A PRO* 5.0 12.4 - - - +
145A MET* 4.1 27.4 - - + -
155A TYR* 3.5 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU 3.2 17.4 + - - +
137A LYS* 4.0 7.2 - - - +
138A LEU 3.3 0.2 - - - -
139A MET* 1.3 76.7 - - - +
141A SER* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS 3.8 8.6 + - - -
138A LEU* 3.2 20.1 + - - +
139A MET 3.3 3.6 - - - +
140A ALA* 1.3 83.0 - - - +
144A PRO* 5.5 8.0 - - - +
151A ASP* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il