Contacts of the helix formed by residues 116 - 139 (chain A) in PDB entry 4B5G
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 ALA 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLY 3.6 9.5 - - - +
114A SER 3.5 0.8 - - - -
115A SER* 1.3 82.5 - - - +
117A GLU* 1.3 66.5 + - - +
118A GLU* 3.3 9.4 - - + +
119A ARG* 3.3 15.9 + - + +
120A GLN 3.1 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 1.3 71.3 - - - +
118A GLU* 1.3 60.7 + - - +
120A GLN* 3.1 18.0 + - - +
121A GLN* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 3.3 5.5 - - + +
117A GLU* 1.3 75.3 - - - +
119A ARG* 1.3 70.0 + - + +
121A GLN* 3.2 9.7 + - + +
122A VAL* 2.9 32.8 + - - +
125A ARG* 3.3 26.7 + - - -
19C GLY* 6.2 0.2 - - - -
22C GLU* 6.0 3.1 - - - +
242C GLU* 5.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.1 25.3 + - - -
92A GLU* 3.4 21.2 + - - -
94A ARG* 3.5 8.7 - - - +
111A PRO* 4.3 8.9 - - - +
112A SER 3.7 19.0 + - - +
113A GLY* 3.7 6.5 - - - -
115A SER* 4.2 4.0 - - - -
116A ALA* 3.3 26.8 + - + +
117A GLU 3.2 0.2 - - - -
118A GLU* 1.3 83.7 + - + +
120A GLN* 1.3 60.0 + - - +
122A VAL* 3.2 32.6 + - - +
123A LYS* 2.9 29.1 + - - +
34U A 5.6 0.9 - - - -
35U C 3.6 24.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
113A GLY* 2.8 24.4 - - - +
116A ALA 3.1 8.0 + - - +
117A GLU* 3.1 25.0 + - - +
119A ARG* 1.3 76.3 - - - +
121A GLN* 1.3 58.9 + - - +
123A LYS* 3.1 10.4 - - - +
124A TYR* 2.9 63.2 + - + -
169A SER* 2.8 27.8 + - - -
172A LEU* 3.7 14.2 - - + +
175A GLU* 2.7 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 3.0 37.7 + - + +
118A GLU* 3.6 11.7 - - + +
119A ARG 3.2 0.2 - - - -
120A GLN* 1.3 75.0 - - - +
122A VAL* 1.3 60.1 + - - +
124A TYR* 3.0 23.6 + - - +
125A ARG* 2.9 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.9 11.9 - - + +
89A PHE* 3.2 27.0 - - + -
92A GLU* 4.5 6.5 - - - +
111A PRO* 4.5 8.1 - - + -
118A GLU* 2.9 23.3 + - - +
119A ARG* 3.7 36.1 - - - +
121A GLN* 1.3 74.6 - - - +
123A LYS* 1.3 58.9 + - - +
125A ARG* 3.4 28.5 + - - +
126A PHE* 2.9 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
----------------------------------------------------------
110A LEU* 3.7 18.6 - - + -
111A PRO* 3.2 34.3 + - + +
112A SER* 4.7 0.2 - - - +
113A GLY 3.8 13.4 - - - +
119A ARG 2.9 14.3 + - - +
120A GLN* 3.1 17.7 - - - +
122A VAL* 1.3 78.6 - - - +
124A TYR* 1.3 54.8 + - + +
126A PHE* 3.2 9.8 + - - +
127A LEU* 2.9 35.3 + - + +
151A ASN* 3.0 31.7 + - - +
152A ILE* 4.1 9.0 - - - -
169A SER* 3.5 12.7 + - - -
170A GLY* 3.8 2.8 - - - +
175A GLU* 3.1 29.3 + - - +
36U 3DR 4.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 2.9 55.6 + - + -
121A GLN* 3.0 24.7 + - - +
123A LYS* 1.3 75.2 - - + +
125A ARG* 1.3 61.1 + - + +
127A LEU* 3.1 18.3 + - + +
128A ASP* 2.9 40.5 + - - +
172A LEU* 3.5 24.8 - - + +
174A GLU* 3.5 47.4 + - + +
175A GLU* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 2.8 27.1 + - - +
89A PHE* 3.7 11.6 - - + -
118A GLU* 3.3 24.4 + - - -
121A GLN* 2.9 31.9 + - - +
122A VAL* 3.4 24.0 - - - +
124A TYR* 1.3 74.6 - - - +
126A PHE* 1.3 56.9 + - - +
128A ASP* 3.7 8.1 - - - +
129A ALA* 2.9 33.3 + - - +
17C LYS* 3.4 28.6 + - - -
18C LYS* 5.3 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 3.4 32.0 - - + +
89A PHE* 3.4 38.6 - + + -
94A ARG* 4.7 8.3 - - + -
108A LEU* 4.0 19.5 - - + -
109A TYR 4.9 1.6 - - - -
110A LEU* 3.7 30.3 - - + -
111A PRO* 3.5 28.5 - - + -
122A VAL 2.9 15.4 + - - +
123A LYS 3.2 10.3 - - - +
124A TYR 3.1 0.2 - - - -
125A ARG* 1.3 78.0 - - - +
127A LEU* 1.3 58.3 + - - +
129A ALA* 3.4 0.9 + - - +
130A PHE* 2.9 57.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.7 27.6 - - + -
123A LYS* 2.9 23.4 + - + +
124A TYR* 3.4 32.8 - - + +
126A PHE* 1.3 77.2 - - + +
128A ASP* 1.3 59.5 + - - +
131A TYR* 2.9 33.4 + - - +
152A ILE* 4.2 13.5 - - + -
174A GLU* 6.0 0.4 - - + -
175A GLU* 4.6 6.7 - - + -
178A TRP* 3.3 63.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 2.9 26.3 + - - +
125A ARG* 3.9 8.0 - - - +
127A LEU* 1.3 80.3 - - - +
129A ALA* 1.3 58.0 + - - +
131A TYR* 4.4 3.8 - - - +
132A PRO* 3.3 19.3 - - - +
174A GLU* 5.7 1.2 - - - +
178A TRP* 4.8 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 5.0 2.2 - - + -
86A ILE* 3.6 28.4 - - + +
89A PHE* 4.5 8.7 - - + -
125A ARG 2.9 17.1 + - - +
126A PHE 4.1 1.8 - - - +
128A ASP* 1.3 77.0 - - - +
130A PHE* 1.3 60.6 + - - +
131A TYR 3.5 0.9 - - - -
132A PRO* 3.5 11.8 - - - +
133A MET* 3.9 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 5.0 9.9 - - + -
95A PHE* 4.0 15.0 - + - -
106A ILE* 6.2 0.2 - - + -
108A LEU* 3.6 31.9 - - + -
110A LEU* 5.1 0.9 - - + -
126A PHE* 2.9 42.0 + + + +
127A LEU* 4.2 1.6 - - - +
129A ALA* 1.3 78.0 - - - +
131A TYR* 1.3 58.5 + - - +
132A PRO 3.5 0.9 - - - -
133A MET* 3.2 31.4 - - + +
134A LEU* 2.9 62.3 + - + +
137A MET* 5.3 2.9 - - - -
146A VAL* 4.8 6.5 - - + -
150A TRP* 4.1 16.2 - + - -
178A TRP* 4.2 11.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU 2.9 19.1 + - - +
128A ASP* 4.4 4.3 - - - +
130A PHE* 1.3 76.6 - - - +
132A PRO* 1.4 72.8 - - + +
134A LEU* 3.1 15.5 + - - +
135A GLU* 3.2 19.1 + - - +
178A TRP* 3.7 28.2 - + - +
181A LYS* 3.6 43.0 - - + +
182A VAL* 4.1 13.7 - - + -
185A LYS* 3.8 12.8 - - - +
186A LEU* 3.2 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP 3.3 22.4 - - - +
129A ALA* 3.5 10.5 - - - +
131A TYR* 1.4 96.6 - - + +
133A MET* 1.3 59.0 + - - +
135A GLU* 3.2 13.9 + - + +
136A ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLN* 5.5 2.9 - - - -
84A MET* 4.2 40.2 - - + +
86A ILE* 5.0 10.3 - - + -
95A PHE* 5.2 8.5 - - + -
129A ALA 3.9 14.8 + - - +
130A PHE* 3.2 35.0 + - + +
132A PRO* 1.3 80.0 - - - +
134A LEU* 1.3 61.2 + - - +
136A ALA* 3.4 6.8 + - - +
137A MET* 3.1 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 2.9 50.2 + - + +
131A TYR* 3.1 8.5 + - - +
133A MET* 1.3 77.8 - - - +
135A GLU* 1.3 61.0 + - - +
137A MET* 3.4 9.2 + - - +
138A LYS 3.2 17.0 + - - -
146A VAL* 4.7 10.3 - - + -
150A TRP* 4.2 12.1 - - + -
178A TRP* 4.1 10.5 - - + -
182A VAL* 3.7 37.0 - - + -
186A LEU* 3.7 12.1 - - + -
188A TRP* 3.4 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 3.2 22.3 + - - +
132A PRO* 3.2 15.0 + - - +
134A LEU* 1.3 77.3 - - - +
136A ALA* 1.3 64.5 + - - +
138A LYS* 3.3 5.7 + - + +
139A ASN* 3.2 43.5 + - - +
186A LEU* 3.4 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO 3.0 13.3 + - - +
133A MET* 3.7 10.5 - - - +
134A LEU 3.4 0.2 - - - -
135A GLU* 1.3 75.5 - - - +
137A MET* 1.3 65.7 + - + +
139A ASN* 3.0 17.7 + - - +
140A GLU* 3.1 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 5.2 2.5 - - - -
97A ARG* 4.2 12.6 - - - +
106A ILE* 3.4 30.1 - - + -
130A PHE* 5.3 2.9 - - - -
133A MET* 3.1 31.9 - - + +
134A LEU* 3.7 18.4 - - - +
135A GLU 3.3 0.4 - - - -
136A ALA* 1.3 76.1 - - + +
138A LYS* 1.3 61.8 + - - +
140A GLU* 3.3 33.4 + - - +
141A GLY 4.4 1.4 + - - -
142A ARG* 4.9 2.4 - - - +
144A ILE* 3.4 50.5 - - + +
146A VAL* 4.3 7.0 - - + -
188A TRP* 4.1 6.5 - - + -
226A THR* 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU 3.2 13.6 + - - +
135A GLU* 3.5 11.9 - - + +
136A ALA 3.2 0.4 - - - -
137A MET* 1.3 76.9 - - - +
139A ASN* 1.3 67.7 + - - +
140A GLU 3.2 3.0 + - - -
141A GLY* 3.7 9.2 + - - -
142A ARG 5.3 0.5 + - - +
186A LEU* 3.3 28.6 + - + +
187A GLY* 4.2 8.1 + - - -
188A TRP* 4.2 17.2 - - + +
226A THR* 4.9 12.1 - - + +
227A PRO* 3.1 43.1 - - + +
228A GLU* 4.8 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 3.2 34.3 + - - +
136A ALA* 3.0 11.7 + - - +
138A LYS* 1.3 83.7 - - - +
140A GLU* 1.3 62.7 + - - +
141A GLY* 3.3 2.4 + - - -
----------------------------------------------------------
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