Contacts of the helix formed by residues 118 - 137 (chain A) in PDB entry 3FR0
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 THR 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 1.3 81.6 - - - +
119A ALA* 1.3 60.0 + - - +
120A GLU* 3.1 28.8 - - + +
121A MET* 3.1 25.4 - - + +
122A LEU* 3.1 22.2 + - - +
173A ALA* 4.9 0.2 - - - -
174A SER* 3.1 22.1 + - - +
175A GLY* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 1.3 72.0 - - - +
120A GLU* 1.3 65.3 + - - +
122A LEU* 2.9 10.4 + - - +
123A PHE* 2.8 34.9 + - + -
173A ALA* 5.1 2.5 - - - -
174A SER 2.8 12.6 + - - +
175A GLY 3.4 25.1 - - - +
176A ALA* 3.6 20.0 - - + -
184A LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.1 24.0 - - + +
119A ALA* 1.3 89.5 + - - +
121A MET* 1.3 58.4 + - + +
123A PHE* 4.5 2.9 - - - +
124A ASP* 3.0 36.6 + - - +
174A SER 4.5 0.5 - - - +
175A GLY* 4.3 8.4 - - - +
184A LEU* 5.2 11.7 - - + +
191A ARG* 3.2 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP* 4.1 5.2 - - + +
114A ALA* 3.5 34.5 - - + +
117A GLY* 3.4 22.2 - - - -
118A THR* 3.1 28.6 + - - +
119A ALA 3.1 0.2 - - - -
120A GLU* 1.3 77.8 - - + +
122A LEU* 1.3 63.8 + - - +
124A ASP* 3.3 7.6 + - - +
125A TYR* 3.1 22.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
79A LEU* 4.6 9.2 - - + -
110A ILE* 4.1 20.9 - - + -
114A ALA* 3.2 30.5 - - + +
115A MET* 3.6 19.3 - - - +
118A THR 3.1 8.1 + - - +
119A ALA* 2.9 14.0 + - - +
121A MET* 1.3 79.2 - - - +
123A PHE* 1.3 67.3 + - + +
125A TYR* 3.1 7.3 + - - +
126A ILE* 3.1 51.2 + - + +
167A TRP* 5.7 4.9 - - + -
171A PHE* 5.2 10.1 - - + -
173A ALA* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.8 10.8 - - + -
119A ALA* 2.8 24.7 + - + +
120A GLU* 4.6 2.2 - - - +
122A LEU* 1.3 81.2 - - + +
124A ASP* 1.3 60.4 + - - +
126A ILE* 3.7 16.5 - - + +
127A SER* 3.0 22.2 + - - -
148A PHE* 4.4 12.8 - + - -
150A PHE* 4.8 3.8 - + - -
167A TRP* 5.5 9.2 - + - -
176A ALA* 5.6 2.7 - - + -
181A VAL* 3.9 27.1 - - + -
184A LEU* 3.8 34.1 - - + +
185A LEU* 3.5 45.0 - - + +
188A ALA* 3.0 24.0 - - + +
191A ARG* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.0 25.4 + - - +
121A MET* 3.4 8.8 - - - +
123A PHE* 1.3 74.0 - - - +
125A TYR* 1.3 65.2 + - - +
127A SER* 3.1 5.8 + - - -
128A GLU* 3.0 22.1 + - - +
188A ALA* 3.7 9.1 - - - +
191A ARG* 2.8 40.6 + - - +
192A ARG* 5.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.5 1.3 - + - -
108A TYR* 4.7 4.5 - - - +
109A SER 3.1 20.6 + - - -
110A ILE* 3.5 26.5 - - + -
111A PRO* 3.4 34.4 - - + +
114A ALA* 4.4 10.8 - - + -
121A MET 3.1 10.1 + - - +
122A LEU 3.1 8.5 + - - +
124A ASP* 1.3 79.0 - - - +
126A ILE* 1.3 61.1 + - - +
128A GLU* 3.4 29.2 + - - +
129A CYS* 3.1 46.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.0 23.3 - - + -
79A LEU* 3.4 36.8 - - + -
84A PHE* 3.8 34.1 - - + -
110A ILE* 4.5 4.0 - - + -
122A LEU* 3.1 30.3 + - + +
123A PHE* 3.7 22.4 - - + +
124A ASP 3.1 0.2 - - - -
125A TYR* 1.3 74.7 - - - +
127A SER* 1.3 65.8 + - - +
129A CYS* 3.3 3.3 + - - +
130A ILE* 3.0 28.8 + - + +
148A PHE* 5.6 0.4 - - + -
185A LEU* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE 3.0 8.3 + - - -
124A ASP* 3.1 10.1 + - - -
126A ILE* 1.3 73.9 - - - +
128A GLU* 1.3 65.9 + - - +
130A ILE* 3.3 13.9 + - - +
131A SER* 3.1 22.2 + - - -
185A LEU* 4.2 2.9 + - - +
188A ALA* 3.0 46.2 - - - +
189A ILE* 3.2 11.9 + - - +
192A ARG* 4.0 12.3 - - - -
195A PHE* 3.7 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP 3.0 11.4 + - - +
125A TYR* 3.4 36.1 - - - +
127A SER* 1.3 76.2 - - - +
129A CYS* 1.3 54.1 + - - +
131A SER* 2.7 26.0 + - - -
132A ASP* 2.7 20.6 + - + +
192A ARG* 3.3 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.6 22.2 - - + -
86A VAL* 4.8 0.4 - - - -
108A TYR* 3.2 46.6 + - + -
125A TYR* 3.1 48.1 + - - -
126A ILE 3.3 2.7 + - - +
128A GLU* 1.3 82.1 - - - +
130A ILE* 1.3 57.8 + - - +
132A ASP* 3.4 8.7 - - - +
133A PHE* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.1 20.0 - - + -
77A LEU* 4.0 25.6 - - + -
86A VAL* 4.5 17.5 - - + -
126A ILE* 3.0 21.8 + - + +
127A SER* 3.4 13.7 - - - +
128A GLU 3.0 0.2 - - - -
129A CYS* 1.3 77.9 - - - +
131A SER* 1.3 56.6 + - - +
133A PHE* 3.3 6.0 + - - +
134A LEU* 2.9 49.1 + - + +
146A LEU* 4.5 12.1 - - + -
185A LEU* 4.6 7.6 - - + -
189A ILE* 5.1 3.6 - - + -
195A PHE* 4.0 18.4 - - + -
197A MET* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 3.1 5.5 + - - -
128A GLU 2.7 14.8 + - - -
130A ILE* 1.3 68.7 - - - +
132A ASP* 1.3 65.5 + - - -
133A PHE 3.1 1.3 - - - -
134A LEU* 3.0 3.5 + - - -
135A ASP* 2.8 31.2 + - - -
140A LYS* 3.6 18.8 - - - +
192A ARG* 3.8 18.7 - - - -
194A ASP* 3.4 12.8 + - - -
195A PHE* 3.1 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 3.2 24.5 + - + +
128A GLU* 2.7 18.6 + - + +
129A CYS* 3.4 12.6 - - - +
131A SER* 1.3 71.4 - - - +
133A PHE* 1.3 60.1 + - - +
135A ASP* 3.7 6.8 - - - +
136A LYS* 3.2 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.9 23.1 - - + -
86A VAL* 3.5 40.4 - - + -
87A MET* 4.0 9.9 - - - -
88A LEU* 4.5 9.4 - - + -
104A LYS* 4.0 22.0 - - + -
105A HIS* 3.7 16.6 - - - -
106A GLN* 3.7 19.1 - - + -
108A TYR* 3.2 11.4 + - - +
129A CYS 2.9 12.6 + - - +
130A ILE 3.5 4.7 - - - +
131A SER 3.1 0.2 - - - -
132A ASP* 1.3 75.7 - - - +
134A LEU* 1.3 70.3 + - + +
136A LYS* 3.5 2.8 + - - +
137A HIS* 3.1 51.4 + + + +
139A MET* 5.9 1.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
75A LEU* 4.5 15.0 - - + -
130A ILE* 2.9 37.7 + - + +
131A SER* 3.0 4.5 + - - +
133A PHE* 1.3 77.2 - - + +
135A ASP* 1.3 63.3 + - - +
138A GLN* 3.2 1.0 + - - -
139A MET* 2.7 54.2 + - + +
140A LYS* 2.9 23.2 + - + +
142A LYS* 6.1 0.2 - - + -
144A LEU* 5.4 2.7 - - + -
195A PHE* 3.6 42.4 - - + -
197A MET* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 2.8 15.5 + - - +
132A ASP* 3.7 7.3 - - - +
134A LEU* 1.3 72.5 - - - +
136A LYS* 1.3 55.2 + - + +
137A HIS 2.5 18.1 + - - -
138A GLN* 2.6 17.5 + - - +
140A LYS* 2.5 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN* 3.5 36.1 + - - +
108A TYR* 4.2 1.6 + - - -
132A ASP* 3.2 35.7 + - - +
133A PHE* 3.5 1.3 + - - +
135A ASP* 1.3 77.7 - - + +
137A HIS* 1.3 82.4 + - + +
138A GLN 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 3.4 46.9 - - + +
105A HIS 4.8 6.1 + - - -
106A GLN* 5.4 1.1 - - + -
133A PHE* 3.1 52.7 + + + +
135A ASP 2.5 5.9 + - - -
136A LYS* 1.3 100.0 + - + +
138A GLN* 1.3 70.2 + - - +
139A MET* 2.9 24.4 + - + +
----------------------------------------------------------
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