Contacts of the helix formed by residues 150 - 165 (chain B) in PDB entry 10GS
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 PHE 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.8 20.4 - - + -
69B LEU* 3.8 31.6 - - + +
70B ARG* 3.6 25.6 - - + -
73B GLY* 4.1 13.5 - - - -
78B LEU* 3.0 27.0 + - - +
79B TYR* 3.5 31.4 - + - -
89B VAL* 3.5 24.0 - - + -
90B ASP* 3.9 7.2 - - - -
93B ASN* 3.7 32.8 - - + -
149B SER* 1.3 73.8 - - - +
151B ALA* 1.3 63.3 + - - +
153B TYR* 3.3 15.4 + - - +
154B ASN* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 3.7 29.4 - - + +
92B VAL* 4.0 20.3 - - + +
93B ASN* 4.0 17.0 - - + +
96B VAL* 4.8 0.9 - - - +
143B ILE* 4.3 5.6 - - + -
149B SER* 3.1 12.2 + - - +
150B PHE* 1.3 78.5 - - - +
152B ASP* 1.3 60.1 + - - +
154B ASN* 3.4 1.4 + - - +
155B LEU* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE* 3.5 13.1 - - - +
143B ILE* 3.0 26.8 + - - +
144B VAL 5.0 0.5 + - - +
147B GLN 4.3 0.3 - - - +
148B ILE* 3.5 26.1 - - + -
149B SER* 2.9 36.7 + - - +
151B ALA* 1.3 78.2 - - - +
153B TYR* 1.3 57.1 + - - +
155B LEU 3.3 0.5 + - - -
156B LEU* 2.8 32.6 + - - +
179B TYR* 2.5 34.1 + - - +
183B LEU* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.7 19.7 - - + +
19B MET* 3.1 25.4 - - + +
20B LEU* 3.6 45.1 - - + -
23B ASP* 2.7 41.6 + - + +
24B GLN* 3.1 18.1 + - - -
69B LEU* 5.5 0.2 - - + -
78B LEU* 4.1 11.0 - - + -
148B ILE* 3.5 25.4 - - + +
149B SER 3.5 17.5 - - - -
150B PHE* 3.3 6.1 + - - +
152B ASP* 1.3 75.7 - - - +
154B ASN* 1.3 57.7 + - - +
156B LEU* 3.4 5.7 + - + +
157B ASP* 3.0 23.0 + - - +
183B LEU* 6.3 0.7 - - + -
189B LEU* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.7 10.9 - - - +
66B ASN* 3.7 14.1 + - - -
69B LEU* 3.7 15.0 - - + +
93B ASN* 2.9 34.6 + - - +
96B VAL* 3.6 18.2 - - + +
97B GLU* 5.1 3.2 + - - +
100B ARG* 2.6 40.0 + - - +
150B PHE 3.2 8.6 + - - +
151B ALA 3.8 4.5 - - - +
152B ASP 3.3 0.2 - - - -
153B TYR* 1.3 77.6 - - - +
155B LEU* 1.3 63.4 + - - +
157B ASP 3.4 0.7 + - - -
158B LEU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 4.7 1.6 - - + -
96B VAL* 4.0 18.5 - - + +
129B PHE* 4.0 37.5 - - + -
143B ILE* 3.7 34.1 - - + -
151B ALA 2.8 19.1 + - - +
152B ASP 3.7 2.7 - - - +
154B ASN* 1.3 72.1 - - - +
156B LEU* 1.3 61.7 + - - +
158B LEU* 3.1 9.1 + - + +
159B LEU* 2.9 57.4 + - + +
176B LEU* 4.9 2.0 - - + -
179B TYR* 3.8 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 4.4 13.5 - - + -
152B ASP 2.8 18.3 + - - +
153B TYR* 3.6 9.4 - - + +
155B LEU* 1.3 76.4 - - - +
157B ASP* 1.3 63.4 + - - +
159B LEU* 3.2 7.9 + - - +
160B LEU* 2.9 42.0 + - + +
179B TYR* 4.7 3.3 - - + -
180B VAL* 4.1 42.0 - - + +
183B LEU* 4.0 25.1 - - + -
184B SER* 4.3 5.6 - - - +
189B LEU* 3.8 29.2 - - + -
193B LEU* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 5.9 0.7 - - - -
12B GLY 4.2 2.8 - - - +
15B ALA* 3.3 29.6 - - - +
16B ALA* 4.2 6.3 + - + +
19B MET* 3.4 23.5 - - + +
100B ARG* 2.8 34.4 + - - +
153B TYR 3.0 11.1 + - - +
154B ASN 3.7 4.5 - - - +
155B LEU 3.3 0.2 - - - -
156B LEU* 1.3 74.4 - - - +
158B LEU* 1.3 64.0 + - - +
160B LEU* 3.2 7.6 + - - +
161B ILE* 3.0 36.2 + - - +
198B TYR* 4.9 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.7 34.3 - - + +
99B LEU* 3.8 23.8 - - + -
100B ARG* 3.9 36.7 - - + +
126B LEU* 5.8 0.7 - - + -
129B PHE* 4.7 4.0 - - + -
154B ASN 3.0 14.0 + - - +
155B LEU* 3.4 16.8 - - + +
157B ASP* 1.3 77.1 - - - +
159B LEU* 1.3 62.0 + - + +
161B ILE* 3.2 20.2 - - + +
162B HIS* 2.7 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.1 26.2 - - + -
129B PHE* 5.7 0.4 - - + -
155B LEU* 2.9 39.1 + - + +
156B LEU* 3.2 6.7 + - - +
158B LEU* 1.3 78.4 - - + +
160B LEU* 1.3 62.8 + - - +
162B HIS* 3.1 7.6 + - + +
163B GLU* 3.0 25.3 + - - +
170B LEU* 4.4 17.2 - - + +
176B LEU* 4.1 21.1 - - + +
179B TYR* 3.9 22.0 - - + -
180B VAL* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 4.7 3.4 - - - -
156B LEU* 2.9 38.5 + - + +
157B ASP* 3.7 8.5 - - - +
159B LEU* 1.3 75.7 - - - +
161B ILE* 1.3 64.2 + - + +
163B GLU* 3.2 20.5 + - + +
164B VAL* 3.3 16.7 + - - +
180B VAL* 4.0 25.8 - - + -
184B SER* 4.6 6.3 - - - +
193B LEU* 4.6 21.3 - - + -
198B TYR* 4.2 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 5.8 3.4 - - + +
100B ARG* 4.0 22.2 - - - +
103B TYR* 3.6 47.8 + - + +
157B ASP* 3.0 27.1 + - - +
158B LEU* 3.2 24.2 - - + +
160B LEU* 1.3 76.7 - - + +
162B HIS* 1.3 60.6 + - - +
164B VAL* 3.5 11.2 + - - +
165B LEU* 3.1 24.3 + - - +
198B TYR* 5.9 1.8 - - - +
203B ILE* 4.0 27.7 - - + +
209B GLN 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.2 9.7 - - + +
103B TYR* 4.0 16.3 - + + -
118B TYR* 2.9 33.2 + + - -
122B LEU* 3.7 31.7 - - + +
126B LEU* 5.5 6.4 - - + +
158B LEU* 2.7 50.0 + - + +
159B LEU* 3.1 12.2 + - - +
161B ILE* 1.3 75.2 - - + +
163B GLU* 1.3 58.8 + - - +
164B VAL 3.1 1.8 - - - -
165B LEU* 3.7 10.2 - - + +
166B ALA* 2.7 35.5 + - - +
169B CYS* 3.6 15.4 - - - -
170B LEU* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU 3.0 15.2 + - - +
160B LEU* 3.2 18.3 + - + +
162B HIS* 1.3 76.0 - - - +
164B VAL* 1.3 61.6 + - + +
166B ALA 4.1 2.9 - - - -
167B PRO* 3.1 30.3 - - - +
168B GLY* 3.7 21.6 + - - -
169B CYS* 4.2 1.5 - - - -
170B LEU* 3.5 45.2 + - + +
171B ASP* 5.5 0.7 - - - +
180B VAL* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 5.9 1.8 - - - +
160B LEU 3.3 14.6 + - - +
161B ILE* 3.6 7.9 - - - +
163B GLU* 1.3 79.9 - - + +
165B LEU* 1.3 62.8 + - - +
167B PRO* 3.9 9.5 - - - +
203B ILE* 4.1 19.3 - - + -
209B GLN* 3.5 42.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 4.2 11.2 - - + -
106B LEU* 4.1 14.6 - - + -
107B ILE* 4.6 5.4 - - + -
111B TYR* 3.9 20.0 - - + -
115B LYS* 3.0 46.2 + - + +
118B TYR* 3.6 35.2 - - + -
119B VAL* 4.9 7.6 - - + +
122B LEU* 5.3 0.7 - - + -
161B ILE 3.1 17.2 + - - +
162B HIS* 3.3 15.9 + - + +
164B VAL* 1.3 79.5 - - - +
166B ALA* 1.3 60.9 + - + +
167B PRO* 3.5 6.1 - - - +
209B GLN 3.3 14.8 + - - +
----------------------------------------------------------
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