Contacts of the helix formed by residues 170 - 179 (chain B) in PDB entry 2GOJ
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 ASP 170 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.0 28.5 + - + +
168B ARG 3.2 1.0 - - - -
169B ASN* 1.3 80.6 - - - +
171B ARG* 1.3 61.2 + - - +
172B ALA* 3.7 9.5 + - - +
173B SER* 2.5 42.5 + - - -
174B TYR 3.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 5.9 2.6 - - - -
114B LEU 2.8 37.4 + - - -
115B CYS* 3.4 22.0 + - + +
117B HIS* 2.8 34.1 + - - +
119B GLY 3.7 17.0 + - - +
158B ILE* 3.9 19.9 + - - +
160B GLU* 5.4 3.0 + - - +
163B TYR* 3.1 49.1 + - + +
169B ASN 2.9 11.8 + - - +
170B ASP* 1.3 72.7 - - - +
172B ALA* 1.3 57.2 + - - +
174B TYR* 3.1 7.6 + - + +
175B VAL* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B CYS* 3.6 23.8 - - - -
170B ASP* 3.2 8.7 - - - +
171B ARG* 1.3 78.1 - - - +
173B SER* 1.3 57.6 + - - +
175B VAL* 3.3 3.8 + - - +
176B LYS* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.7 22.3 - - - -
170B ASP* 2.5 32.6 + - - -
171B ARG 3.2 0.4 - - - -
172B ALA* 1.3 75.5 - - - +
174B TYR* 1.3 60.3 + - - +
176B LYS* 3.7 10.2 - - - +
177B ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS 5.1 0.4 - - - -
18B ILE* 4.0 18.4 - - + -
76B TYR* 2.8 31.1 + - - -
156B CYS* 3.7 17.8 - - - -
157B ASP 2.6 29.6 + - - -
158B ILE* 4.1 4.3 - - + -
162B ALA* 3.8 19.8 - - + +
163B TYR* 3.4 43.3 - + + -
167B TYR* 3.7 25.8 - + + -
170B ASP 3.4 3.8 + - - +
171B ARG* 3.1 14.0 + - + +
173B SER* 1.3 79.0 - - - +
175B VAL* 1.3 64.0 + - + +
177B ALA* 3.3 2.6 + - - +
178B TRP* 2.9 30.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 3.8 34.1 - - - +
114B LEU* 3.8 39.7 - - + -
115B CYS* 4.0 12.6 - - - -
156B CYS* 5.3 0.4 - - - -
158B ILE* 4.7 2.5 - - + -
171B ARG* 2.9 23.7 + - + +
172B ALA 3.6 7.9 - - - +
174B TYR* 1.3 85.9 - - + +
176B LYS* 1.3 63.9 + - - +
178B TRP* 3.2 18.7 + - + +
179B TRP* 3.1 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LYS* 6.3 2.9 - - - +
172B ALA 2.9 17.0 + - - +
173B SER* 3.7 11.0 - - - +
174B TYR 3.2 0.2 - - - -
175B VAL* 1.3 76.4 - - - +
177B ALA* 1.3 64.7 + - - +
179B TRP* 3.2 26.6 + - + +
180B ASN* 4.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 3.6 28.6 - - + +
18B ILE* 6.0 0.2 - - + -
167B TYR* 3.2 27.8 - - + +
173B SER 3.0 14.4 + - - +
174B TYR 3.5 4.7 - - - +
176B LYS* 1.3 77.7 - - - +
178B TRP* 1.3 61.1 + - - +
180B ASN* 3.1 31.7 + - - +
181B LEU* 3.9 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.9 2.2 - - + +
76B TYR* 4.2 5.8 - + - -
79B SER* 4.7 11.0 - - - -
80B MET* 3.6 36.5 - - + +
110B PHE* 3.8 31.2 - + - -
114B LEU* 4.8 3.4 - - + -
154B LEU* 4.9 10.8 - - + -
155B THR 3.5 23.2 + - - -
156B CYS* 3.7 29.2 - - + +
174B TYR* 2.9 22.2 + + + +
175B VAL* 3.2 14.3 + - - +
177B ALA* 1.3 76.6 - - - +
179B TRP* 1.3 81.9 + + - +
181B LEU* 2.9 26.8 + - + +
182B VAL* 3.2 37.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY* 3.1 20.3 - - - -
86B GLY* 3.1 9.6 + - - +
103B PHE* 4.0 24.9 - + + -
106B PHE* 3.7 26.2 - + - -
107B LYS* 3.5 57.8 - - + +
110B PHE* 3.6 32.3 - + - -
111B SER* 3.0 21.3 + - - -
114B LEU* 5.3 0.4 - - + -
154B LEU* 6.3 0.4 - - + -
175B VAL* 3.1 29.9 + - + +
176B LYS* 3.2 15.2 + - + +
177B ALA 3.2 0.8 - - - -
178B TRP* 1.3 90.5 - + - +
180B ASN* 1.3 57.8 + - - +
181B LEU 3.1 0.7 - - - -
182B VAL* 3.8 19.6 + - + +
184B TRP* 4.4 5.6 - + - -
----------------------------------------------------------
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