Contacts of the strand formed by residues 176 - 182 (chain B) in PDB entry 3NSH
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 VAL 176 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.3 8.5 - - - -
14B GLY* 2.8 50.6 + - - +
15B LYS 4.0 8.7 - - - +
16B SER* 4.4 14.4 - - - +
19B GLY 4.7 0.4 - - - +
20B TYR* 3.5 26.2 - - + +
161B CYS 3.5 19.3 - - - +
162B GLY* 4.7 1.6 - - - -
163B ALA* 3.7 23.6 - - + +
167B LEU* 3.8 9.1 - - - +
174B ALA 3.6 1.2 - - - -
175B SER* 1.4 85.3 + - - +
177B GLY* 1.3 58.4 + - - +
345B GLU* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 4.8 1.3 - - - -
12B LEU 3.3 15.5 - - - -
13B ARG* 3.5 12.3 - - - -
20B TYR* 3.3 12.3 - - - -
161B CYS* 2.9 33.3 + - - +
162B GLY 5.5 0.2 + - - -
167B LEU* 4.3 8.2 - - - +
176B VAL* 1.3 73.0 - - - +
178B GLY* 1.3 57.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 3.1 18.5 + - - -
12B LEU* 3.1 33.3 + - - +
13B ARG* 4.2 1.4 - - - +
159B GLN* 2.9 16.8 - - - -
160B LEU* 4.6 0.2 - - - -
161B CYS* 4.2 8.7 - - - -
177B GLY* 1.3 74.4 - - - -
179B SER* 1.3 63.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET 3.6 7.4 - - - -
9B VAL* 3.7 4.5 - - - +
10B ASP* 2.9 25.9 + - - -
11B ASN* 3.3 4.9 - - - -
12B LEU* 3.8 6.6 - - - +
157B SER 3.8 0.9 - - - +
158B LEU* 3.5 2.8 - - - -
159B GLN* 2.7 51.5 + - - +
178B GLY* 1.3 72.6 - - - -
180B MET* 1.3 60.8 + - - +
181B ILE* 3.9 3.3 + - - +
189B LEU* 3.8 26.3 - - - +
348B TYR* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B MET* 3.5 6.2 - - - +
11B ASN* 2.8 28.3 + - - +
12B LEU* 3.9 11.0 - - + +
22B VAL* 3.9 34.5 - - + -
37B VAL* 4.0 25.6 - - + -
93B ILE* 5.1 2.7 - - + -
125B LEU* 4.5 10.3 - - + -
127B LEU* 4.3 14.8 - - - -
156B PHE* 4.9 7.6 - - + -
157B SER 3.5 5.8 - - - +
158B LEU* 3.6 17.0 - - + -
179B SER* 1.3 72.7 - - - +
181B ILE* 1.3 65.4 + - - +
182B ILE* 3.5 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.6 40.6 - - + +
8B MET* 3.7 33.7 - - + +
9B VAL* 4.0 6.3 - - + +
156B PHE* 3.2 6.1 - - - +
157B SER* 3.0 38.0 + - - +
179B SER* 4.0 3.1 - - - -
180B MET* 1.3 74.1 - - - +
182B ILE* 1.3 60.7 + - - +
184B GLY 3.3 21.4 - - - +
185B ILE 4.3 0.4 - - - +
186B ASP* 4.0 5.8 - - + +
189B LEU* 3.5 33.2 - - + -
348B TYR* 3.7 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 4.7 1.7 - - - -
8B MET* 3.4 32.2 - - - +
11B ASN* 5.7 0.4 - - - +
93B ILE* 3.5 35.4 - - + -
96B GLY* 4.8 0.4 - - - -
97B PRO* 3.6 30.1 - - + +
142B PHE* 5.9 0.4 - - + -
143B PHE* 4.2 8.5 - - + -
146B LEU* 3.7 24.5 - - + -
152B VAL* 3.8 8.1 - - + +
156B PHE* 4.3 7.9 - - + -
180B MET* 4.0 32.1 - - + +
181B ILE* 1.3 71.7 - - - +
183B GLY* 1.4 62.5 + - - +
184B GLY 3.5 0.8 + - - -
----------------------------------------------------------
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