Contacts of the helix formed by residues 161 - 174 (chain B) in PDB entry 1W1W
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 SER 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA 3.7 0.4 + - - -
160B GLN* 1.3 74.1 - - - +
162B PRO* 1.3 69.1 - - - +
163B VAL* 3.5 11.1 + - - +
164B GLU* 2.6 45.9 + - - +
165B LEU* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN 4.3 2.2 - - - +
161B SER* 1.3 86.0 - - - +
163B VAL* 1.3 61.3 + - + +
165B LEU* 3.4 1.6 + - + +
166B SER* 2.8 24.9 + - - -
1102B GLU* 4.3 10.5 - - - +
1111B GLY* 3.1 21.2 - - - -
1112B ILE 3.0 34.6 + - - +
1113B LYS* 4.3 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B SER* 3.1 9.6 - - - +
162B PRO* 1.3 80.7 - - + +
164B GLU* 1.3 61.0 + - + +
166B SER* 3.2 6.2 + - - -
167B ARG* 2.9 28.0 + - + +
1110B ALA* 4.5 5.4 - - - +
1111B GLY* 4.0 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLN* 4.5 6.1 - - - +
160B GLN* 3.4 28.0 - - - +
161B SER* 2.6 48.3 + - - +
163B VAL* 1.3 76.7 - - + +
165B LEU* 1.3 58.9 + - - +
167B ARG* 3.1 9.7 + - - +
168B MET* 2.9 25.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
158B ALA 6.1 0.9 - - - +
160B GLN* 3.5 28.2 + - + +
161B SER 2.8 14.3 + - - +
162B PRO* 3.6 8.1 - - + +
164B GLU* 1.3 71.6 - - - +
166B SER* 1.3 64.0 + - - +
168B MET* 3.2 11.8 + - - +
169B PHE* 3.0 43.3 + - + -
1099B LEU* 3.9 5.8 - - + -
1112B ILE* 3.3 35.0 - - + +
1114B TYR* 3.8 25.1 - - + -
1141B LEU* 4.3 14.8 - - + -
1145B ILE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO 2.8 10.7 + - - -
163B VAL* 3.3 10.1 - - - -
164B GLU 3.1 0.2 - - - -
165B LEU* 1.3 77.2 - - - +
167B ARG* 1.3 56.3 + - - +
169B PHE* 3.1 6.1 + - - +
170B GLU* 2.8 29.4 + - - +
1064B PHE* 3.9 3.8 - - - -
1107B PRO 3.5 11.8 + - - -
1108B PHE* 3.9 13.9 + - - -
1110B ALA 2.9 29.7 + - - -
1112B ILE* 3.6 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 2.9 15.0 + - + +
164B GLU* 3.1 14.3 + - - +
166B SER* 1.3 75.1 - - - +
168B MET* 1.3 51.4 + - - +
170B GLU* 3.3 12.2 + - - +
171B GLU* 2.8 73.9 + - - +
176B ILE* 4.0 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA* 5.4 7.6 - - + +
146B ASN* 5.6 6.3 - - + -
157B ILE* 4.8 12.3 - - + -
160B GLN* 3.0 37.7 - - - +
164B GLU 2.9 9.8 + - - +
165B LEU* 3.4 10.5 - - - +
167B ARG* 1.3 75.4 - - - +
169B PHE* 1.3 55.7 + - - +
171B GLU* 2.8 9.0 + - + +
172B VAL* 2.6 53.8 + - + +
1145B ILE* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.0 48.5 + - + -
166B SER 3.1 7.2 + - - +
168B MET* 1.3 74.1 - - - +
170B GLU* 1.3 54.1 + - - +
172B VAL* 4.0 3.8 - - + +
173B SER* 2.6 43.1 + - - -
1064B PHE* 3.5 17.5 - - + +
1067B THR* 4.2 15.9 - - + -
1068B PHE* 3.9 20.9 - + - -
1071B VAL* 3.9 30.3 - - + -
1099B LEU* 3.7 24.7 - - + -
1112B ILE* 4.0 28.5 - - + -
1141B LEU* 4.7 0.4 - - + -
1145B ILE* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 2.8 12.8 + - - +
167B ARG* 3.3 14.8 - - - +
169B PHE* 1.3 76.5 - - - +
171B GLU* 1.3 58.0 + - - +
173B SER* 3.6 0.2 - - - -
174B GLY 3.2 5.2 + - - -
175B SER* 2.7 40.4 + - - +
176B ILE* 3.0 47.6 + - + +
179B LYS* 5.8 0.2 + - - -
1060B ARG* 2.5 43.9 + - - -
1064B PHE* 3.9 4.9 - - + -
1108B PHE* 3.2 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 5.1 2.1 - - - +
143B LYS* 3.0 68.6 - - + +
144B ALA* 4.2 10.1 - - + +
167B ARG* 2.8 51.1 + - - +
168B MET* 2.8 15.7 + - + +
170B GLU* 1.3 76.1 - - - +
172B VAL* 1.3 62.3 + - + +
174B GLY* 3.8 5.4 + - - -
176B ILE* 3.4 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.7 26.3 - - + +
144B ALA* 3.7 21.8 - - + -
146B ASN* 4.3 11.9 - - + +
168B MET* 2.6 38.7 + - + +
169B PHE* 4.0 4.5 - - - +
171B GLU* 1.3 73.3 - - - +
173B SER* 1.3 66.0 + - - +
174B GLY* 3.5 0.3 + - - -
1067B THR* 4.5 11.2 + - + +
1145B ILE* 4.0 34.1 - - + +
1148B TYR* 5.8 3.3 - - + -
1149B GLN* 4.5 9.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
169B PHE 2.6 24.5 + - - -
170B GLU 3.4 5.0 + - - -
172B VAL* 1.3 77.2 - - - +
174B GLY* 1.3 59.8 + - - +
175B SER* 3.4 12.9 + - - -
1063B LEU* 3.1 43.0 - - - +
1064B PHE* 3.8 6.5 - - - -
1067B THR* 3.2 28.0 + - - +
1148B TYR* 5.7 0.4 - - - -
1149B GLN* 4.9 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS* 5.7 3.3 + - - -
170B GLU 3.2 6.7 + - - -
171B GLU 3.8 6.9 + - - -
172B VAL 3.3 2.2 - - - -
173B SER* 1.3 80.0 + - - +
175B SER* 1.3 58.1 + - - +
176B ILE* 2.8 16.5 + - - +
177B GLN* 3.0 29.1 + - - +
1063B LEU* 3.1 8.7 - - - -
----------------------------------------------------------
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