Contacts of the helix formed by residues 80 - 98 (chain B) in PDB entry 1WSQ
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 ASN 80 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.7 1.6 - - - +
79B ASN* 1.3 98.5 + - - +
81B GLU* 1.3 64.5 + - - +
82B HIS* 3.2 13.0 + - - +
83B ASP* 2.8 50.9 + - - +
84B LEU* 3.1 22.0 + - - +
120B TRP* 4.2 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 1.3 72.4 - - - +
82B HIS* 1.3 65.3 + - - +
84B LEU* 3.5 22.3 + - - +
85B GLN* 3.0 54.4 + - + +
88B LYS* 5.3 0.5 + - - -
120B TRP* 4.3 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 3.2 9.5 + - + +
81B GLU* 1.3 79.7 - - - +
83B ASP* 1.3 69.8 + - - +
85B GLN* 3.2 9.4 + - - +
86B VAL* 3.0 42.4 + - + +
216B GLU* 5.2 7.9 + - - -
220B TYR* 5.3 4.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.7 25.9 - - + +
79B ASN* 4.4 2.8 - - - +
80B ASN* 2.8 36.2 + - - +
82B HIS* 1.3 85.4 - - - +
84B LEU* 1.3 65.0 + - - +
86B VAL* 3.3 8.4 + - - +
87B CYS* 3.1 26.3 + - - -
219B LYS* 4.4 18.3 + - - +
220B TYR* 4.0 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.0 22.1 - - + +
80B ASN 3.1 14.9 + - - +
81B GLU* 3.5 33.0 - - - +
83B ASP* 1.3 76.5 - - - +
85B GLN* 1.3 56.9 + - - +
87B CYS* 3.1 6.1 + - - +
88B LYS* 2.9 45.1 + - - +
111B ILE* 3.8 37.0 - - + -
120B TRP* 3.9 30.3 - - + +
122B VAL* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.0 40.7 + - + +
82B HIS* 3.2 11.6 + - - +
84B LEU* 1.3 73.2 - - - +
86B VAL* 1.3 59.9 + - + +
88B LYS* 3.2 35.2 + - - +
89B ARG* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B HIS* 3.0 37.3 + - + +
83B ASP* 3.5 10.1 - - - +
84B LEU 3.2 0.4 - - - -
85B GLN* 1.3 75.7 - - + +
87B CYS* 1.3 60.6 + - - +
89B ARG* 3.2 9.3 + - + +
90B GLU* 2.9 27.3 + - + +
196B GLY* 3.8 22.2 - - - +
198B ALA 5.9 2.9 - - - +
220B TYR* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 4.1 20.9 - - - -
78B VAL* 3.9 20.2 - - - -
83B ASP 3.1 18.1 + - - +
84B LEU* 3.1 9.2 + - + +
86B VAL* 1.3 78.7 - - - +
88B LYS* 1.3 63.6 + - - +
90B GLU* 3.2 17.2 + - - +
91B ILE* 3.0 27.9 + - - +
111B ILE* 5.2 1.6 - - + -
122B VAL* 4.0 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 5.3 0.8 + - - -
84B LEU* 2.9 36.1 + - - +
85B GLN* 3.2 38.8 + - - +
87B CYS* 1.3 75.5 - - - +
89B ARG* 1.3 56.8 + - - +
91B ILE* 3.3 10.1 + - - +
92B GLN* 2.9 28.7 + - - +
111B ILE* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLN 2.9 13.5 + - - +
86B VAL* 3.4 12.1 - - - +
88B LYS* 1.3 73.1 - - - +
90B GLU* 1.3 65.3 + - - +
92B GLN* 3.2 6.5 + - - +
93B ILE* 2.9 38.5 + - + +
198B ALA 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS* 2.7 35.1 + - - +
76B MET* 4.8 2.6 - - - +
86B VAL* 2.9 12.8 + - - +
87B CYS* 3.4 23.6 - - - +
89B ARG* 1.3 74.9 - - - +
91B ILE* 1.3 64.1 + - - +
93B ILE* 3.4 5.8 + - - +
94B MET* 3.1 40.5 + - + +
122B VAL* 5.6 0.2 - - - +
124B ILE* 3.8 13.8 - - + +
194B ASP* 4.8 0.2 - - - +
195B PHE* 3.6 30.1 + - - +
196B GLY* 3.6 23.7 + - - -
404B KSA 5.3 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B CYS 3.0 17.3 + - - +
88B LYS* 3.6 8.7 - - - +
89B ARG 3.2 0.2 - - - -
90B GLU* 1.3 77.0 - - - +
92B GLN* 1.3 58.1 + - - +
94B MET* 3.2 9.0 + - - +
95B ARG* 2.9 53.1 + - - +
106B TYR* 4.0 5.3 - - + -
109B SER* 3.5 33.4 - - - +
111B ILE* 4.2 28.5 - - + -
122B VAL* 4.4 6.1 - - + -
124B ILE* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS 2.9 16.5 + - - +
89B ARG* 3.2 7.4 + - - +
91B ILE* 1.3 77.1 - - - +
93B ILE* 1.3 64.1 + - + +
95B ARG* 3.4 29.0 + - - +
96B ASP* 2.9 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG* 2.9 29.6 + - + +
90B GLU* 3.7 6.7 - - - +
92B GLN* 1.3 77.7 - - + +
94B MET* 1.3 63.6 + - - +
96B ASP* 3.2 7.1 + - - +
97B LEU* 2.9 45.0 + - + +
172B ILE* 4.4 27.8 - - + -
195B PHE* 4.3 23.6 - - + +
198B ALA* 4.0 28.0 - - + +
199B THR* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS* 6.4 0.2 - - + -
90B GLU* 3.1 46.2 + - + +
91B ILE* 3.2 6.9 + - - +
93B ILE* 1.3 76.5 - - - +
95B ARG* 1.3 63.7 + - - +
97B LEU* 5.2 0.9 - - - -
98B SER* 2.6 42.0 + - - +
103B ILE* 6.0 1.3 - - - -
104B VAL* 5.2 4.3 - - - +
106B TYR* 4.2 12.3 - - + -
124B ILE* 3.6 32.5 - - + -
126B MET* 4.2 26.5 - - + +
195B PHE* 3.9 31.4 - - + +
404B KSA 6.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 2.9 31.4 + - - +
92B GLN* 3.7 30.7 + - - +
94B MET* 1.3 76.9 - - - +
96B ASP* 1.3 65.4 + - - +
98B SER* 4.3 3.3 + - - -
106B TYR* 3.1 51.0 + - + -
109B SER* 3.7 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLN* 2.9 49.1 + - - +
93B ILE* 3.6 6.4 - - - +
94B MET 3.2 0.2 - - - -
95B ARG* 1.3 80.9 - - - +
97B LEU* 1.3 72.5 + - + +
99B GLY 5.3 0.5 + - - -
164B ARG* 4.1 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 30.9 + - + +
94B MET* 5.2 0.7 - - - -
96B ASP* 1.3 96.7 - - + +
98B SER* 1.3 64.3 + - - +
99B GLY 3.1 4.8 + - - -
100B HIS* 3.1 14.7 + - - +
103B ILE* 4.0 13.5 - - + +
164B ARG* 3.3 31.1 + - + +
165B LEU* 3.5 44.4 - - + +
168B CYS* 4.5 21.1 - - - -
172B ILE* 5.5 5.2 - - + -
195B PHE* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B MET* 2.6 30.9 + - - +
95B ARG* 4.3 2.5 + - - -
96B ASP 3.8 0.8 - - - -
97B LEU* 1.3 76.3 - - - +
99B GLY* 1.3 58.2 + - - +
100B HIS 2.9 15.8 + - - +
103B ILE* 3.5 19.7 - - - +
104B VAL 3.1 16.2 + - - -
105B GLY* 3.8 6.6 - - - -
106B TYR* 3.1 32.5 + - - +
----------------------------------------------------------
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