Contacts of the strand formed by residues 70 - 78 (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 LYS 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 4.8 20.2 - - - +
49B ASP* 3.5 25.1 - - - +
62B LEU* 4.5 18.2 - - + -
63B VAL 3.4 4.9 - - - +
64B ARG* 3.5 18.2 - - + -
68B GLY 3.6 5.5 + - - +
69B MET* 1.3 73.8 - - - +
71B CYS* 1.3 61.9 - - - +
128B PHE* 4.1 15.7 + - + +
130B ARG* 5.1 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.5 6.2 - - - +
63B VAL* 2.9 33.6 + - + +
65B THR* 3.8 27.4 - - - -
69B MET* 4.0 13.0 - - - -
70B LYS* 1.3 78.5 - - - +
72B ALA* 1.3 61.1 + - - +
107B ILE* 3.6 22.4 - - - -
125B LEU* 3.6 24.0 - - + -
126B MET 3.4 12.1 - - - +
128B PHE* 4.0 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.4 5.8 - - + -
60B VAL* 4.3 6.1 - - + -
61B PHE 3.3 7.9 - - - +
71B CYS* 1.3 75.0 - - - +
73B LEU* 1.3 61.0 + - - +
74B LYS 4.2 0.6 + - - -
124B ILE 3.7 1.0 - - - +
125B LEU* 3.5 4.7 - - - +
126B MET* 2.8 39.3 + - + +
127B ASP 4.0 3.8 - - - +
128B PHE* 4.0 4.4 - - - +
404B KSA 3.3 46.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.6 35.7 - - + -
46B VAL* 3.8 18.8 - - + -
59B ILE 3.4 1.7 - - - +
60B VAL* 3.1 8.2 - - - -
61B PHE* 2.8 44.5 + - + +
63B VAL* 3.7 24.5 - - + -
72B ALA* 1.3 74.0 - - - +
74B LYS* 1.3 65.2 + - - +
75B ARG* 4.7 1.1 - - + +
123B LEU* 4.0 18.8 - - + -
124B ILE 3.5 28.9 - - - +
125B LEU* 4.2 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 4.1 26.2 - - + -
59B ILE 3.5 5.2 - - - +
60B VAL* 4.2 7.4 - - + -
73B LEU* 1.3 74.8 - - - +
75B ARG* 1.3 62.3 + - - +
76B MET* 4.1 16.9 - - - +
90B GLU* 2.7 36.7 + - - +
94B MET* 6.4 0.2 - - + -
122B VAL* 3.4 4.9 - - - +
123B LEU* 3.5 2.1 - - - -
124B ILE* 2.9 45.8 + - + +
126B MET* 3.5 19.3 - - + +
194B ASP* 4.9 4.3 - - - -
196B GLY* 5.5 0.9 - - - -
404B KSA 3.5 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 4.6 11.3 + - - -
37B ARG* 3.9 17.0 - - - +
39B PHE* 3.2 45.2 - - - -
58B ALA* 3.5 3.1 - - - -
59B ILE* 3.0 32.5 + - + +
61B PHE* 4.1 19.1 - - + -
73B LEU* 3.9 1.5 + - + -
74B LYS* 1.3 74.8 - - - +
76B MET* 1.3 70.2 + - - +
77B PHE* 3.1 38.9 - - + -
121B GLU* 2.9 25.6 + - + +
122B VAL 3.3 4.3 - - - +
123B LEU* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 5.5 2.0 - - - +
57B PHE* 3.7 27.4 - - + +
58B ALA* 4.0 6.3 - - + -
74B LYS* 4.1 24.9 - - - +
75B ARG* 1.3 78.5 - - - +
77B PHE* 1.3 81.6 + - - +
78B VAL* 4.1 12.6 - - + -
87B CYS* 4.1 16.6 - - - -
90B GLU* 4.8 2.5 - - - +
121B GLU* 3.7 2.9 - - - +
122B VAL* 2.8 46.7 + - + +
219B LYS* 6.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE 5.0 2.0 + - - +
75B ARG* 3.1 46.9 - - + -
76B MET* 1.3 85.6 - - - +
78B VAL* 1.3 68.8 + - - +
114B VAL* 4.9 10.3 - - + -
119B VAL* 4.1 19.3 - - + -
120B TRP 3.3 13.9 - - - +
121B GLU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 4.1 9.6 - - + -
77B PHE* 1.3 79.9 - - - +
79B ASN* 1.3 61.1 + - - +
80B ASN 3.7 0.7 - - - +
83B ASP* 3.7 28.0 - - + +
84B LEU* 4.0 26.7 - - + +
87B CYS* 3.9 24.0 - - - -
118B ASP 3.5 0.5 - - - +
119B VAL* 3.4 4.7 - - - +
120B TRP* 2.8 52.7 + - + +
122B VAL* 4.3 7.9 - - + -
----------------------------------------------------------
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