Contacts of the strand formed by residues 74 - 82 (chain B) in PDB entry 6QPA
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 MET 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 4.2 2.9 - - - -
15B ILE* 2.8 49.9 + - + +
16B ALA 4.8 0.7 - - - +
17B ASN* 3.6 30.3 - - + +
22B TYR* 3.6 28.9 - - - +
25B MET* 6.3 0.2 - - - -
49B LEU* 4.0 24.0 - - + -
50B GLN 3.2 22.4 - - - +
68B ARG* 4.7 11.9 - - + +
71B LEU* 3.8 23.8 - - + +
72B ASN* 4.1 0.8 - - - +
73B PRO* 1.3 74.6 - - - +
75B GLY* 1.3 65.8 + - - +
76B MET 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.5 7.9 - - - -
14B LYS* 4.4 10.3 - - - +
49B LEU* 3.6 4.9 - - - +
50B GLN* 2.9 52.1 + - - +
73B PRO 4.3 0.2 - - - -
74B MET* 1.3 74.7 - - - +
76B MET* 1.3 59.9 + - - +
77B PHE* 4.2 3.4 - - - -
297B MET* 4.6 9.0 - - - -
299B PHE* 4.4 3.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
11B ASN 3.4 3.5 - - - +
13B ALA* 2.8 40.9 + - + +
15B ILE* 3.9 29.2 - - + -
25B MET* 4.1 23.6 - - + +
47B GLN* 4.4 11.9 - - + +
48B LEU 3.4 8.5 - - - +
49B LEU* 3.7 24.0 - - + -
75B GLY* 1.3 72.9 - - - -
77B PHE* 1.3 61.9 + - - +
78B GLN* 3.5 35.2 - - - +
109B MET* 4.3 13.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
10B ILE* 3.8 22.0 - - + -
11B ASN 3.4 2.9 - - - -
12B MET* 3.8 42.4 - - + -
13B ALA 4.7 3.6 - - - -
14B LYS* 5.8 3.6 - - + -
46B GLU 3.6 1.7 - - - +
47B GLN* 3.9 0.2 - - - -
48B LEU* 2.7 53.4 + - + +
75B GLY* 4.2 1.5 - - - -
76B MET* 1.3 84.3 - - - +
78B GLN* 1.3 60.4 + - - +
79B TYR* 4.0 0.9 - - + -
162B ILE* 3.6 31.6 - - + -
254B LEU* 5.0 1.1 - - + -
297B MET* 4.3 21.3 - - + -
299B PHE* 3.8 28.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 3.4 2.1 - - - +
11B ASN* 2.9 55.3 + - + +
29B GLY* 6.3 0.6 - - - -
32B VAL* 4.9 13.5 - - - +
33B CSS 4.7 17.9 - - - -
45B PHE* 6.6 0.2 - - + -
46B GLU 3.3 4.7 - - - +
47B GLN* 4.2 21.2 + - + +
76B MET* 3.5 33.2 - - - +
77B PHE* 1.3 74.6 - - - +
79B TYR* 1.3 66.5 + - - +
80B THR* 3.7 7.5 + - + +
103B CSS 5.7 5.6 - - - -
116B GLU* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.0 23.1 - - + -
9B ALA 3.4 4.9 - - - -
10B ILE* 3.7 32.1 - - + -
45B PHE* 3.0 10.4 - - - +
46B GLU* 2.7 57.1 + - + +
48B LEU* 3.6 24.5 - - + -
77B PHE* 4.6 1.8 - - + -
78B GLN* 1.3 75.3 - - - +
80B THR* 1.3 61.8 + - - +
81B VAL* 4.7 4.5 - - + -
162B ILE* 3.4 21.8 - - + +
197B MET* 3.9 13.9 - - + -
199B MET* 3.5 13.3 - - + +
256B HIS* 2.7 37.9 + + - -
308B TRP* 5.0 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.5 1.9 - - - -
9B ALA* 2.9 43.8 + - - +
33B CSS 4.5 10.3 - - - -
36B THR* 4.4 10.3 - - + +
42B PHE* 4.0 16.6 - - + -
44B GLY 3.6 3.6 - - - -
45B PHE* 4.2 5.6 - - + -
78B GLN* 3.7 8.7 + - + +
79B TYR* 1.3 78.9 - - - +
81B VAL* 1.3 62.1 + - - +
82B TRP* 2.9 32.8 + - + -
88B HIS* 3.9 7.1 + - - -
116B GLU* 4.2 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.5 31.9 - - + -
7B ILE 3.5 6.3 - - - +
8B ILE* 4.1 20.4 - - + -
42B PHE* 3.9 1.7 - - - -
43B LEU* 2.8 28.0 + - + -
44B GLY 2.9 16.7 + - - +
79B TYR* 4.7 6.3 - - + -
80B THR* 1.3 76.8 - - - +
82B TRP* 1.3 69.2 + - - +
308B TRP* 3.7 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.1 6.8 - - - +
7B ILE* 2.9 45.5 + - + -
9B ALA* 4.5 2.0 - - + -
36B THR* 3.5 34.3 - - + -
39B HIS* 4.2 6.1 - - + -
41B GLY 3.4 21.5 - - - -
42B PHE* 3.6 24.7 - + + -
43B LEU* 3.6 6.5 - - - -
80B THR* 2.9 45.0 + - + -
81B VAL* 1.3 75.0 - - - +
83B LYS* 1.3 61.4 + - - +
84B ASP 3.4 17.0 - - - +
87B SER* 3.7 15.7 - - - -
88B HIS* 3.2 48.6 - + + -
91B MET* 3.7 22.4 - - + -
----------------------------------------------------------
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