Contacts of the strand formed by residues 82 - 94 (chain B) in PDB entry 2G1Y
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 THR 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B THR* 3.5 25.4 - - + -
76B LEU 3.1 13.9 - - - +
77B ARG* 3.4 35.8 + - + +
78B TYR* 4.3 1.8 + - - -
80B THR 5.2 0.2 + - - -
81B GLY* 1.3 75.7 + - - -
83B VAL* 1.3 68.6 + - - +
84B SER* 4.7 1.3 - - - +
108B GLU* 5.7 0.5 - - - +
110B PRO* 3.0 31.2 - - - +
114B PHE* 4.0 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 4.0 21.5 - - + +
74B LEU* 6.0 0.4 - - + -
75B THR* 3.3 1.9 - - - +
76B LEU* 2.7 56.0 + - + +
78B TYR* 4.8 3.1 - - + -
82B THR* 1.3 75.1 - - - +
84B SER* 1.3 65.3 + - - +
106B VAL* 3.6 24.7 - - + -
108B GLU* 3.4 16.2 - - - +
109B MET* 4.5 2.7 - - + -
110B PRO* 4.3 3.1 - - + -
114B PHE* 3.4 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 6.3 0.9 - - - -
74B LEU* 3.2 13.7 - - - -
75B THR* 3.1 22.1 + - - +
82B THR* 4.7 1.7 - - - +
83B VAL* 1.3 77.0 + - - +
85B GLY* 1.3 59.4 + - - +
106B VAL* 3.2 9.5 - - - +
107B THR* 2.7 24.1 + - - -
108B GLU* 3.1 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.5 9.7 - - - +
74B LEU* 2.8 39.0 + - - +
84B SER* 1.3 77.2 - - - +
86B PHE* 1.3 62.4 + - - -
105B GLU 2.9 14.6 - - - -
107B THR* 3.9 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 3.7 2.2 - - - -
45B LYS* 3.6 31.2 - - + -
67B TYR* 4.9 7.6 - - - -
69B HIS* 5.9 3.4 - + - -
71B GLY* 3.5 28.3 - - - +
72B THR 3.2 4.7 - - - +
73B GLU* 4.6 2.2 - - + -
74B LEU* 4.8 1.8 - - - -
85B GLY* 1.3 75.8 - - - +
87B LEU* 1.3 74.6 + - - +
88B SER* 3.9 0.7 - - - -
104B GLY* 4.4 2.5 - - - -
105B GLU* 2.8 80.1 + - + +
107B THR* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASN* 5.8 0.2 - - - +
67B TYR* 5.5 0.2 + - - -
70B ASN* 2.6 40.7 + - - +
72B THR* 2.5 37.2 + - + +
74B LEU* 3.6 30.5 - - + +
86B PHE* 1.3 78.3 - - - +
88B SER* 1.3 69.2 + - - +
102B MET* 4.2 17.5 - - + +
103B PHE* 3.5 22.7 - - - +
104B GLY* 4.3 0.4 - - - +
133B GLY* 5.1 5.8 - - - +
135B VAL* 3.9 30.1 - - + -
986B NAG 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.9 15.4 + - - -
68B LYS 4.3 5.4 - - - -
70B ASN* 4.4 4.9 - - - +
86B PHE* 3.8 3.8 + - - -
87B LEU* 1.3 83.1 + - - +
89B GLN* 1.3 60.1 + - - +
102B MET* 3.2 9.2 - - - +
103B PHE* 2.8 50.2 + - - -
105B GLU* 2.5 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER 5.4 0.7 - - - +
67B TYR* 3.5 2.8 - - - -
68B LYS* 2.9 64.5 + - + +
70B ASN* 5.8 0.4 - - + -
88B SER* 1.3 77.4 - - - +
90B ASP* 1.3 69.9 + - - +
100B THR* 3.2 29.5 - - + +
101B GLN 3.5 7.4 - - - +
102B MET* 3.7 29.7 - - - +
103B PHE* 4.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.1 4.7 - - + -
22B GLY* 3.0 20.6 - - - -
59B PHE* 3.8 5.8 - - + -
64B SER* 2.8 23.6 + - - -
66B SER* 2.7 32.0 + - - -
67B TYR* 3.3 12.2 - - - +
89B GLN* 1.3 81.2 - - - +
91B ILE* 1.3 82.9 + - - +
92B ILE* 3.6 3.4 + - - +
100B THR* 4.3 3.8 - - - -
101B GLN* 2.8 29.9 + - - +
103B PHE* 3.8 17.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
20B GLY 3.7 0.9 - - - +
21B ILE* 3.5 2.6 - - - -
22B GLY 3.0 28.1 + - - +
23B THR* 3.6 21.5 - - + +
66B SER* 4.3 12.1 - - - +
90B ASP* 1.3 91.9 + - - +
92B ILE* 1.3 60.4 + - - +
93B THR* 5.1 5.3 + - - +
98B THR* 4.8 17.7 - - + -
99B VAL 3.6 10.8 - - - +
100B THR* 4.0 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.1 17.9 - - + -
20B GLY 3.0 9.0 - - - +
21B ILE* 4.1 20.0 - - + -
39B VAL* 4.2 19.7 - - + -
90B ASP 4.0 3.1 - - - +
91B ILE* 1.3 78.1 - - - +
93B THR* 1.3 64.4 + - - +
94B VAL* 3.7 20.1 + - + -
97B ILE 3.3 1.9 - - - +
98B THR* 3.1 5.6 - - - -
99B VAL* 2.8 39.6 + - - +
101B GLN* 3.6 33.9 - - + +
103B PHE* 4.6 9.0 - - + -
123B VAL* 6.3 0.4 - - + -
138B ILE* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 3.1 9.2 - - - +
20B GLY* 2.5 45.0 + - - -
22B GLY 5.4 0.3 + - - -
25B PRO* 4.2 16.5 - - + +
91B ILE* 5.1 7.3 + - - +
92B ILE* 1.3 72.3 - - - +
94B VAL* 1.3 61.3 + - - +
95B GLY* 3.9 3.2 + - - +
96B GLY* 4.6 14.4 - - - +
97B ILE 3.2 7.2 - - - +
98B THR* 4.1 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 3.0 10.8 + - - +
5B VAL* 4.3 12.8 - - + -
18B GLU 5.1 0.4 - - - +
19B ILE* 4.6 8.1 - - + -
32B PHE* 4.3 23.8 - - + -
92B ILE* 3.8 21.8 - - + +
93B THR* 1.3 75.6 - - - +
95B GLY* 1.3 70.2 + - - +
96B GLY 3.5 0.4 - - - -
97B ILE* 2.6 25.9 + - + +
99B VAL* 4.9 1.3 - - + -
123B VAL* 6.3 1.6 - - + -
138B ILE* 4.5 17.5 - - + -
142B ILE* 4.7 8.1 - - + -
173B LEU* 4.0 24.5 - - + -
----------------------------------------------------------
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