Contacts of the strand formed by residues 71 - 82 (chain B) in PDB entry 2G3T
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 ILE 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ARG* 4.4 1.3 - - - +
13B ASP* 4.3 14.4 - - - +
16B ASP* 3.9 39.3 - - + +
17B ILE* 5.2 0.2 - - + -
19B ARG* 2.8 31.3 + - - +
20B LEU* 3.5 15.8 - - + +
56B VAL* 3.3 41.1 - - + -
57B ALA 3.3 3.8 - - - +
58B GLU* 4.0 11.2 - - + +
69B HIS* 4.5 1.0 - - - +
70B SER* 1.3 95.9 - - - +
72B VAL* 1.3 64.1 + - - +
73B GLY 3.5 12.8 - - - +
97B MET* 4.1 0.2 - - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.2 0.7 - - - -
57B ALA* 3.0 12.8 + - + +
59B VAL* 3.5 36.1 - - + -
65B THR* 3.9 14.6 - - + -
70B SER 4.2 0.2 - - - +
71B ILE* 1.3 77.1 - - - +
73B GLY* 1.3 57.8 + - - +
96B VAL* 3.6 5.2 - - - +
97B MET* 2.8 36.8 + - - +
100B TYR* 3.6 52.0 - - + -
105B ILE* 4.2 11.0 - - + -
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 3.4 11.5 - - - +
56B VAL* 3.6 0.7 - - - -
57B ALA* 3.1 31.7 + - - -
71B ILE* 3.5 10.0 - - - +
72B VAL* 1.3 79.8 - - - +
74B PHE* 1.3 64.3 + - - +
95B PHE 3.0 14.8 - - - -
96B VAL* 4.0 5.8 - - - -
109B ILE* 5.8 0.4 - - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 3.8 25.1 - - + -
20B LEU* 3.5 39.9 - - + -
21B ILE* 3.8 22.9 - - + -
24B LEU* 4.2 16.2 - - + -
54B CYS* 4.3 10.3 - - - -
55B LEU 3.1 14.8 - - - +
56B VAL* 4.4 0.4 - - - +
57B ALA 4.8 0.2 - - - +
73B GLY* 1.3 74.4 - - - +
75B ALA* 1.3 69.0 + - - +
76B MET* 4.0 22.9 - - + -
93B ASP* 4.5 8.7 - - + -
94B PHE* 3.0 5.4 - - - +
95B PHE* 2.9 54.4 + - + +
96B VAL* 5.4 1.0 - - - +
109B ILE* 5.3 7.4 - - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B HIS 3.7 0.3 - - - +
54B CYS* 3.1 7.1 - - - +
55B LEU* 2.9 40.6 + - + -
74B PHE* 1.3 78.2 - - - +
76B MET* 1.3 60.5 + - - +
77B TYR* 4.2 1.7 + - - -
91B LEU* 4.6 0.7 - - + -
93B ASP 3.2 7.2 - - - +
94B PHE* 3.8 7.4 - - + -
109B ILE* 3.4 31.2 - - + -
113B LEU* 4.4 15.3 - - + -
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 5.0 0.4 - - + -
21B ILE* 4.4 23.1 - - + -
36B LEU* 5.8 3.4 - - + -
41B LEU* 4.4 9.6 - - + -
52B TYR* 3.9 39.3 - - + -
53B HIS 3.4 8.3 - - - +
54B CYS* 4.0 12.6 - - - -
74B PHE* 4.0 12.5 - - + -
75B ALA* 1.3 73.0 - - - +
77B TYR* 1.3 64.6 + - - +
78B TYR* 5.2 2.5 - - + -
91B LEU* 3.6 3.9 - - - +
92B GLU* 2.8 50.0 + - + +
93B ASP* 2.7 16.1 + - + +
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.6 1.7 - - - -
53B HIS* 2.7 76.2 + + + +
54B CYS 4.5 0.4 - - - -
55B LEU* 4.1 28.0 - - + +
75B ALA 4.6 1.8 - - - -
76B MET* 1.3 76.7 - - - +
78B TYR* 1.3 72.6 + - - +
79B PHE* 3.9 12.8 - + - -
89B LEU* 3.7 21.3 - - + -
90B TYR 3.1 15.9 - - - +
91B LEU* 4.3 3.8 - - - -
92B GLU 4.3 1.3 - - - +
113B LEU* 3.6 23.6 - - + -
116B VAL* 3.8 32.9 - - + +
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE 3.7 25.6 - - - +
52B TYR* 4.2 8.1 - - + -
53B HIS* 4.3 8.1 - - + +
76B MET* 5.2 2.2 - - + -
77B TYR* 1.3 86.4 - - - +
79B PHE* 1.3 66.7 + - - +
80B THR* 3.7 17.9 - - + -
89B LEU* 3.8 3.3 - - - +
90B TYR* 2.8 62.0 + + + +
92B GLU* 2.8 41.4 + - + -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B HIS* 3.9 31.4 - + - -
77B TYR* 3.9 17.7 - + - -
78B TYR* 1.3 81.7 - - - +
80B THR* 1.3 66.3 + - - +
87B LYS* 4.0 21.1 - - + -
88B LEU 3.3 4.0 - - - +
89B LEU* 4.4 7.2 - - + -
116B VAL* 4.1 8.3 - - + -
120B CYS* 3.8 29.8 - - + -
122B CYS* 3.6 32.5 - - - -
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TYR* 3.7 15.0 + - + -
79B PHE* 1.3 79.8 - - - +
81B TYR* 1.3 66.2 + - - +
87B LYS* 3.5 8.7 - - - +
88B LEU* 2.8 51.1 + - - +
89B LEU 4.8 0.2 + - - -
90B TYR* 3.7 32.9 - - + +
126B HIS* 5.6 0.7 - - - +
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B THR* 1.3 80.2 - - - +
82B ASP* 1.3 79.9 + - - +
83B PRO* 4.2 11.2 - - + +
86B GLY* 3.5 12.8 - - - -
87B LYS* 3.5 30.3 - - + -
88B LEU* 4.6 3.7 - - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 1.3 80.1 - - - +
83B PRO* 1.3 68.9 - - - +
84B TRP* 2.8 43.6 + - - +
85B ILE* 3.1 19.1 + - + +
86B GLY* 2.7 44.6 + - - +
88B LEU* 4.0 17.4 - - + +
126B HIS* 5.4 2.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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