Contacts of the strand formed by residues 71 - 82 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG* 4.6 11.2 - - - +
13A ASP* 4.2 16.2 - - - +
16A ASP* 3.2 45.2 + - + +
19A ARG* 3.0 23.7 + - - -
20A LEU* 3.6 15.4 - - + +
56A VAL* 4.0 18.2 - - + -
57A ALA 3.3 8.1 - - - +
58A GLU* 5.0 3.4 - - + -
69A HIS* 4.3 1.7 - - - +
70A SER* 1.3 95.5 - - - +
72A VAL* 1.3 64.1 + - - +
73A GLY 3.5 20.4 - - - +
97A MET* 4.0 1.0 - - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.3 2.0 - - - -
57A ALA* 2.9 16.1 + - + +
59A VAL* 3.9 31.2 - - + -
65A THR* 3.8 12.1 - - - +
70A SER 4.5 0.4 - - - -
71A ILE* 1.3 77.7 - - - +
73A GLY* 1.3 57.5 + - - +
96A VAL* 3.6 3.1 - - - +
97A MET* 2.8 39.4 + - - -
100A TYR* 3.5 55.9 - - + -
105A ILE* 4.0 13.7 - - + -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.7 9.3 - - - +
56A VAL* 3.4 2.8 - - - -
57A ALA* 3.0 32.5 + - - -
71A ILE* 3.5 8.9 - - - +
72A VAL* 1.3 80.3 - - - +
74A PHE* 1.3 64.5 + - - +
95A PHE 3.1 13.7 - - - -
96A VAL* 4.1 6.5 - - - -
109A ILE* 5.0 0.9 - - - -
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.7 12.6 - - + -
20A LEU* 3.5 48.0 - - + -
21A ILE* 3.8 22.9 - - + -
24A LEU* 4.2 17.3 - - + -
54A CYS* 4.3 10.3 - - - -
55A LEU 3.2 14.8 - - - +
56A VAL* 4.3 8.3 - - + +
73A GLY* 1.3 75.5 - - - +
75A ALA* 1.3 71.3 + - - +
76A MET* 4.1 22.2 - - + -
93A ASP* 4.5 9.9 - - + -
94A PHE* 3.5 0.9 - - - -
95A PHE* 2.9 50.5 + - + +
109A ILE* 4.4 9.8 - - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A CYS* 3.1 7.1 - - - +
55A LEU* 3.0 37.5 + - + +
74A PHE* 1.3 78.5 - - - +
76A MET* 1.3 60.2 + - - +
77A TYR* 4.3 1.9 + - - -
91A LEU* 4.5 1.3 - - + -
93A ASP 3.2 10.8 - - - +
94A PHE* 4.7 2.7 - - + -
109A ILE* 3.4 31.4 - - + +
113A LEU* 4.4 17.5 - - + -
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.4 22.9 - - + -
36A LEU* 5.6 2.9 - - + -
41A LEU* 4.4 9.6 - - + -
52A TYR* 4.0 32.1 - - + -
53A HIS 3.3 9.2 - - - +
54A CYS* 3.9 19.3 - - - -
74A PHE* 4.0 13.4 - - + -
75A ALA* 1.3 73.9 - - - +
77A TYR* 1.3 65.6 + - - +
78A TYR* 5.2 2.5 - - + -
91A LEU* 3.7 3.3 - - - +
92A GLU* 2.9 48.9 + - + -
93A ASP* 2.8 14.2 + - + +
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.6 1.9 - - - +
53A HIS* 2.8 72.9 + + + +
54A CYS 4.7 0.4 + - - -
55A LEU* 4.0 30.8 - - + +
75A ALA 4.6 2.0 - - - -
76A MET* 1.3 76.5 - - - +
78A TYR* 1.3 72.5 + - - +
79A PHE* 3.9 10.9 - + - -
89A LEU* 3.4 21.1 - - + -
90A TYR 3.2 16.8 - - - +
91A LEU* 4.3 2.5 - - - -
92A GLU 4.3 1.3 - - - +
113A LEU* 3.6 26.0 - - + -
116A VAL* 3.9 32.9 - - + +
119A ARG* 4.3 6.8 + - - -
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Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE 3.8 25.1 - - - +
52A TYR* 4.3 8.1 - - + -
53A HIS* 4.4 8.3 - - + +
76A MET* 5.2 1.8 - - + -
77A TYR* 1.3 86.6 - - - +
79A PHE* 1.3 68.1 + - - +
80A THR* 3.8 18.6 - - + -
89A LEU* 3.9 3.6 - - - +
90A TYR* 2.9 61.3 + + + +
92A GLU* 2.7 42.5 + - + -
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 3.8 30.3 - + - -
77A TYR* 3.9 17.5 - + - -
78A TYR* 1.3 81.1 - - - +
80A THR* 1.3 66.3 + - - +
87A LYS* 4.0 17.0 - - + -
88A LEU 3.4 13.2 - - - +
89A LEU* 3.9 18.6 - - + -
116A VAL* 4.1 3.1 - - + -
119A ARG* 5.4 0.9 - - - -
120A CYS* 3.8 37.5 - - + -
122A CYS* 3.8 13.0 - - - -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.8 14.8 + - + -
79A PHE* 1.3 81.6 - - - +
81A TYR* 1.3 65.8 + - - +
87A LYS* 3.5 8.8 - - - +
88A LEU* 2.9 48.4 + - - +
90A TYR* 3.7 34.1 - - + +
126A HIS* 5.5 0.9 - - - +
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR* 1.3 80.4 - - - +
82A ASP* 1.3 81.3 + - - +
83A PRO* 4.2 11.1 - - + +
86A GLY* 3.5 12.6 - - - -
87A LYS* 3.4 32.5 - - + -
88A LEU* 4.6 3.9 - - - +
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 1.3 81.2 - - - +
83A PRO* 1.3 68.1 - - - +
84A TRP* 2.7 45.4 + - - +
85A ILE* 3.3 18.1 + - + -
86A GLY* 2.7 43.5 + - - +
88A LEU* 4.0 17.0 - - + +
126A HIS* 5.3 3.5 + - - -
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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