Contacts of the strand formed by residues 86 - 96 (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 GLY 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.5 24.5 - - - -
82A ASP* 2.7 42.3 + - - +
83A PRO 4.8 0.4 + - - -
84A TRP 3.9 0.4 - - - -
85A ILE* 1.3 75.2 - - - +
87A LYS* 1.3 66.3 + - - +
88A LEU* 3.5 6.2 + - - +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 4.0 19.2 - - + -
80A THR 3.5 12.6 - - - +
81A TYR* 3.4 17.4 - - + -
85A ILE 4.2 0.8 + - - -
86A GLY* 1.3 72.7 - - - -
88A LEU* 1.3 65.7 + - - +
120A CYS* 2.9 36.8 + - - +
121A ARG* 4.0 9.7 + - - +
122A CYS* 3.3 17.5 - - - -
123A SER* 3.3 24.1 + - - -
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Residues in contact with LEU 88 (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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79A PHE* 3.4 8.8 - - - +
80A THR* 2.9 44.9 + - - +
81A TYR 4.9 1.6 - - - -
82A ASP* 4.0 20.4 - - + +
85A ILE* 4.0 22.4 - - + -
86A GLY 3.7 7.6 - - - +
87A LYS* 1.3 83.5 - - - +
89A LEU* 1.3 62.9 + - - +
122A CYS* 3.6 8.1 - - - -
123A SER* 4.2 1.1 - - - -
124A SER* 3.4 34.5 - - - +
126A HIS* 3.7 33.9 - - + +
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Residues in contact with LEU 89 (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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77A TYR* 3.4 36.6 - - + -
78A TYR 3.9 2.2 - - - +
79A PHE* 3.9 17.3 - - + -
88A LEU* 1.3 75.5 - - - +
90A TYR* 1.3 67.2 + - - +
113A LEU* 3.4 34.1 - - + +
116A VAL* 4.2 4.5 - - + -
117A ALA* 3.8 13.7 - - + +
122A CYS* 3.6 15.1 - - + -
124A SER 3.1 12.2 + - - +
125A MET* 3.1 29.1 - - + -
126A HIS* 2.9 25.1 + - - +
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Residues in contact with TYR 90 (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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77A TYR* 3.2 8.1 - - - +
78A TYR* 2.9 81.0 + + + +
80A THR* 3.7 20.2 - - + +
88A LEU 4.0 0.2 + - - -
89A LEU* 1.3 75.0 - - - +
91A LEU* 1.3 73.8 + - - +
92A GLU* 3.4 14.6 + - - -
126A HIS* 3.4 29.4 - + + -
127A PHE* 4.2 7.4 - - - -
128A LEU* 3.2 36.1 + - + +
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Residues in contact with LEU 91 (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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75A ALA* 4.5 4.3 - - + -
76A MET 3.7 8.3 - - - +
77A TYR* 4.3 2.9 - - + -
89A LEU* 4.1 1.0 + - - -
90A TYR* 1.3 78.3 - - - +
92A GLU* 1.3 60.7 + - - +
93A ASP* 3.5 29.2 - - - +
94A PHE* 4.5 9.4 - - + -
110A LEU* 4.5 6.5 - - + -
113A LEU* 3.7 34.1 - - + -
125A MET* 4.1 26.2 - - + +
126A HIS 2.9 8.0 + - - +
127A PHE* 3.3 34.7 - - + +
128A LEU 4.6 1.6 + - - -
140A TYR* 4.3 17.5 - - + +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A MET* 2.9 40.4 + - + +
78A TYR* 2.7 44.9 + - + -
90A TYR* 3.4 12.7 + - - -
91A LEU* 1.3 76.3 - - - +
93A ASP* 1.3 77.1 + - + +
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.7 32.3 - - + +
28A GLU* 5.1 4.0 - - - +
74A PHE* 4.6 12.1 - - + -
75A ALA* 3.2 3.7 - - - -
76A MET* 2.8 29.3 + - + -
91A LEU* 3.5 7.2 - - - +
92A GLU* 1.3 97.1 - - + +
94A PHE* 1.3 68.1 + - - +
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Residues in contact with PHE 94 (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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24A LEU* 5.0 3.3 - - - +
74A PHE* 3.5 6.3 - - - -
75A ALA* 4.3 0.7 - - + +
91A LEU* 4.5 15.5 - - + -
93A ASP* 1.3 82.8 + - - +
95A PHE* 1.3 68.0 + - - +
96A VAL* 4.1 15.5 - - + -
106A GLY* 3.0 47.3 - - - -
109A ILE* 3.7 29.8 - - + -
110A LEU* 3.8 22.7 - - + -
113A LEU* 4.8 1.3 - - + -
139A PHE* 6.2 3.1 - + - -
140A TYR* 4.9 7.0 - - - +
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Residues in contact with PHE 95 (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* 3.8 30.1 - - + -
23A GLU* 3.7 43.5 - - + -
24A LEU* 3.8 26.5 - - + -
27A TYR* 4.2 24.5 - + + -
73A GLY* 3.1 3.5 - - - -
74A PHE* 2.9 48.0 + - + +
94A PHE* 1.3 78.9 - - - +
96A VAL* 1.3 81.8 + - - +
97A MET* 4.0 3.1 - - - -
98A SER 4.9 0.9 - - - -
101A ARG* 3.5 23.1 - - - -
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Residues in contact with VAL 96 (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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72A VAL 3.6 10.3 - - - +
73A GLY* 4.6 1.3 - - - -
94A PHE* 4.1 21.0 - - + -
95A PHE* 1.3 84.3 - - - +
97A MET* 1.3 66.3 + - - +
100A TYR* 3.8 25.4 - - + +
101A ARG* 2.6 52.2 + - + +
105A ILE* 3.8 33.9 - - + -
106A GLY* 4.4 4.5 - - - +
109A ILE* 4.3 5.6 - - + -
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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