Contacts of the strand formed by residues 86 - 96 (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 GLY 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.7 24.7 - - - -
82B ASP* 2.7 48.4 + - - +
83B PRO 4.8 0.2 - - - -
84B TRP 3.8 0.6 - - - -
85B ILE* 1.3 74.2 - - - +
87B LYS* 1.3 65.3 + - - +
88B LEU* 3.6 2.3 + - - +
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Residues in contact with LYS 87 (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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79B PHE* 4.0 19.8 - - + -
80B THR 3.5 11.9 - - - +
81B TYR* 3.5 15.5 - - + -
85B ILE 4.0 1.2 + - - +
86B GLY* 1.3 71.2 - - - -
88B LEU* 1.3 67.9 + - - +
120B CYS* 2.9 36.1 + - - +
121B ARG* 4.0 12.6 - - - +
122B CYS* 3.4 18.1 - - - -
123B SER* 3.2 23.7 + - - -
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Residues in contact with LEU 88 (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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79B PHE* 3.3 9.0 - - - +
80B THR* 2.8 46.1 + - - +
81B TYR 4.9 1.8 - - - +
82B ASP* 4.0 21.1 - - + +
85B ILE* 3.9 11.7 - - + -
86B GLY 3.8 7.2 - - - +
87B LYS* 1.3 76.6 - - - +
89B LEU* 1.3 63.3 + - - +
122B CYS* 3.7 6.5 - - - -
123B SER* 3.2 22.9 - - - +
124B SER* 3.1 28.7 - - - +
126B HIS* 3.7 34.5 - - + +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.7 28.9 - - + -
78B TYR 3.9 3.4 - - - +
79B PHE* 4.4 11.2 - - + -
88B LEU* 1.3 76.1 - - - +
90B TYR* 1.3 93.7 + - - +
91B LEU* 4.1 2.0 - - + +
113B LEU* 3.4 31.0 - - + +
116B VAL* 4.4 4.7 - - + -
117B ALA* 3.7 17.9 - - + +
122B CYS* 3.7 14.2 - - + -
124B SER 3.1 12.0 + - - +
125B MET* 3.1 25.7 - - + +
126B HIS* 2.9 24.4 + - - +
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Residues in contact with TYR 90 (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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77B TYR* 3.1 6.6 - - - +
78B TYR* 2.8 79.0 + + + +
80B THR* 3.7 19.3 - - + +
88B LEU 4.0 0.2 + - - -
89B LEU* 1.3 77.6 - - - +
91B LEU* 1.3 73.0 + - - +
92B GLU* 3.4 14.2 + - - -
126B HIS* 3.4 30.7 - + + -
127B PHE* 4.2 7.4 - - - -
128B LEU* 3.2 36.7 - - + +
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Residues in contact with LEU 91 (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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75B ALA* 4.6 2.2 - - + -
76B MET 3.6 9.4 - - - +
77B TYR* 4.3 3.1 - - + -
89B LEU* 4.1 1.4 - - + +
90B TYR* 1.3 78.6 - - - +
92B GLU* 1.3 61.8 + - - +
93B ASP* 3.6 29.4 - - - +
94B PHE* 4.4 12.3 - - + -
110B LEU* 4.5 4.0 - - + -
113B LEU* 3.7 33.0 - - + -
125B MET* 4.1 26.2 - - + +
126B HIS 2.9 8.4 + - - +
127B PHE* 3.3 33.8 - - + +
128B LEU 4.7 1.2 + - - -
140B TYR* 4.1 18.8 - - + +
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Residues in contact with GLU 92 (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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76B MET* 2.8 41.1 + - + +
78B TYR* 2.8 43.5 + - + -
90B TYR* 3.4 12.2 + - - -
91B LEU* 1.3 74.4 - - - +
93B ASP* 1.3 74.9 + - + +
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Residues in contact with ASP 93 (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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24B LEU* 3.7 31.9 - - + +
28B GLU* 4.8 8.2 - - - +
74B PHE* 4.8 9.0 - - + -
75B ALA* 3.2 0.3 - - - -
76B MET* 2.7 29.0 + - + -
91B LEU* 3.6 10.1 - - - +
92B GLU* 1.3 93.0 - - + +
94B PHE* 1.3 74.0 + - - +
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Residues in contact with PHE 94 (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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24B LEU* 5.1 1.7 - - - +
74B PHE* 3.0 16.2 - - - +
75B ALA* 3.8 12.8 - - + -
91B LEU* 4.4 12.6 - - + -
93B ASP* 1.3 87.1 + - - +
95B PHE* 1.3 67.1 + - - +
96B VAL* 4.4 12.8 - - + -
106B GLY* 3.9 28.0 - - - -
109B ILE* 4.4 9.4 - - + -
110B LEU* 3.8 19.7 - - + -
139B PHE* 5.4 7.6 - + - -
140B TYR* 3.1 29.4 - + - -
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Residues in contact with PHE 95 (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* 3.8 22.0 - - + -
23B GLU* 3.3 39.0 - - + -
24B LEU* 3.7 29.6 - - + -
27B TYR* 4.2 21.5 - + + -
73B GLY* 3.0 4.5 - - - -
74B PHE* 2.9 45.5 + - + -
94B PHE* 1.3 77.2 - - - +
96B VAL* 1.3 70.5 + - - +
97B MET* 3.8 21.5 - - + -
98B SER* 4.4 4.3 - - - -
101B ARG* 3.3 28.3 - - - -
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Residues in contact with VAL 96 (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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72B VAL 3.6 7.9 - - - +
73B GLY* 4.8 2.0 - - - -
74B PHE 5.4 0.7 - - - +
94B PHE* 4.4 11.1 - - + -
95B PHE* 1.3 81.4 - - - +
97B MET* 1.3 70.8 + - - +
98B SER 3.2 2.4 + - - -
100B TYR* 3.9 0.7 - - + -
101B ARG* 3.4 51.3 + - + +
105B ILE* 3.5 50.9 - - + -
106B GLY* 3.9 20.4 - - - +
109B ILE* 5.1 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