Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 2GRU
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 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 4.3 3.2 - - - -
35B ASP* 3.1 8.5 + - - -
36B GLN* 2.6 37.9 + - - +
38B ILE* 3.4 18.4 - - + -
92B ALA* 4.3 3.4 - - + -
93B ASN* 3.0 27.5 + - - -
94B ARG 4.3 1.0 - - - +
95B ARG* 1.3 81.5 - - - +
97B ALA* 1.3 75.8 + - - +
98B ILE* 5.2 0.2 - - + -
121B ILE* 3.7 32.5 - - + +
122B ALA* 3.9 4.2 + - - +
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Residues in contact with ALA 97 (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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34B PHE* 3.7 26.2 - - + -
36B GLN 3.1 4.6 + - - -
37B TYR* 3.4 22.8 - - + -
38B ILE 3.0 24.9 + - - -
95B ARG 4.0 0.4 + - - -
96B THR* 1.3 79.7 - - - +
98B ILE* 1.3 59.9 + - - +
99B VAL 3.9 0.2 + - - -
122B ALA* 3.4 15.0 - - + +
124B ILE* 4.0 12.8 - - + -
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Residues in contact with ILE 98 (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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38B ILE* 3.3 28.3 - - + +
40B ILE* 3.8 30.7 - - + -
87B ALA* 5.1 1.8 - - + -
97B ALA* 1.3 72.5 - - - +
99B VAL* 1.3 57.5 + - - +
100B ALA 4.0 0.2 + - - -
110B ALA* 3.9 26.7 - - + +
113B ALA* 5.3 1.3 - - + -
114B ALA* 3.9 19.7 - - + +
117B MET* 4.2 16.4 - - - -
121B ILE* 3.7 26.5 - - + -
122B ALA 2.7 12.1 + - - +
123B LEU* 3.6 3.3 - - + +
124B ILE* 2.6 35.0 + - - +
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Residues in contact with VAL 99 (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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37B TYR* 3.5 40.2 - - + -
38B ILE 2.8 9.8 + - - +
39B MET* 3.3 16.1 - - + +
40B ILE 2.9 27.0 + - - +
57B PHE* 4.0 21.3 - - + -
98B ILE* 1.3 78.3 - - - +
100B ALA* 1.3 62.4 + - - +
101B VAL* 3.5 10.5 + - + -
124B ILE* 3.4 16.4 - - + +
126B VAL* 3.7 28.0 - - + -
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Residues in contact with ALA 100 (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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40B ILE 3.7 5.8 - - - -
98B ILE 4.0 0.8 + - - -
99B VAL* 1.3 70.7 - - - +
101B VAL* 1.3 56.9 + - - +
102B GLY 3.8 1.9 + - - +
106B THR* 4.2 9.2 - - + +
107B GLY* 4.2 4.7 - - - -
110B ALA* 3.4 29.4 - - + -
123B LEU* 4.2 3.6 - - + -
124B ILE 2.6 15.7 + - - +
125B HIS* 3.7 20.1 - - + -
126B VAL 2.8 32.1 + - - +
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Residues in contact with VAL 101 (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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39B MET* 3.7 36.6 - - + -
40B ILE 3.0 7.9 + - - -
41B SER* 2.9 39.3 + - - +
45B VAL* 3.7 4.5 - - + +
49B ILE* 3.8 29.4 - - + -
50B VAL* 4.4 7.6 - - - -
53B ALA* 4.0 12.6 - - + -
99B VAL* 4.0 5.4 - - + -
100B ALA* 1.3 73.0 - - - +
102B GLY* 1.3 58.5 + - - +
106B THR* 3.6 2.1 - - - +
126B VAL* 3.5 20.9 - - + +
128B THR* 4.0 6.1 - - + -
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Residues in contact with GLY 102 (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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45B VAL* 3.7 15.5 - - - -
100B ALA 3.8 2.1 + - - +
101B VAL* 1.3 76.2 - - - +
103B GLY* 1.3 65.2 + - - +
106B THR* 3.8 6.7 - - - -
107B GLY 5.1 0.2 - - - -
126B VAL 3.4 6.5 + - - -
127B PRO* 3.5 8.0 - - - +
128B THR* 2.9 37.6 + - - +
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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