Contacts of the strand formed by residues 36 - 42 (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 GLN 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.2 7.5 + - - +
35B ASP* 1.3 95.4 + - - +
37B TYR* 1.3 69.3 + - - +
38B ILE* 3.5 13.7 - - + +
61B ALA* 3.8 3.2 - - - +
62B PRO* 3.5 19.1 - - + +
64B HIS* 3.4 25.7 + - + +
90B LEU 3.2 26.9 + - - -
91B GLY 4.1 4.7 - - - +
92B ALA* 3.4 10.7 - - - -
96B THR* 2.6 35.0 + - - +
97B ALA 3.1 23.7 + - - -
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Residues in contact with TYR 37 (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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29B ILE* 3.5 15.8 - - - +
30B PRO 4.8 0.7 + - - -
34B PHE* 3.4 41.4 + + + +
36B GLN* 1.3 73.6 - - - +
38B ILE* 1.3 63.1 + - - +
39B MET* 3.7 0.8 + - + -
57B PHE* 3.7 33.9 - + + -
60B LEU* 3.8 24.4 - - + +
61B ALA* 3.7 30.5 - - + -
62B PRO 2.9 5.5 + - - +
63B VAL* 3.2 18.7 - - + -
64B HIS 2.9 26.2 + - - +
97B ALA* 3.4 14.1 - - + -
99B VAL* 3.5 27.8 - - + -
124B ILE* 4.0 7.0 - - + -
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Residues in contact with ILE 38 (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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36B GLN* 3.5 31.6 - - - +
37B TYR* 1.3 72.5 - - - +
39B MET* 1.3 61.2 + - - +
40B ILE* 3.5 11.6 + - + -
64B HIS* 3.4 15.5 - - + +
66B LEU* 3.6 35.4 - - + -
87B ALA* 4.3 16.4 - - + -
90B LEU* 4.4 13.7 - - + -
92B ALA* 4.4 7.2 - - + -
96B THR* 3.4 21.1 - - + -
97B ALA 3.0 8.3 + - - +
98B ILE* 3.3 17.4 - - + +
99B VAL* 2.8 23.3 + - - -
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Residues in contact with MET 39 (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 3.7 0.6 - - - -
38B ILE* 1.3 72.0 - - - +
40B ILE* 1.3 59.9 + - - +
41B SER* 4.3 7.4 - - - +
50B VAL* 3.6 22.2 - - + +
53B ALA* 3.6 18.4 - - + +
54B ALA* 3.6 38.8 - - - +
57B PHE* 4.0 16.6 - - + -
63B VAL* 4.0 12.6 - - + -
64B HIS 2.8 13.6 + - - +
65B ILE* 3.4 6.1 - - + +
66B LEU 2.8 27.6 + - - +
99B VAL* 3.3 15.3 - - + +
101B VAL* 3.7 27.4 - - + -
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Residues in contact with ILE 40 (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* 4.1 18.8 - - + +
39B MET* 1.3 73.7 - - - +
41B SER* 1.3 67.5 + - - +
66B LEU* 3.3 14.8 - - + +
68B PHE* 3.7 28.3 - - + -
83B LEU* 3.9 28.9 - - + +
98B ILE* 3.8 30.5 - - + -
99B VAL 2.9 9.5 + - - +
100B ALA* 3.7 0.2 - - - -
101B VAL 3.0 20.4 + - - -
106B THR* 3.2 6.5 - - + +
110B ALA* 4.2 26.5 - - + +
113B ALA* 4.6 4.9 - - + -
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Residues in contact with SER 41 (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* 4.1 2.8 + - - +
40B ILE* 1.3 75.5 + - - +
42B ASP* 1.3 68.5 + - - +
45B VAL* 4.1 2.5 - - - -
50B VAL* 3.6 30.9 - - - +
66B LEU 3.1 7.1 + - - -
67B ARG* 3.0 34.4 + - - +
68B PHE* 3.5 4.8 + - - -
101B VAL* 2.9 35.9 + - - +
106B THR* 3.8 3.6 - - - -
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Residues in contact with ASP 42 (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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41B SER* 1.3 74.7 - - - +
43B SER* 1.3 62.3 + - - +
44B GLY* 2.8 28.8 + - - -
45B VAL* 3.2 11.7 + - - +
67B ARG* 2.8 18.2 + - - -
68B PHE* 3.3 33.9 - - + -
70B GLY* 3.7 15.3 - - - -
71B GLY 5.3 0.2 - - - -
103B GLY 4.7 0.7 + - - -
105B LEU* 4.2 9.4 - - + +
106B THR* 2.6 37.0 + - - +
604B NAD 3.0 27.9 + - - -
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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