Contacts of the strand formed by residues 75 - 83 (chain B) in PDB entry 2MGZ
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 SER 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.0 5.3 - - - +
44B TYR* 3.2 27.0 + - - +
46B THR* 2.9 39.7 + - - -
47B SER 4.6 0.2 - - - -
66B VAL* 3.3 23.0 - - - +
67B ILE 4.0 4.9 - - - -
68B THR* 4.1 5.1 - - - +
73B GLN 3.8 0.6 + - - -
74B LYS* 1.3 75.8 - - - +
76B ARG* 1.3 57.9 + - - +
77B GLY* 3.0 21.7 + - - -
78B TYR 3.9 1.0 + - - -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.3 31.3 + - - -
67B ILE* 3.0 24.1 + - + +
68B THR* 5.2 2.9 - - - -
69B ASP 5.8 0.4 - - - +
74B LYS 3.8 0.8 + - - -
75B SER* 1.3 71.2 + - - +
77B GLY* 1.3 58.9 + - - +
78B TYR* 3.6 28.8 - - + +
7C G 4.4 2.2 + - - +
8C U 2.8 41.1 + - - +
9C G 6.1 0.3 - - - -
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY* 4.3 3.5 - - - -
41B GLY 4.1 20.5 - - - +
42B LEU* 5.1 4.5 - - - -
44B TYR* 4.1 16.5 - - - -
75B SER* 3.0 14.1 + - - -
76B ARG* 1.3 78.4 - - - +
78B TYR* 1.3 62.5 + - - +
8C U 4.5 7.7 - - - -
9C G 3.5 18.4 - - - -
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Residues in contact with TYR 78 (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 PHE* 3.8 20.9 - + + -
39B VAL 3.4 13.9 - - - +
40B GLY* 4.7 1.8 - - - -
42B LEU* 5.2 3.2 - - - +
66B VAL* 3.6 8.2 - - - +
67B ILE* 3.2 54.1 + - + +
75B SER* 3.9 2.8 + - - -
76B ARG* 3.7 34.8 - - + +
77B GLY* 1.3 81.9 - - - +
79B GLY* 1.3 58.1 + - - +
80B PHE* 3.7 17.0 - + - -
8C U 5.9 0.2 - - - -
9C G 3.3 20.2 - - + +
10C U 3.6 30.3 - - - -
11C G 3.6 13.9 + - - -
12C C 4.7 1.4 + - - -
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Residues in contact with GLY 79 (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 PHE* 3.8 1.4 - - - -
39B VAL* 2.9 38.0 + - - +
40B GLY 5.2 0.8 + - - -
42B LEU* 5.8 1.4 - - - +
51B LEU* 4.4 8.5 - - - -
65B VAL 3.5 11.2 - - - -
66B VAL* 4.1 6.1 - - - -
78B TYR* 1.3 74.3 - - - +
80B PHE* 1.3 76.5 + - - -
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Residues in contact with PHE 80 (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 ILE 3.5 6.3 - - - -
38B PHE* 3.5 35.9 - + + -
39B VAL* 4.7 0.2 - - - +
51B LEU* 3.6 3.9 - - - +
63B GLU 4.4 0.2 - - - +
64B ALA* 3.3 2.6 - - - -
65B VAL* 2.8 40.5 + - + +
67B ILE* 3.8 13.7 - - + -
78B TYR* 3.7 20.6 - + - -
79B GLY* 1.3 82.3 - - - -
81B VAL* 1.3 63.5 + - - +
110B ALA* 4.6 3.6 - - + -
10C U 3.4 25.4 - + - -
11C G 3.1 78.3 - + + +
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Residues in contact with VAL 81 (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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35B THR 4.5 0.2 - - - -
36B LYS* 3.6 0.5 - - - +
37B ILE* 2.8 46.1 + - + +
39B VAL* 3.7 21.1 - - + -
51B LEU* 4.0 7.2 - - + -
55B PHE* 3.7 30.1 - - + -
61B ILE* 4.2 13.0 - - + -
63B GLU 3.7 4.5 - - - -
64B ALA* 3.9 11.9 - - + -
80B PHE* 1.3 78.8 - - - +
82B THR* 1.3 65.7 + - - +
83B MET* 3.6 29.4 - - + -
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Residues in contact with THR 82 (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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33B MET* 3.5 37.0 - - + +
35B THR* 3.3 24.9 - - - +
36B LYS* 4.1 3.8 - - - +
61B ILE* 3.5 6.4 - - - +
62B GLU* 2.8 51.7 + - + +
63B GLU* 2.9 16.8 + - - -
81B VAL* 1.3 76.0 + - - +
83B MET* 1.3 58.2 + - - +
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Residues in contact with MET 83 (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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35B THR* 2.9 36.4 + - - +
37B ILE* 4.3 8.7 - - + -
55B PHE* 3.6 30.1 - - + +
58B PHE* 4.4 4.9 - - + -
60B ASP 3.5 21.3 - - - +
61B ILE* 4.0 10.8 - - + -
62B GLU* 3.9 6.9 - - - +
81B VAL* 3.6 27.1 - - - -
82B THR* 1.3 76.8 - - - +
84B LYS* 1.3 64.2 + - - +
85B ASP 3.4 15.7 - - - +
88B SER* 3.8 32.3 - - - +
89B ALA* 4.0 11.7 - - + +
92B ALA* 5.4 0.4 - - - -
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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