Contacts of the helix formed by residues 55 - 64 (chain B) in PDB entry 2GMF
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 LEU 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.8 27.8 - - + -
53B THR 2.7 8.3 + - - +
54B CYS* 1.3 72.7 - - - +
56B GLN* 1.3 68.6 + - - +
58B ARG* 3.1 10.0 + - - +
59B LEU* 3.0 29.4 + - + +
84B TYR* 3.6 34.8 - - + -
91B THR* 3.5 18.6 + - + +
93B GLU* 3.0 2.4 + - - -
113B PHE* 4.2 23.6 - - + -
117B ILE* 4.7 0.4 - - + -
122B TRP* 3.3 35.9 - - + -
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Residues in contact with GLN 56 (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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24A ARG* 6.4 0.2 - - - -
55B LEU* 1.3 80.6 - - + +
57B THR* 1.3 57.7 + - - +
59B LEU* 4.0 4.5 - - - +
60B GLU* 3.1 27.2 + - - +
81B ALA* 3.1 44.9 + - - +
84B TYR* 4.0 11.1 - - - +
85B LYS* 3.9 29.5 - - + +
91B THR* 4.7 5.2 - - - +
93B GLU* 3.0 21.9 + - + +
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Residues in contact with THR 57 (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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24A ARG* 3.3 30.2 + - - +
28A LEU* 3.9 22.9 - - + -
43B ILE* 3.6 23.6 - - + -
54B CYS* 3.6 8.3 - - - -
56B GLN* 1.3 71.1 - - - +
58B ARG* 1.3 66.4 - - - +
60B GLU* 3.0 7.4 + - + +
61B LEU* 2.9 35.2 + - + +
93B GLU* 2.8 26.7 + - - +
96B CYS* 4.3 4.0 - - + -
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Residues in contact with ARG 58 (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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43B ILE* 3.9 34.9 + - + +
45B GLU* 3.0 28.3 + - - +
46B MET* 3.9 3.2 + - - +
47B PHE* 3.7 30.1 - - - +
53B THR* 2.9 35.4 + - - -
54B CYS* 2.6 17.7 + - - +
55B LEU* 3.5 10.1 - - - +
57B THR* 1.3 72.7 - - - +
59B LEU* 1.3 62.8 + - - +
61B LEU* 3.8 2.5 - - - +
62B TYR* 2.9 60.0 + - + +
113B PHE* 3.7 21.9 - - + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.0 26.6 + - + +
56B GLN* 4.1 7.0 - - - +
58B ARG* 1.3 75.8 - - - +
60B GLU* 1.3 62.8 + - - +
62B TYR* 3.3 6.4 + - + +
63B LYS* 3.1 28.4 + - + +
77B LEU* 3.9 28.8 - - + +
80B MET* 4.3 9.9 - - + +
81B ALA* 3.5 42.4 - - + +
84B TYR* 4.5 12.1 - - + -
113B PHE* 3.5 34.1 - - + -
117B ILE* 5.7 0.2 - - + -
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Residues in contact with GLU 60 (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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24A ARG* 3.2 38.6 + - - -
25A LEU* 4.9 3.3 - - - +
28A LEU* 5.2 3.3 - - - +
72A LYS* 5.7 1.0 + - - -
56B GLN 3.1 19.8 + - - +
57B THR* 3.0 7.3 + - - +
59B LEU* 1.3 77.8 - - - +
61B LEU* 1.3 59.5 + - + +
63B LYS* 3.3 16.3 + - - +
64B GLN* 3.0 47.5 + - - +
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Residues in contact with LEU 61 (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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28A LEU* 4.8 10.1 - - + -
41B GLU* 3.7 38.3 - - + +
42B VAL* 4.3 10.1 - - + -
43B ILE* 4.0 11.4 - - + +
57B THR* 2.9 35.2 + - + +
58B ARG* 4.0 3.4 - - - +
60B GLU* 1.3 76.2 - - + +
62B TYR* 1.3 67.6 + - + +
64B GLN* 3.2 25.2 + - + +
65B GLY* 3.1 19.2 + - - -
98B THR* 3.6 28.5 - - + -
106B PHE* 4.5 2.5 - - - -
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Residues in contact with TYR 62 (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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42B VAL* 4.7 9.2 - - + -
58B ARG* 2.9 52.9 + - + +
59B LEU* 3.6 12.8 - - + +
60B GLU 3.3 0.2 - - - -
61B LEU* 1.3 75.6 - - + +
63B LYS* 1.3 63.2 + - - +
65B GLY 3.2 4.0 + - - -
66B LEU* 3.3 8.7 - - - +
77B LEU* 4.2 13.7 - - + -
106B PHE* 3.2 44.3 - + + -
109B ASN* 2.5 34.5 + - - -
110B LEU* 3.9 26.5 - - + -
113B PHE* 3.6 43.2 - + + +
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Residues in contact with LYS 63 (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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59B LEU* 3.1 16.2 + - + +
60B GLU* 3.5 14.6 - - - +
61B LEU 3.2 0.2 - - - -
62B TYR* 1.3 79.7 - - - +
64B GLN* 1.3 62.7 + - + +
65B GLY 3.2 0.5 + - - -
66B LEU* 3.4 26.1 + - - +
74B LYS* 3.9 45.5 + - + +
77B LEU* 3.9 21.3 - - + -
78B THR* 3.0 36.6 + - - +
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Residues in contact with GLN 64 (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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72A LYS* 4.2 20.7 + - - +
60B GLU* 3.0 41.8 + - + +
61B LEU* 3.2 28.6 + - + +
63B LYS* 1.3 78.9 - - + +
65B GLY* 1.3 57.9 + - - +
66B LEU 3.6 2.8 + - - +
67B ARG* 3.6 8.3 + - - -
74B LYS* 5.3 3.4 - - - +
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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