Contacts of the helix formed by residues 76 - 90 (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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLU 3.8 22.0 - - - +
74B TYR* 3.2 4.1 + - - -
75B LYS* 1.3 81.2 - - - +
77B LEU* 1.3 59.5 + - - +
78B SER* 3.5 11.9 + - - -
79B THR* 3.0 37.8 + - - -
80B VAL* 3.2 13.9 + - - +
109B VAL* 5.5 0.2 - - - +
144B VAL* 3.7 9.4 - - - +
145B ASN* 3.6 18.2 - - + +
146B LEU* 5.9 1.8 - - - -
147B THR 6.0 0.7 - - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.2 31.4 - - + +
81A THR* 3.3 30.9 - - + +
84A GLN* 3.5 24.7 - - - +
116A MET* 3.6 27.4 - - + -
76B THR* 1.3 74.3 - - - +
78B SER* 1.3 58.1 + - - +
80B VAL* 3.3 5.7 + - + +
81B THR* 2.9 32.9 + - - -
112B VAL* 4.0 11.4 - - + -
144B VAL* 3.6 23.7 - - + +
145B ASN 4.3 2.8 + - - +
146B LEU* 5.7 0.7 - - + -
153B VAL* 3.9 10.8 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 5.1 3.3 + - - +
76B THR* 3.2 11.4 - - - -
77B LEU* 1.3 76.4 - - - +
79B THR* 1.3 62.8 + - - +
81B THR* 4.0 6.5 - - - -
82B ASN* 3.3 21.5 + - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.5 41.7 - - + -
74B TYR* 2.4 33.5 + - - +
75B LYS* 5.2 0.2 - - - -
76B THR* 3.0 15.2 + - - -
78B SER* 1.3 73.3 - - - +
80B VAL* 1.3 65.7 + - - +
82B ASN* 3.3 6.6 + - - +
83B LEU* 3.0 31.0 + - + +
109B VAL* 4.1 7.4 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.6 7.6 - - + -
76B THR 3.2 11.3 + - - +
77B LEU* 3.3 12.8 + - - +
79B THR* 1.3 79.5 - - - +
81B THR* 1.3 57.9 + - - +
83B LEU* 3.0 10.4 + - - +
84B GLN* 2.9 55.1 + - - +
109B VAL* 3.5 29.6 - - + +
112B VAL* 3.9 24.7 - - + -
113B ALA* 3.8 14.1 - - - +
116B MET* 5.1 0.7 - - - -
144B VAL* 4.1 9.9 - - + -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.4 30.0 - - + +
78A SER* 5.2 3.5 + - - +
146A LEU* 4.3 11.9 - - + -
77B LEU 2.9 17.4 + - - -
78B SER* 4.0 8.2 - - - -
79B THR 3.3 0.2 - - - -
80B VAL* 1.3 76.5 - - - +
82B ASN* 1.3 62.9 + - - +
84B GLN* 3.2 11.2 + - - +
85B GLU* 3.0 44.6 + - + +
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Residues in contact with ASN 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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68B PHE* 5.6 1.6 - - - +
78B SER 3.3 15.8 + - - +
79B THR* 3.7 7.5 - - - +
80B VAL 3.3 0.6 - - - -
81B THR* 1.3 79.0 - - - +
83B LEU* 1.3 63.6 + - - +
85B GLU* 3.8 7.5 - - - +
86B ARG* 3.0 64.1 + - - +
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Residues in contact with LEU 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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40B ILE* 3.9 26.8 - - + +
66B LEU* 3.5 34.7 - - + +
68B PHE* 3.7 29.4 - - + -
79B THR* 3.0 18.3 + - + +
80B VAL* 3.4 7.9 - - - +
82B ASN* 1.3 78.4 - - - +
84B GLN* 1.3 56.5 + - - +
86B ARG* 3.8 22.0 - - - +
87B ALA* 3.0 28.2 + - - +
109B VAL* 3.4 33.9 - - + +
113B ALA* 5.0 4.5 - - + -
117B MET* 5.6 0.2 - - - -
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.4 5.1 - - - +
146A LEU* 4.2 15.8 - - + +
153A VAL* 3.5 20.8 - - - +
80B VAL* 2.9 29.4 + - - +
81B THR* 3.2 25.0 + - - +
83B LEU* 1.3 75.7 - - - +
85B GLU* 1.3 55.7 + - - +
87B ALA* 3.2 3.3 + - - +
88B ILE* 2.9 38.9 + - - +
113B ALA* 3.2 25.6 - - + +
116B MET* 3.6 19.2 - - - +
117B MET* 3.7 27.2 - - + +
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Residues in contact with GLU 85 (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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146A LEU* 3.5 23.0 - - + +
147A THR* 2.9 52.2 + - - +
148A SER* 3.8 11.8 + - - -
81B THR* 3.0 35.7 + - + +
82B ASN* 3.8 7.4 - - - +
84B GLN* 1.3 74.4 - - - +
86B ARG* 1.3 60.5 + - + +
88B ILE* 3.2 5.0 + - - +
89B ALA* 2.8 29.0 + - - +
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Residues in contact with ARG 86 (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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65B ILE 5.0 0.2 + - - -
66B LEU* 3.6 37.5 - - + +
67B ARG* 3.0 42.2 + - - +
68B PHE* 4.7 3.0 - - - +
82B ASN* 3.0 48.8 + - - +
83B LEU* 3.8 12.5 - - - +
85B GLU* 1.3 76.0 - - + +
87B ALA* 1.3 65.4 + - - +
89B ALA* 3.4 9.0 + - + +
90B LEU* 3.2 28.5 + - + +
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Residues in contact with ALA 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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38B ILE* 4.3 21.5 - - + -
40B ILE* 6.4 0.4 - - + -
66B LEU* 3.9 4.7 - - - +
83B LEU 3.0 19.4 + - - +
84B GLN 3.2 5.8 + - - +
86B ARG* 1.3 78.2 - - - +
88B ILE* 1.3 58.8 + - - +
90B LEU* 3.1 15.4 + - - +
91B GLY 3.3 0.3 + - - -
92B ALA* 2.9 31.3 + - + +
98B ILE* 5.1 2.0 - - + -
117B MET* 3.7 21.5 - - + -
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Residues in contact with ILE 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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146A LEU* 3.6 22.2 - - + -
148A SER* 3.1 34.1 - - - +
152A LEU* 4.6 9.4 - - + -
321A ASN* 5.2 8.7 - - - +
84B GLN 2.9 19.2 + - - +
85B GLU 3.6 6.5 - - - +
87B ALA* 1.3 71.3 - - - +
89B ALA* 1.3 59.1 + - - +
90B LEU 3.0 4.3 - - - -
91B GLY* 2.8 22.5 + - - -
92B ALA 4.0 9.0 - - - +
117B MET* 3.9 11.2 - - + -
118B PHE* 3.5 37.5 - - + -
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Residues in contact with ALA 89 (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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148A SER* 5.8 0.4 - - - -
85B GLU 2.8 20.4 + - - +
86B ARG* 3.6 10.3 - - + +
87B ALA 3.4 0.2 - - - -
88B ILE* 1.3 72.4 - - - +
90B LEU* 1.3 61.2 + - + +
91B GLY 3.3 0.6 + - - -
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Residues in contact with LEU 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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36B GLN* 3.2 16.9 + - - +
38B ILE* 4.4 6.3 - - + -
64B HIS* 3.8 50.4 + - + +
66B LEU* 3.9 23.1 - - + -
86B ARG 3.2 17.0 + - - +
87B ALA* 3.1 12.4 + - - +
88B ILE 2.9 1.4 + - - -
89B ALA* 1.3 78.1 - - + +
91B GLY* 1.3 58.5 + - - +
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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