Contacts of the helix formed by residues 83 - 94 (chain B) in PDB entry 2Q4E
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ARG* 6.0 5.2 - - - +
63B TYR* 4.6 9.4 - - + +
79B LEU* 4.4 18.9 - - + +
80B PRO* 3.0 38.9 + - + +
82B SER* 1.3 91.9 - - - +
84B HIS* 1.3 65.3 + - - +
86B GLU* 4.2 3.6 - - - +
87B TRP* 3.2 49.6 + - + +
179B LEU* 5.0 4.5 - - + -
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Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 4.2 1.3 + - + -
79B LEU* 2.5 36.4 + - + -
80B PRO 2.9 22.3 + - - -
81B THR* 2.9 19.2 + - - +
83B LEU* 1.3 77.7 - - - +
85B VAL* 1.3 62.1 + - - +
88B ALA* 2.8 37.5 + - - +
100B LEU* 3.4 27.6 - - + +
101B GLU* 3.0 29.4 - - + -
102B LYS 5.5 0.4 - - - -
103B PRO 3.8 7.8 + - - -
104B VAL 2.5 32.9 + - - +
105B ALA* 4.9 1.6 - - - -
114B ILE* 3.9 6.5 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR 4.6 0.4 + - - -
82B SER 4.3 12.3 + - - +
84B HIS* 1.3 77.1 - - - +
86B GLU* 1.3 63.3 + - + +
89B ILE* 3.0 46.5 - - + +
105B ALA* 5.5 1.0 - - + +
110B GLU* 3.7 57.9 - - + +
113B LYS* 4.6 10.1 - - + +
114B ILE* 3.6 11.3 - - + +
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Residues in contact with GLU 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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82B SER 5.4 1.1 - - - +
83B LEU* 3.8 5.4 + - - +
84B HIS 3.1 1.2 - - - -
85B VAL* 1.3 89.0 - - + +
87B TRP* 1.3 101.2 + - + +
89B ILE* 3.8 2.3 - - - +
90B LYS* 3.2 49.7 + - - +
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Residues in contact with TRP 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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12B MSE 4.4 6.7 - - - +
63B TYR* 3.8 35.7 - + + -
64B GLU* 4.1 20.0 - - + -
67B LEU* 4.4 13.8 - - + +
77B VAL* 5.8 2.6 - - + +
79B LEU* 4.1 18.2 - - + -
83B LEU* 3.2 50.2 + - + +
86B GLU* 1.3 105.9 + - + +
88B ALA* 1.3 65.7 + - - +
90B LYS* 4.0 28.8 - - + +
91B ALA* 3.2 20.6 + - - +
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Residues in contact with ALA 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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77B VAL* 5.8 6.2 - - + +
84B HIS* 2.8 28.0 + - - +
87B TRP* 1.3 71.4 - - - +
89B ILE* 1.3 63.8 + - - +
91B ALA* 2.8 16.7 + - - +
92B ALA* 2.9 11.5 + - - +
98B ILE* 3.4 19.2 - - + +
100B LEU* 4.6 16.8 - - + -
114B ILE* 3.9 26.7 - - + -
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Residues in contact with ILE 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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85B VAL* 3.0 38.3 + - + +
86B GLU 3.7 3.1 + - - +
87B TRP 3.4 0.2 - - - -
88B ALA* 1.3 78.8 - - - +
90B LYS* 1.3 68.1 + - + +
92B ALA* 2.9 10.7 + - - +
93B GLU* 2.8 38.6 + - + +
113B LYS* 4.1 23.1 - - + +
114B ILE* 3.9 20.4 - - + +
117B ALA* 4.1 13.9 - - + -
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Residues in contact with LYS 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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64B GLU* 4.2 14.2 + - - +
67B LEU* 3.9 15.3 - - + -
86B GLU* 3.2 43.4 + - - +
87B TRP* 4.0 32.4 - - + +
89B ILE* 1.3 77.6 - - + +
91B ALA* 1.3 63.3 + - - +
93B GLU* 3.1 20.2 + - - +
94B LYS* 3.1 17.8 + - + +
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Residues in contact with ALA 91 (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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67B LEU* 3.5 27.8 - - + +
75B LEU* 4.1 12.6 - - + -
77B VAL* 5.8 2.9 - - + -
87B TRP 3.2 12.5 + - - +
88B ALA* 2.8 15.1 + - - +
90B LYS* 1.3 75.7 - - - +
92B ALA* 1.3 64.1 + - - +
94B LYS* 3.0 10.5 + - - -
96B LYS* 3.0 25.7 + - + +
98B ILE* 4.2 12.1 - - + -
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Residues in contact with ALA 92 (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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88B ALA 2.9 10.7 + - - +
89B ILE* 2.9 8.0 + - - +
91B ALA* 1.3 75.4 - - - +
93B GLU* 1.3 61.6 + - - +
95B GLY* 3.1 13.0 + - - -
96B LYS 3.8 11.8 + - - -
98B ILE* 4.2 0.8 - - + +
117B ALA* 4.0 21.1 - - + +
118B CYS* 4.1 21.1 - - - +
121B ASN* 3.3 32.0 - - - +
123B VAL* 4.4 3.5 - - + +
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Residues in contact with GLU 93 (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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89B ILE* 2.8 34.5 + - + +
90B LYS* 3.1 13.7 + - - +
92B ALA* 1.3 76.7 - - - +
94B LYS* 1.3 63.2 + - + +
95B GLY 3.3 1.6 + - - -
117B ALA* 5.0 5.7 - - - +
120B ALA* 5.4 0.7 - - - +
121B ASN* 2.8 39.6 + - - +
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Residues in contact with LYS 94 (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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64B GLU* 3.8 8.5 - - - +
67B LEU* 3.6 31.9 - - + +
68B GLU* 3.5 37.7 + - + +
90B LYS* 3.1 12.8 + - + +
91B ALA 3.0 8.4 + - - +
93B GLU* 1.3 83.8 - - - +
95B GLY* 1.3 61.4 + - - +
96B LYS* 3.3 18.9 + - + -
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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