Contacts of the helix formed by residues 79 - 88 (chain B) in PDB entry 6BJV
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.8 1.4 - - - -
77B ASP* 3.4 20.6 - - + +
78B ARG* 1.3 82.0 - - - +
80B GLU* 1.3 54.2 + - - +
81B ALA* 3.8 8.2 + - - +
82B SER* 2.8 32.0 + - - -
83B LEU* 2.7 36.0 + - - +
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Residues in contact with GLU 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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79B THR* 1.3 73.0 - - - +
81B ALA* 1.3 88.0 + - - +
83B LEU* 3.2 13.5 + - + +
84B HIS* 3.0 28.0 + - + +
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Residues in contact with ALA 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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79B THR* 3.2 7.4 + - - +
80B GLU* 1.3 92.7 + - - +
82B SER* 1.3 62.6 + - - +
84B HIS* 3.5 6.2 + - - +
85B ARG* 3.2 19.6 + - - +
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Residues in contact with SER 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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75B ARG 5.1 2.5 - - - -
76B TYR* 3.4 8.9 - - - -
77B ASP* 3.4 33.0 + - - -
79B THR* 2.8 42.9 + - - -
81B ALA* 1.3 75.5 - - - +
83B LEU* 1.3 65.0 + - - +
85B ARG* 3.2 10.8 + - - +
86B VAL* 3.0 28.1 + - - +
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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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76B TYR* 3.5 22.2 - - + +
79B THR 2.7 21.4 + - - +
80B GLU* 3.4 13.5 - - + +
82B SER* 1.3 70.8 + - - +
84B HIS* 1.3 66.8 + - - +
86B VAL* 3.0 5.3 + - - +
87B LEU* 2.8 55.5 + - + +
142B GLN* 4.9 2.0 - - - +
145B LEU* 3.9 24.7 - - + -
146B GLN* 3.3 40.2 - - + +
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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
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80B GLU* 3.0 21.9 + - + +
81B ALA* 3.7 7.2 + - - +
83B LEU* 1.3 76.4 - - - +
85B ARG* 1.3 64.6 + - - +
87B LEU* 3.8 11.3 + - + +
88B GLY* 3.8 12.8 + - - -
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Residues in contact with ARG 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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32B LEU* 3.2 34.1 - - + +
35B GLU* 5.6 7.1 + - - -
75B ARG 5.9 2.0 - - - -
81B ALA 3.2 13.1 + - - +
82B SER* 3.4 14.4 - - - +
83B LEU 3.0 0.6 - - - -
84B HIS* 1.3 82.4 + - - +
86B VAL* 1.3 62.8 + - + +
88B GLY* 3.7 6.1 + - - -
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Residues in contact with VAL 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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32B LEU* 4.6 0.7 - - + -
35B GLU* 5.4 1.3 - - - +
59B PHE* 3.6 24.7 - - + -
74B LEU* 4.4 15.3 - - + -
75B ARG 3.7 23.3 - - - +
76B TYR* 4.0 7.6 - - + -
82B SER 3.0 13.6 + - - +
83B LEU* 3.2 18.4 - - + +
85B ARG* 1.3 77.8 - - + +
87B LEU* 1.3 58.3 + - - +
88B GLY 3.2 2.2 - - - -
89B SER* 3.1 9.1 + - - -
141B LYS* 2.7 28.4 + - - -
145B LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 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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83B LEU* 2.8 51.4 + - + +
84B HIS* 4.2 10.5 - - + +
85B ARG 3.4 0.2 - - - -
86B VAL* 1.3 78.1 - - - +
88B GLY* 1.3 57.4 + - - +
89B SER 3.2 3.2 + - - -
90B TRP* 3.4 13.7 + - - +
138B ILE* 4.3 23.5 - - + +
141B LYS* 4.2 20.0 + - + +
142B GLN* 4.1 40.6 - - + +
145B LEU* 4.6 1.3 - - + -
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Residues in contact with GLY 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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31B LYS* 3.5 26.1 - - - +
32B LEU* 4.2 6.3 - - - +
84B HIS 3.8 7.0 + - - -
85B ARG 3.7 10.1 + - - -
86B VAL 3.2 1.2 - - - -
87B LEU* 1.3 76.3 - - - +
89B SER* 1.3 62.7 + - - -
90B TRP 3.1 6.5 + - - -
91B THR* 6.2 0.2 - - - -
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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