Contacts of the helix formed by residues 63 - 69 (chain B) in PDB entry 2BV1
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 ALA 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LYS* 2.8 25.8 + - + +
60A VAL* 3.6 25.2 - - + +
62B SER* 1.3 72.2 - - - +
64B ALA* 1.3 58.1 + - - +
65B GLU 3.3 0.2 + - - -
66B VAL* 3.3 6.3 + - - +
67B MET* 2.8 37.7 + - + +
187B LEU* 3.9 13.8 - - + +
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Residues in contact with ALA 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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62B SER* 3.1 8.7 + - - +
63B ALA* 1.3 79.2 - - - +
65B GLU* 1.3 62.7 + - - +
67B MET* 3.3 18.7 + - + +
68B GLN* 3.0 34.4 + - - +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.8 15.0 - - + -
62B SER* 3.0 23.4 + - - +
64B ALA* 1.3 76.8 - - - +
66B VAL* 1.3 63.5 + - - +
68B GLN* 3.0 28.7 + - - +
69B TRP* 3.0 43.5 + - - +
75B LYS* 4.5 3.3 - - - +
79B ASN* 3.4 34.5 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 4.0 10.5 - - + -
61B LEU* 3.5 34.5 - - + -
62B SER 3.3 10.0 + - - +
63B ALA* 3.6 7.4 - - - +
65B GLU* 1.3 74.3 - - - +
67B MET* 1.3 58.3 + - - +
69B TRP* 3.2 25.7 + - + +
183B TYR* 2.6 54.4 + - + +
186B LEU* 4.1 5.4 - - + -
187B LEU* 3.7 26.0 - - + +
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Residues in contact with MET 67 (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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63B ALA* 2.8 27.5 + - - +
64B ALA* 3.3 19.5 + - + +
66B VAL* 1.3 70.8 - - - +
68B GLN* 1.3 63.2 + - + +
70B SER* 3.1 24.4 + - - -
71B GLN* 4.3 3.0 + - - +
183B TYR* 3.7 5.8 - - - -
187B LEU* 3.4 20.6 - - + -
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Residues in contact with GLN 68 (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 ALA* 3.0 22.5 + - + +
65B GLU* 3.0 28.2 + - - +
67B MET* 1.3 73.7 - - + +
69B TRP* 1.3 63.5 + - - +
70B SER 3.1 0.4 - - - -
71B GLN* 3.0 44.2 + - - +
75B LYS* 3.5 22.1 - - + +
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Residues in contact with TRP 69 (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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61B LEU* 3.8 35.2 - - + -
65B GLU* 3.0 34.2 + - - +
66B VAL* 3.2 15.4 + - + +
68B GLN* 1.3 78.0 - - - +
70B SER* 1.3 50.1 + - - +
71B GLN 3.2 0.7 - - - -
72B SER 3.3 8.4 - - - +
75B LYS 4.1 2.9 - - - -
76B LEU* 3.5 44.5 - - + +
79B ASN* 3.5 16.2 - - - +
81B THR* 4.1 5.6 - - + -
82B GLY* 3.3 32.7 - - - -
85B VAL* 4.2 12.3 - - + -
174B TYR* 2.7 32.2 + - - -
177B PHE* 4.5 1.3 - + + -
178B LEU* 4.4 3.4 - - + -
183B TYR* 3.7 26.0 - + + -
186B LEU* 3.9 21.3 - - + -
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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