Contacts of the strand formed by residues 67 - 72 (chain B) in PDB entry 2VZE
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 PRO 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PRO 4.2 4.5 - - - +
66B SER* 1.3 86.8 - - - +
68B ALA* 1.3 59.9 + - - +
70B TRP* 5.8 4.5 - - + -
80B MET* 3.9 29.6 - - + -
81B TRP 3.9 5.4 - - - +
83B PHE* 3.5 7.8 - - - -
256B ILE* 6.3 2.7 - - + -
280B GLY 4.5 1.0 - - - +
281B ALA 4.0 0.2 - - - -
282B CYS* 3.2 38.3 + - + +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER 3.4 0.4 + - - -
67B PRO* 1.3 74.4 - - - +
69B LEU* 1.3 57.6 + - - +
81B TRP 2.8 15.9 + - - +
82B ASN 3.9 7.2 - - - +
83B PHE* 3.5 42.4 - - + -
86B LEU* 3.9 15.9 - - + -
277B TRP* 2.8 21.5 + - - -
282B CYS* 3.9 3.8 - - - +
283B THR* 2.9 15.4 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 1.3 79.6 - - - +
70B TRP* 1.3 66.2 + - - +
71B TRP* 4.9 2.9 - - + +
80B MET* 3.2 6.9 - - - +
81B TRP* 2.8 68.3 + - + -
86B LEU* 4.5 11.4 - - + -
117B PRO* 4.2 15.5 - - + +
120B TRP* 4.2 26.0 - - + -
121B LEU* 5.4 2.0 - - + -
277B TRP* 4.1 9.4 - - + -
282B CYS* 4.3 1.3 - - - -
283B THR* 3.5 21.1 - - + +
285B VAL* 3.8 22.4 - - + -
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Residues in contact with TRP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 5.8 3.8 - - + -
69B LEU* 1.3 75.7 - - - +
71B TRP* 1.3 68.3 + - - +
72B VAL* 3.9 8.2 - - + +
78B GLU* 3.0 24.1 + - + +
79B LEU 3.5 11.2 - - - -
80B MET* 4.4 12.8 - - + +
256B ILE* 3.6 33.4 - - + -
282B CYS* 3.9 15.3 - - - -
283B THR 3.0 8.1 + - - +
284B PHE* 3.4 22.4 - + + -
285B VAL 2.9 25.6 + - - +
303B TYR* 3.6 27.6 - + - -
304B PRO* 4.1 16.6 - - + -
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Residues in contact with TRP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.1 4.2 - - + -
70B TRP* 1.3 72.1 - - - +
72B VAL* 1.3 74.3 + - - +
73B ASN* 3.7 29.6 - - + -
77B LYS* 3.9 30.1 - - + -
78B GLU* 3.1 5.7 - - - +
79B LEU* 2.8 67.3 + - + +
81B TRP* 4.8 3.1 - - + -
115B ARG 2.9 26.5 + - - -
116B VAL* 4.5 9.4 - - + -
117B PRO* 3.6 36.8 - - + +
285B VAL* 3.2 30.3 - - + -
287B LEU* 4.1 10.8 - - + +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TRP* 3.9 9.2 - - - +
71B TRP* 1.3 88.2 + - - +
73B ASN* 1.3 58.7 + - - +
74B GLY* 4.3 3.8 - - - +
77B LYS 3.4 8.5 - - - +
78B GLU* 3.5 30.1 - - + +
284B PHE* 3.9 22.2 - - + -
285B VAL 2.9 6.9 + - - +
286B HIS* 3.2 33.7 - - + +
287B LEU 3.0 23.2 + - - -
303B TYR* 3.6 15.3 - - + +
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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