Contacts of the strand formed by residues 64 - 67 (chain B) in PDB entry 2VM8
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 MET 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS* 3.4 23.0 - - - +
25B VAL* 4.3 2.2 - - + -
62B SER 3.9 1.0 + - - -
63B ARG* 1.3 77.8 - - - +
65B VAL* 1.3 58.7 + - - +
66B ILE* 3.3 28.5 - - + -
366B TRP* 3.6 34.8 - - + -
377B GLU* 3.5 31.6 - - + +
380B PHE* 4.8 1.1 - - + -
411B ILE* 3.2 23.7 - - - +
412B TRP* 3.3 32.7 + - + +
414B PRO* 3.9 19.2 - - + +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.5 13.2 - - + -
22B GLY* 3.9 16.8 - - - -
23B LYS 2.8 10.3 + - - +
24B ILE* 3.5 8.6 - - + +
25B VAL 2.9 24.4 + - - +
35B ILE* 3.5 31.6 - - + -
60B ALA* 4.7 0.7 - - + -
63B ARG 3.4 11.2 - - - +
64B MET* 1.3 79.9 - - - +
66B ILE* 1.3 63.6 + - - +
401B ILE* 4.8 1.8 - - + +
409B LEU* 4.2 15.7 - - + -
410B VAL 3.2 11.7 - - - +
411B ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.9 12.3 - - + -
64B MET* 3.3 29.6 - - + -
65B VAL* 1.3 80.1 - - - +
67B PRO* 1.3 82.7 - - + +
68B GLY 3.4 0.2 + - - -
362B MET* 3.9 15.3 - - + -
380B PHE* 3.7 26.5 - - + -
381B VAL* 3.9 11.0 - - + -
401B ILE* 4.2 4.9 - - - -
409B LEU* 3.5 4.0 - - - +
410B VAL* 2.9 41.8 + - + +
412B TRP* 4.0 22.4 - - + -
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 3.3 17.7 - - - +
26B ASN* 4.0 8.7 - - - +
66B ILE* 1.3 100.1 - - + +
68B GLY* 1.3 66.2 + - - +
69B GLY* 3.4 2.1 + - - -
362B MET* 4.7 2.9 - - - +
381B VAL* 3.6 24.5 - - + +
384B THR* 5.2 1.0 + - - -
385B SER* 3.8 10.5 + - - +
399B GLY* 3.6 33.4 - - - +
400B ARG* 3.8 6.5 - - - +
401B ILE* 3.9 13.4 - - + -
408B ASP 3.8 8.1 - - - +
410B VAL* 4.6 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
------------------------------------------------------------
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