Contacts of the strand formed by residues 334 - 338 (chain B) in PDB entry 3V4R
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 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 3.8 28.0 - - + -
49B VAL* 5.4 0.9 - - + +
52B LEU* 3.9 23.3 - - + -
53B ILE* 4.4 13.7 - - + +
56B VAL* 4.1 15.7 - - + -
58B LYS* 4.0 15.4 - - + +
59B PRO 3.0 9.3 + - - +
60B THR* 3.0 35.5 + - + +
61B LEU 2.9 24.3 + - - -
333B PHE* 1.3 76.5 - - - +
335B ILE* 1.3 74.2 + - - +
336B VAL* 3.8 16.6 - - + -
388B ASN* 3.4 18.2 - - + +
390B VAL* 4.6 3.8 - - + -
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.2 16.2 - - + +
63B ILE* 3.8 29.6 - - + -
326B LEU* 4.9 4.7 - - + -
333B PHE* 3.5 41.1 - - + +
334B MET* 1.3 72.5 - - - +
336B VAL* 1.3 65.8 + - - +
337B VAL* 4.1 5.8 - - + -
382B PHE* 5.1 6.5 - - + -
385B HIS* 4.3 1.3 - - + +
386B MET* 4.1 26.2 - - + +
387B HIS 4.7 0.9 - - - +
388B ASN 3.0 10.4 + - - +
389B ILE* 3.4 28.3 - - + +
390B VAL 2.9 25.1 + - - -
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.0 28.3 - - + -
52B LEU* 4.9 2.2 - - + -
60B THR* 4.4 5.4 - - + +
61B LEU 2.7 12.0 + - - +
62B VAL* 3.3 19.9 - - + +
63B ILE 2.9 25.3 + - - -
334B MET* 3.8 27.4 - - + -
335B ILE* 1.3 77.0 - - - +
337B VAL* 1.3 63.7 - - - +
338B ASP* 5.0 1.1 - - + +
390B VAL* 3.3 14.8 - - + +
392B VAL* 3.7 26.7 - - + -
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.8 9.9 - - + +
335B ILE* 4.3 7.0 - - + -
336B VAL* 1.3 74.4 - - - +
338B ASP* 1.3 57.0 + - - +
340B SER* 3.7 15.9 + - - -
343B THR* 3.6 35.4 - - + -
344B ILE* 4.1 15.9 - - + -
382B PHE* 5.5 1.6 - - + -
389B ILE* 3.9 27.8 - - + -
390B VAL 2.9 8.4 + - - +
391B TYR* 4.1 18.2 - - + -
392B VAL* 2.8 34.0 + - - +
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Residues in contact with ASP 338 (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 VAL* 5.0 4.3 - - + -
63B ILE 2.9 17.1 + - - +
64B ALA* 4.7 0.2 - - - -
65B HIS* 4.5 3.0 + - - -
69B LEU* 4.1 13.0 - - + -
73B LEU* 4.0 26.9 - - + -
336B VAL* 3.7 3.7 + - + +
337B VAL* 1.3 70.0 - - - +
339B GLU* 1.4 59.6 + - - +
340B SER 3.3 0.2 + - - -
343B THR* 2.7 28.6 + - - -
392B VAL* 3.9 9.0 - - + -
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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