Contacts of the strand formed by residues 395 - 398 (chain K) in PDB entry 1VYH
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 VAL 395 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ILE 5.5 0.2 - - - +
96K PRO* 4.1 15.7 - - + +
116K PHE* 4.7 0.9 - - - -
354K LEU* 3.8 25.8 - - + -
362K LEU* 4.4 10.5 - - + -
386K LEU* 5.0 2.5 - - + -
387K ASP 3.3 25.1 - - - +
388K PHE* 3.7 21.1 - - + +
394K TYR* 1.3 78.3 - - - +
396K VAL* 1.3 67.6 + - - +
406K VAL* 3.3 4.5 - - - +
407K TRP* 2.6 57.0 + - + +
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Residues in contact with VAL 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K VAL* 3.8 17.5 - - + -
115K ILE 5.2 0.4 - - - +
116K PHE* 3.7 22.2 - - + -
123K MET* 3.9 20.9 - - + -
137K TYR* 5.1 0.4 - - + -
386K LEU* 3.1 7.8 - - - +
387K ASP* 3.0 50.2 + - + +
395K VAL* 1.3 77.9 - - - +
397K THR* 1.3 63.5 + - - +
404K VAL* 3.8 13.2 - - + -
405K LYS 3.0 13.0 - - - +
406K VAL* 3.9 18.6 - - + -
407K TRP* 4.5 0.2 - - - -
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Residues in contact with THR 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K VAL* 3.9 2.5 - - - -
356K CYS* 5.2 0.2 - - - +
362K LEU* 3.7 23.4 - - - +
378K ALA* 4.6 4.5 - - + -
379K HIS* 2.9 35.1 + - + +
383K VAL* 3.4 21.7 - - + +
385K SER 3.6 6.0 + - - -
386K LEU* 4.2 2.6 - - - +
396K VAL* 1.3 77.7 + - - +
398K GLY* 1.3 60.8 + - - +
403K THR 3.2 2.4 - - - +
404K VAL* 2.9 8.3 - - - -
405K LYS 2.7 33.9 + - - +
407K TRP* 3.7 16.5 + - - -
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Residues in contact with GLY 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K VAL* 3.5 21.5 - - - -
114K VAL* 3.3 10.0 - - - +
383K VAL* 3.4 11.3 - - - +
384K THR* 2.9 18.3 + - - -
385K SER* 3.3 12.1 + - - -
397K THR* 1.3 75.4 - - - +
399K SER* 1.3 66.1 + - - -
403K THR 3.4 7.6 - - - -
404K VAL* 4.5 1.3 - - - -
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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