Contacts of the strand formed by residues 362 - 366 (chain P) 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 LEU 362 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P PRO 4.6 10.1 - - - +
354P LEU* 3.9 19.5 - - + -
355P SER 3.3 16.2 - - - +
356P CYS* 4.6 3.8 - - + +
361P THR* 1.3 75.3 - - - +
363P ARG* 1.3 58.7 + - - +
364P VAL* 3.9 3.1 + - + +
374P LYS 4.0 0.5 - - - +
375P THR* 3.7 1.9 - - - -
376P LEU* 2.9 58.0 + - + +
378P ALA* 4.3 9.1 - - + +
383P VAL* 5.7 0.7 - - + -
386P LEU* 3.5 28.7 - - + -
395P VAL* 4.8 11.0 - - + -
397P THR* 4.4 16.2 - - + +
407P TRP* 4.9 11.9 - - + +
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Residues in contact with ARG 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318P LYS 4.3 3.8 + - - -
320P ILE* 4.4 2.0 - - - +
337P HIS* 3.1 72.5 + - + +
339P ASN 3.7 5.5 + - - -
341P VAL* 4.2 14.5 - - - +
354P LEU* 3.8 1.5 - - - +
355P SER* 2.8 63.6 + - - +
356P CYS 4.6 0.7 - - - +
357P ALA* 3.4 22.8 - - - +
359P ASP* 2.8 25.7 + - - -
361P THR* 3.5 7.4 - - + +
362P LEU* 1.3 71.7 - - - +
364P VAL* 1.3 60.9 + - - +
365P TRP* 3.4 38.6 - - + +
372P CYS* 4.5 1.8 - - - -
374P LYS 3.5 4.9 - - - +
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Residues in contact with VAL 364 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P PRO* 4.1 26.7 - - + +
352P PHE* 4.4 10.5 - - + -
353P ILE 4.0 2.2 - - - -
354P LEU* 3.7 35.0 - - + -
362P LEU* 4.6 7.2 - - + +
363P ARG* 1.3 71.6 - - - +
365P TRP* 1.3 62.5 + - - +
372P CYS* 3.5 2.4 - - - -
373P MET* 2.7 45.0 + - + -
374P LYS* 2.7 41.3 + - + +
376P LEU* 5.7 2.0 - - + -
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Residues in contact with TRP 365 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318P LYS 5.6 0.4 - - - -
320P ILE* 3.6 11.9 - - + +
334P LEU* 3.1 61.2 - - + -
335P VAL 3.3 37.2 - - - -
336P GLY* 3.3 9.4 - - - -
337P HIS* 4.4 4.7 - + - -
352P PHE* 3.7 13.2 - - - +
353P ILE* 2.9 40.4 + - + +
355P SER* 3.4 25.7 + - - -
363P ARG* 3.4 48.4 - - + +
364P VAL* 1.3 77.5 - - - +
366P ASP* 1.3 62.9 - - - +
367P TYR 3.9 1.6 - - - +
370P LYS 4.7 6.1 - - - -
371P ARG 4.0 2.9 - - - -
372P CYS* 4.2 18.6 - - + +
373P MET* 5.1 0.2 - - - -
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Residues in contact with ASP 366 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P LEU* 5.9 0.2 - - - -
351P LYS 4.0 11.0 - - - +
352P PHE* 4.7 6.8 - - + -
365P TRP* 1.3 74.5 - - - +
367P TYR* 1.3 57.2 + - - +
368P LYS* 2.7 60.0 + - - +
369P ASN* 3.2 13.0 + - - -
370P LYS* 3.0 13.9 + - - -
371P ARG* 2.7 28.4 + - + +
373P MET* 3.9 24.1 - - + +
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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