Contacts of the strand formed by residues 331 - 336 (chain A) in PDB entry 5VZH
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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A VAL* 3.7 24.5 - - + -
295A VAL* 4.0 19.3 - - + -
298A LEU* 3.8 23.6 - - + -
317A LEU* 3.8 16.4 - - + -
321A PHE* 4.7 2.7 - - + -
330A ASP* 1.3 79.5 - - - +
332A ASP* 1.3 64.2 + - - +
333A PHE* 3.4 35.0 - - + -
415A VAL* 4.3 3.4 - - + -
416A ARG 3.0 5.3 + - - +
417A VAL* 3.3 6.1 - - + +
418A ASP 2.8 26.7 + - - +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A LEU* 3.6 11.4 - - - +
318A THR* 2.9 39.4 + - - +
319A GLY* 3.5 12.1 - - - +
320A GLY 4.1 0.5 + - - -
321A PHE* 5.6 1.7 - - - -
330A ASP* 2.9 5.3 - - - +
331A VAL* 1.3 74.6 - - - +
333A PHE* 1.3 60.8 + - - +
418A ASP* 3.1 9.8 - - + +
434A HIS* 5.0 1.8 - - + +
501A MG 2.0 31.1 - - - -
502A MG 2.1 28.1 - - - -
506A UTP 2.9 14.4 + - - -
507A GOA 2.9 7.5 - - - +
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Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A VAL* 4.5 2.0 - - + -
298A LEU* 4.2 6.1 - - + -
299A GLN* 3.7 49.4 - - + -
302A VAL* 4.1 14.4 - - + -
315A VAL* 3.6 24.2 - - + -
316A THR 3.3 7.9 - - - +
317A LEU* 4.0 15.7 - - + -
318A THR* 4.1 3.5 + - - -
331A VAL* 3.4 26.0 - - + -
332A ASP* 1.3 79.6 - - - +
334A LEU* 1.3 61.5 + - - +
335A ILE* 5.0 1.8 - - + -
417A VAL* 4.0 16.6 - - + -
418A ASP 2.8 12.0 + - - +
419A LEU* 3.8 26.2 - - + -
420A VAL* 3.1 29.9 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A THR* 3.8 0.9 + - - +
315A VAL* 3.6 1.2 - - - -
316A THR* 2.8 42.9 + - - +
318A THR* 3.7 15.0 - - + +
333A PHE* 1.3 74.5 - - - +
335A ILE* 1.3 63.1 + - - +
336A THR 4.4 0.2 + - - -
420A VAL* 3.4 28.7 - - + +
422A ALA* 4.1 11.7 - - + -
427A PHE* 3.4 33.1 - - + -
430A ALA* 3.8 21.5 - - + +
431A LEU* 3.4 41.1 - - + +
434A HIS* 5.1 3.1 - - + -
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 4.5 3.4 - - + -
306A VAL* 3.9 29.4 - - + -
314A THR 3.2 12.3 - - - +
315A VAL* 4.3 13.0 - - + -
333A PHE* 5.0 1.6 - - + -
334A LEU* 1.3 81.9 - - - +
336A THR* 1.3 67.2 + - - +
346A LEU* 3.6 29.4 - - + -
347A LEU* 4.7 4.3 - - + -
350A VAL* 5.0 2.7 - - + -
419A LEU* 4.4 34.8 - - + -
420A VAL 2.7 14.4 + - - +
421A VAL* 3.2 14.7 - - + +
422A ALA 3.0 26.7 + - - -
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Residues in contact with THR 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ALA* 3.3 8.6 - - - +
314A THR* 2.9 43.4 + - - +
335A ILE* 1.3 75.7 - - - +
337A HIS* 1.3 70.7 + - - +
338A PRO* 5.8 0.4 - - + -
343A GLU* 4.8 6.3 - - - -
346A LEU* 5.4 0.4 - - - -
422A ALA 2.7 24.7 + - - -
424A VAL* 3.3 25.5 + - + -
427A PHE* 3.6 34.3 - - + -
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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