Contacts of the strand formed by residues 431 - 437 (chain B) in PDB entry 6VXX
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 GLY 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B CYS* 3.5 1.9 - - - -
380B TYR* 2.9 30.1 + - - -
381B GLY* 3.1 9.7 + - - +
382B VAL* 5.2 2.0 - - - -
429B PHE* 3.5 12.3 - - - -
430B THR* 1.3 79.4 - - - +
432B CYS* 1.3 60.3 + - - -
513B LEU 3.3 10.8 - - - -
515B PHE* 3.4 13.5 - - - -
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Residues in contact with CYS 432 (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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377B PHE* 4.1 17.3 - - + -
378B LYS 3.4 6.5 - - - +
379B CYS* 2.1 49.1 - - - -
382B VAL* 4.3 5.2 - - - -
387B LEU* 4.3 17.0 - - - -
429B PHE* 3.9 1.3 - - - -
431B GLY* 1.3 76.9 - - - -
433B VAL* 1.3 63.9 + - - +
434B ILE* 4.0 7.5 + - + +
511B VAL 4.0 0.5 - - - +
512B VAL* 3.8 1.0 - - - +
513B LEU* 2.9 36.2 + - + +
515B PHE* 4.0 9.3 - - + -
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Residues in contact with VAL 433 (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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376B THR* 3.9 7.1 - - + +
377B PHE* 3.7 1.0 + - - -
378B LYS* 2.9 35.5 + - + +
380B TYR* 3.9 19.5 - - + +
407B VAL* 5.3 9.0 - - + +
410B ILE* 3.6 42.0 - - + +
425B LEU* 4.5 1.8 - - + -
429B PHE* 4.5 4.9 - - + -
432B CYS* 1.3 75.0 - - - +
434B ILE* 1.3 63.0 + - - +
435B ALA* 4.2 3.0 + - + -
510B VAL* 3.9 23.6 - - + -
511B VAL 4.0 2.7 - - - -
512B VAL* 4.2 13.2 - - + -
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Residues in contact with ILE 434 (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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342B PHE* 3.8 26.5 - - + -
368B LEU* 4.6 4.0 - - + -
374B PHE* 3.3 46.2 - - + -
376B THR 3.5 5.6 - - - +
377B PHE* 3.5 41.3 - - + -
432B CYS* 4.5 4.3 - - + +
433B VAL* 1.3 80.2 - - - +
435B ALA* 1.3 60.8 + - - +
436B TRP* 4.0 2.0 - - - -
509B ARG 3.9 0.7 - - - +
510B VAL* 3.4 1.5 - - - +
511B VAL 2.9 37.8 + - - +
513B LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 435 (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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374B PHE* 3.7 1.0 - - - -
375B SER* 2.8 30.4 + - - -
376B THR* 3.1 31.1 + - + +
407B VAL* 4.5 20.4 - - + -
433B VAL* 5.4 0.7 - - + -
434B ILE* 1.3 77.7 - - - +
436B TRP* 1.3 59.2 + - - +
508B TYR* 4.6 5.4 - - + -
509B ARG 3.3 11.7 - - - +
510B VAL* 4.0 15.0 - - + -
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Residues in contact with TRP 436 (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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342B PHE* 3.3 57.3 + + + -
347B PHE* 3.7 22.0 - + - -
373B SER* 3.5 26.7 - - - +
374B PHE* 3.5 18.8 - + - -
375B SER* 3.7 9.2 - - - +
434B ILE 4.0 8.7 - - - -
435B ALA* 1.3 82.6 - - - +
437B ASN* 1.3 81.2 + - - +
438B SER* 5.3 0.6 - - - -
508B TYR* 3.4 6.6 - - - -
509B ARG* 2.9 64.7 + - + +
511B VAL* 3.7 5.4 - - + -
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Residues in contact with ASN 437 (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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505A TYR* 5.7 2.8 + - - -
375B SER* 3.8 9.1 + - - -
436B TRP* 1.3 89.8 - - - +
438B SER* 1.3 59.7 + - - +
439B ASN* 3.0 25.7 + - - +
440B ASN* 4.3 9.9 - - - +
506B GLN* 4.5 9.3 + - - +
507B PRO 3.6 9.9 - - - +
508B TYR* 3.5 30.3 + - + +
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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