Contacts of the strand formed by residues 451 - 460 (chain A) in PDB entry 3VI4
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 ILE 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.8 7.4 - - + -
2A ASN* 3.5 27.8 - - + +
362A ASP* 3.4 44.6 - - + +
430A TYR* 2.8 24.6 + - + +
449A ARG 3.7 7.9 - - - +
450A PRO* 1.3 72.5 - - - +
452A VAL* 1.3 66.0 + - - +
453A SER* 4.6 3.4 - - - +
491A SER 4.0 0.2 - - - +
492A GLY* 3.2 22.9 - - - -
493A LYS 4.1 0.5 + - - -
495A VAL* 3.6 3.1 - - - +
585A ALA* 3.5 7.2 - - + +
587A HIS* 4.1 31.6 - - + +
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Residues in contact with VAL 452 (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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451A ILE* 1.3 78.3 - - - +
453A SER* 1.3 61.6 + - - +
490A ALA* 4.3 4.9 - - + -
491A SER 3.4 10.1 - - - +
495A VAL* 3.9 19.1 - - + -
499A ILE* 4.1 22.7 - - + -
501A PHE* 4.2 12.6 - - + -
571A LEU* 3.9 27.6 - - + -
584A PRO* 3.8 28.3 - - + -
585A ALA 2.7 11.5 + - - +
586A LEU* 3.3 7.0 - - + +
587A HIS 2.9 22.6 + - - -
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Residues in contact with SER 453 (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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451A ILE* 4.1 4.1 + - - +
452A VAL* 1.3 74.2 - - - +
454A ALA* 1.3 60.8 - - - +
489A ASN 4.0 0.5 - - - +
490A ALA* 3.3 1.3 - - - -
491A SER* 2.8 47.1 + - - -
587A HIS* 3.6 30.5 - - - +
590A SER* 4.5 4.5 - - - -
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Residues in contact with ALA 454 (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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452A VAL 4.2 1.6 + - - -
453A SER* 1.3 74.0 - - - +
455A SER* 1.3 63.6 + - - +
488A LEU* 4.1 5.6 - - + -
489A ASN 2.9 14.1 - - - +
490A ALA* 3.9 12.6 - - + -
501A PHE* 3.9 13.2 - - + -
569A PHE* 3.8 26.2 - - + -
586A LEU* 4.5 5.5 - - + +
590A SER* 3.1 28.7 + - - -
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Residues in contact with SER 455 (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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454A ALA* 1.3 79.3 - - - +
456A ALA* 1.3 61.9 + - - +
487A CYS 3.9 0.7 - - - +
488A LEU* 3.7 4.2 - - - -
489A ASN* 2.9 39.8 + - - +
569A PHE* 4.5 4.5 - - - -
590A SER* 5.3 1.6 - - - -
591A LYS 5.2 4.0 - - - +
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Residues in contact with ALA 456 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A SER* 1.3 76.7 + - - +
457A SER* 1.3 61.6 + - - +
486A PHE* 6.0 0.4 - - + -
487A CYS 3.1 12.8 - - - +
488A LEU* 4.2 6.1 - - + -
567A LEU* 3.9 22.7 - - + -
569A PHE* 3.6 27.3 - - + -
591A LYS 4.8 3.5 + - - +
594A ILE* 3.5 22.2 - - + +
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Residues in contact with SER 457 (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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455A SER 4.4 0.2 + - - -
456A ALA* 1.3 77.4 - - - +
458A LEU* 1.3 62.0 + - - +
459A THR* 4.3 6.3 - - - -
486A PHE* 3.1 7.0 - - - +
487A CYS* 2.9 39.0 + - - +
541A GLU* 2.8 26.2 + - - -
594A ILE* 4.6 4.0 - - - -
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Residues in contact with LEU 458 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A SER* 1.3 76.1 - - - +
459A THR* 1.3 65.3 + - - +
460A ILE* 5.5 0.7 - - + -
484A LEU* 3.6 26.7 - - + -
485A SER 3.4 17.5 - - - +
486A PHE* 4.1 10.8 - - + -
505A LEU* 4.3 11.0 - - + -
565A ILE* 4.4 16.6 - - + +
567A LEU* 3.8 31.9 - - + +
594A ILE* 4.1 31.5 - - + +
596A ASP* 3.6 29.6 - - + +
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Residues in contact with THR 459 (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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457A SER* 5.4 5.3 + - - -
458A LEU* 1.3 80.1 - - - +
460A ILE* 1.3 64.7 + - - +
461A PHE 4.0 0.6 + - - -
483A ASN 3.8 1.4 - - - +
484A LEU* 4.1 1.8 - - - +
485A SER* 3.0 46.1 + - - +
487A CYS* 6.0 1.7 - - - -
596A ASP* 4.5 2.2 - - - +
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Residues in contact with ILE 460 (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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458A LEU* 5.4 0.9 - - + -
459A THR* 1.3 73.8 - - - +
461A PHE* 1.3 64.6 + - - +
463A ALA* 3.8 31.3 + - + +
482A ILE* 3.5 29.6 - - + -
483A ASN 3.6 2.9 - - - -
484A LEU* 3.5 24.2 - - + -
548A ILE* 5.7 1.6 - - + -
565A ILE* 3.8 23.3 - - + -
596A ASP* 3.5 25.2 + - + +
597A LYS 3.2 26.9 - - - +
598A ALA* 4.5 6.7 - - + -
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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