Contacts of the strand formed by residues 563 - 571 (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 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A PHE* 3.8 18.6 - - + -
508A ASP* 3.2 28.0 - - - +
518A ARG* 4.0 20.2 - - + +
519A ALA* 3.8 21.8 - - + -
550A LEU* 4.1 6.7 - - + -
562A PRO* 1.3 70.5 - - - +
564A HIS* 1.3 61.2 + - - +
565A ILE* 3.8 19.7 - - + +
597A LYS* 3.3 1.6 - - - -
598A ALA* 2.7 55.1 + - + +
600A ILE* 3.7 34.5 - - + -
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Residues in contact with HIS 564 (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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507A LEU 3.6 0.2 - - - -
508A ASP* 2.7 35.3 + - - +
509A TRP* 3.1 28.8 + - + -
510A GLN* 3.1 57.0 + - + +
562A PRO* 3.5 28.8 + - + +
563A ILE* 1.3 74.6 - - - +
565A ILE* 1.3 61.6 + - - +
596A ASP 3.7 3.2 + - - -
597A LYS* 3.6 45.0 + - + +
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Residues in contact with ILE 565 (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* 4.4 16.9 - - + +
460A ILE* 3.8 22.4 - - + -
484A LEU* 4.3 16.8 - - + -
505A LEU* 5.1 2.9 - - + -
506A GLN 3.2 6.3 - - - +
507A LEU* 3.7 34.1 - - + -
509A TRP* 4.2 2.8 - - - -
519A ALA* 5.4 0.2 - - + -
548A ILE* 4.9 7.9 - - + -
563A ILE* 3.8 24.0 - - + +
564A HIS* 1.3 84.1 - - - +
566A ALA* 1.3 64.9 + - - +
567A LEU 4.3 0.2 - - - -
595A GLU* 3.4 5.7 - - - +
596A ASP 2.7 44.6 + - - +
597A LYS 4.5 0.7 - - - -
598A ALA* 4.7 6.5 - - + -
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Residues in contact with ALA 566 (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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504A GLU 3.2 6.2 - - - +
505A LEU* 3.4 3.5 - - - -
506A GLN* 2.8 49.1 + - - +
509A TRP* 4.2 12.1 - - + -
565A ILE* 1.3 76.8 - - - +
567A LEU* 1.3 60.5 + - - +
568A ASN* 3.9 0.9 + - - +
593A ARG* 3.5 30.3 - - + +
594A ILE 3.5 3.8 - - - +
595A GLU* 4.1 9.6 - - + -
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Residues in contact with LEU 567 (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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456A ALA* 3.9 8.7 - - + -
457A SER 4.7 2.0 - - - +
458A LEU* 3.8 15.3 - - + +
486A PHE* 3.3 46.2 - - + -
503A VAL* 4.1 11.0 - - + -
504A GLU 3.5 4.5 - - - -
505A LEU* 3.5 19.7 - - + -
566A ALA* 1.3 72.9 - - - +
568A ASN* 1.3 63.9 + - - +
569A PHE* 3.7 31.9 - - + -
592A SER 4.8 0.2 - - - +
593A ARG* 3.4 2.3 - - - +
594A ILE* 2.7 58.4 + - + +
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Residues in contact with ASN 568 (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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503A VAL* 3.7 0.9 - - - +
504A GLU* 2.9 44.6 + - - +
506A GLN* 4.4 2.9 + - - -
566A ALA 4.5 2.1 - - - +
567A LEU* 1.3 76.6 - - - +
569A PHE* 1.3 62.0 + - - +
592A SER 3.2 12.8 - - - +
593A ARG* 4.1 27.1 + - + +
2016A NAG 1.5 63.3 + - - +
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Residues in contact with PHE 569 (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* 3.8 31.6 - - + -
455A SER* 4.5 2.2 - - - -
456A ALA* 3.6 26.5 - - + -
488A LEU* 4.3 8.1 - - + -
501A PHE* 3.9 21.5 - + + -
502A THR 3.3 11.9 - - - +
503A VAL* 3.8 18.4 - - + -
567A LEU* 3.7 16.8 - - + -
568A ASN* 1.3 75.5 - - - +
570A SER* 1.3 66.7 + - - +
586A LEU* 4.3 9.4 - - + +
590A SER* 5.5 1.8 - - - -
591A LYS 3.6 11.7 - - - -
592A SER* 2.9 57.9 + - - +
593A ARG 6.0 0.2 - - - -
594A ILE* 6.1 0.4 - - + -
2016A NAG 3.7 4.8 - - - +
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Residues in contact with SER 570 (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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501A PHE* 3.4 7.2 - - - -
502A THR* 3.0 35.5 + - - -
569A PHE* 1.3 76.9 - - - +
571A LEU* 1.3 71.3 + - - +
573A PRO* 5.5 1.9 - - - +
586A LEU* 4.3 12.8 - - - -
2016A NAG 3.1 19.1 + - - -
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Residues in contact with LEU 571 (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* 3.9 14.8 - - + -
499A ILE* 3.8 29.4 - - + -
500A GLY 3.6 5.4 - - - +
501A PHE* 3.8 19.0 - - + -
570A SER* 1.3 77.5 - - - +
572A ASP* 1.3 67.5 + - - +
573A PRO* 3.1 10.6 - - - +
584A PRO* 3.6 23.3 - - + +
585A ALA 3.6 8.1 - - - -
586A LEU* 3.4 47.1 - - + +
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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
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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