Contacts of the strand formed by residues 528 - 536 (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 THR 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A GLU* 5.2 6.5 - - + +
505A LEU 3.2 7.0 - - - +
506A GLN* 3.5 33.9 - - + +
512A GLN* 6.0 0.4 - - - +
517A ARG* 4.0 17.3 + - - +
521A PHE* 3.6 6.5 - - - -
524A SER* 4.7 2.1 + - - -
526A GLN* 4.6 9.8 + - - +
527A ALA* 1.3 83.4 + - - +
529A LEU* 1.3 65.2 + - - +
530A THR* 4.3 2.5 - - - -
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Residues in contact with LEU 529 (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 3.2 6.1 - - - +
504A GLU* 4.9 0.2 - - - -
505A LEU* 3.1 36.1 + - + +
521A PHE* 3.7 24.5 - - + -
523A ALA* 6.3 2.5 - - + -
524A SER* 4.8 15.0 - - - +
528A THR* 1.3 77.3 - - - +
530A THR* 1.3 70.9 + - - +
531A GLN* 4.4 12.7 - - + +
546A MET* 3.8 35.0 - - + -
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Residues in contact with THR 530 (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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502A THR* 6.1 2.5 - - - -
503A VAL 3.2 5.6 - - - -
504A GLU* 3.2 36.8 - - + +
528A THR* 4.3 2.9 - - - +
529A LEU* 1.3 81.1 - - - +
531A GLN* 1.3 64.6 + - - +
2016A NAG 5.6 2.7 - - + -
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Residues in contact with GLN 531 (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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486A PHE* 3.6 23.1 - - - -
502A THR* 3.1 13.1 - - - +
503A VAL* 3.0 34.3 + - + +
529A LEU* 4.4 12.4 - - + +
530A THR* 1.3 78.5 - - - +
532A THR* 1.3 74.8 + - - +
533A LEU* 3.4 26.9 - - + +
544A ARG* 3.7 18.6 - - - +
546A MET* 4.2 12.4 - - - +
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Residues in contact with THR 532 (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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500A GLY* 5.4 2.0 - - - -
501A PHE 3.4 9.9 - - - +
502A THR* 3.8 9.7 - - - +
531A GLN* 1.3 85.2 + - - +
533A LEU* 1.3 83.4 + - - +
534A LEU* 4.5 13.0 - - + -
544A ARG* 4.8 3.1 + - - -
572A ASP* 4.1 15.1 + - - +
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Residues in contact with LEU 533 (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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486A PHE* 3.7 27.8 - - + -
488A LEU* 3.8 25.6 - - + -
499A ILE 3.5 2.8 - - - +
500A GLY* 3.6 3.1 - - - -
501A PHE* 2.9 34.1 + - + +
503A VAL* 4.1 10.5 - - + -
531A GLN* 3.4 15.5 - - - +
532A THR* 1.3 82.8 - - - +
534A LEU* 1.3 66.2 + - - +
535A ILE* 3.9 18.1 + - + -
542A ASP* 5.0 6.3 - - - +
544A ARG* 3.2 42.6 - - + +
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Residues in contact with LEU 534 (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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498A SER* 4.1 27.1 - - - +
499A ILE 3.8 5.2 - - - +
500A GLY* 5.0 7.9 - - - +
532A THR* 4.5 14.4 - - + -
533A LEU* 1.3 76.7 - - - +
535A ILE* 1.3 63.0 + - - +
536A GLN 4.3 0.3 + - - -
542A ASP* 3.6 14.7 - - - +
544A ARG* 5.6 1.8 - - - +
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Residues in contact with ILE 535 (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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488A LEU* 3.6 46.4 - - + +
489A ASN* 4.8 0.7 - - - -
490A ALA* 3.9 21.8 - - + +
497A ASP 3.7 0.2 - - - +
498A SER* 3.3 3.3 - - - -
499A ILE* 2.7 37.1 + - + +
501A PHE* 3.7 25.4 - - + -
533A LEU* 4.2 15.0 - - + -
534A LEU* 1.3 76.7 - - - +
536A GLN* 1.3 74.2 + - - +
539A ALA* 5.1 4.3 - - + -
540A ARG 5.4 0.7 - - - +
542A ASP* 3.5 29.2 - - + +
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Residues in contact with GLN 536 (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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490A ALA 3.4 9.9 + - - +
497A ASP* 3.3 32.6 - - + +
498A SER* 4.7 5.4 - - - +
499A ILE* 4.7 0.9 - - - -
534A LEU 4.3 0.6 + - - -
535A ILE* 1.3 80.1 - - - +
537A ASN* 1.3 67.0 + - + +
538A GLY 3.5 2.2 - - - -
539A ALA* 3.2 33.7 + - + +
542A ASP* 5.5 0.6 + - - -
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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