Contacts of the strand formed by residues 581 - 587 (chain A) in PDB entry 3VN4
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 581 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A ARG 2.5 25.5 + - - -
545A CYS* 3.6 16.1 - - - +
546A GLN* 3.4 39.0 - - + +
555A CYS* 4.5 0.7 - - - +
579A ASN* 3.7 13.2 - - - +
580A LEU* 1.3 78.5 - - - +
582A SER* 1.3 68.4 + - - +
583A VAL* 3.1 4.5 + - - +
677A TYR* 3.5 2.3 - - - +
678A PHE* 2.8 44.5 + - - +
679A GLN* 6.2 0.2 - - - -
680A PRO* 6.1 0.2 - - + -
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Residues in contact with SER 582 (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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516A ASP* 4.8 8.7 + - - -
543A ASP 4.9 0.3 + - - -
544A ARG* 3.2 25.8 + - - +
546A GLN* 4.8 4.4 - - - +
581A THR* 1.3 75.1 - - - +
583A VAL* 1.3 63.2 + - - +
584A TYR* 3.4 5.5 + - - +
645A ILE 5.0 6.0 + - - -
676A THR* 3.4 8.8 + - - +
677A TYR* 3.7 2.9 - - - -
678A PHE* 3.8 20.9 - - - -
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Residues in contact with VAL 583 (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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574A LEU* 5.3 1.6 - - + -
576A VAL* 4.0 31.4 - - + -
580A LEU* 4.0 27.4 - - + +
581A THR* 3.9 5.2 - - - +
582A SER* 1.3 77.7 - - - +
584A TYR* 1.3 61.5 + - - +
585A ILE* 4.2 16.4 - - + -
643A ILE 5.8 0.2 - - - +
644A ARG* 3.7 6.9 + - - +
645A ILE* 3.3 49.2 + - + +
676A THR 3.5 6.3 - - - +
677A TYR* 3.7 20.9 - - + -
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Residues in contact with TYR 584 (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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582A SER 3.4 3.3 + - - +
583A VAL* 1.3 76.1 - - - +
585A ILE* 1.3 67.8 + - - +
586A ALA* 3.5 27.0 - - + +
588A HIS* 5.5 2.9 - + - -
640A LEU* 5.0 2.4 - - - +
642A GLU* 2.5 41.0 + - + +
643A ILE 3.7 1.6 - - - -
644A ARG* 3.8 45.5 - - + +
674A THR* 5.0 4.9 - - - -
675A PHE* 3.1 7.5 - - - +
676A THR* 2.8 58.0 + - + +
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Residues in contact with ILE 585 (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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573A PHE* 3.9 24.0 - - + -
574A LEU* 4.4 7.9 - - + -
576A VAL* 4.6 0.2 - - + -
583A VAL* 4.2 20.0 - - + -
584A TYR* 1.3 82.6 - - - +
586A ALA* 1.3 64.3 + - - +
595A LEU* 4.4 10.5 - - + -
642A GLU* 3.4 3.5 - - - +
643A ILE* 2.7 55.2 + - + +
645A ILE* 5.2 0.4 - - + -
655A ILE* 3.5 43.3 - - + -
673A ILE* 4.0 6.7 - - + -
674A THR 3.7 9.2 - - - +
675A PHE* 3.9 11.2 - - + -
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Residues in contact with ALA 586 (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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584A TYR* 3.5 30.1 - - + +
585A ILE* 1.3 78.2 - - - +
587A ASN* 1.3 59.0 + - - +
588A HIS* 4.0 15.0 - - + +
595A LEU* 4.7 1.1 - - - -
640A LEU* 4.5 3.1 - - + -
641A GLU 3.2 12.3 - - - +
672A ASP 3.8 0.3 - - - +
673A ILE* 3.1 7.3 - - - +
674A THR* 2.9 43.4 + - - +
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Residues in contact with ASN 587 (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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586A ALA* 1.3 72.5 - - - +
588A HIS* 1.3 62.1 + - - +
589A ARG 3.1 15.8 + - - -
590A PRO* 3.9 6.4 - - - +
593A THR* 2.9 29.1 + - - -
594A HIS* 4.4 2.0 - - - +
595A LEU* 4.0 12.8 - - + +
640A LEU* 3.6 4.0 - - - +
641A GLU* 2.8 57.8 + - + +
657A VAL* 4.8 1.8 - - - +
672A ASP 3.2 21.3 + - - +
673A ILE* 3.8 18.3 - - + +
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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