Contacts of the strand formed by residues 582 - 585 (chain D) in PDB entry 4JVG
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 582 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536D SER* 3.2 5.7 - - - -
537D LEU* 2.8 39.6 + - + -
556D ILE* 5.3 0.9 - - + -
560D THR* 4.1 18.8 - - + +
577D LEU* 3.7 22.2 - - + -
578D LYS 2.9 33.7 - - - +
579D SER* 3.0 12.5 + - - +
580D ASN 4.1 1.3 - - - -
581D ASN* 1.3 80.0 - - - +
583D PHE* 1.3 64.3 + - - +
584D LEU* 3.7 22.0 - - + -
590D VAL* 3.7 18.6 - - + -
591D LYS 4.0 2.2 - - - -
592D ILE* 4.6 11.7 - - + -
645D VAL* 4.5 13.2 - - + -
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Residues in contact with PHE 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D LEU* 6.1 2.0 - - + -
532D CYS* 3.3 49.1 - - + -
533D GLU 3.9 2.9 - - - -
534D GLY 3.6 17.5 - - - -
535D SER* 4.0 17.9 - - - -
536D SER* 4.3 5.2 - - - +
581D ASN 3.8 0.2 + - - -
582D ILE* 1.3 72.3 - - - +
584D LEU* 1.3 97.9 + - - +
585D HIS* 3.7 6.1 - - + -
590D VAL* 3.3 5.2 - - - -
591D LYS* 2.9 46.7 + - + +
595D PHE* 4.2 25.8 - + + -
801D B96 3.7 20.4 - - - -
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Residues in contact with LEU 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D GLY* 3.0 28.4 - - - -
535D SER 3.0 16.9 + - - +
537D LEU* 4.1 20.0 - - + +
540D HIS* 3.5 28.5 - - + +
548D PHE* 4.2 6.7 - - + -
552D LYS* 5.6 0.2 - - - +
556D ILE* 4.1 25.8 - - + -
582D ILE* 3.7 18.4 - - + -
583D PHE* 1.3 85.6 - - - +
585D HIS* 1.3 61.8 + - - +
587D ASP* 3.5 25.1 + - - +
588D ASN 5.3 1.6 - - - +
589D THR 3.7 3.4 - - - +
590D VAL* 4.1 12.3 - - + -
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Residues in contact with HIS 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C VAL* 5.2 6.0 - - + +
530D GLN* 4.4 8.6 + - - -
531D TRP 4.7 2.9 + - - -
532D CYS* 2.9 42.9 - - + +
533D GLU* 3.4 10.4 + - + -
583D PHE* 3.7 6.1 - - + -
584D LEU* 1.3 69.3 - - - +
586D GLU* 1.3 96.5 + - + +
587D ASP 2.7 4.3 - - - -
588D ASN 2.7 23.6 + - - -
589D THR* 2.9 31.9 + - - +
591D LYS* 4.0 25.8 - - + -
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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