Contacts of the strand formed by residues 504 - 510 (chain A) in PDB entry 4RS6
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 VAL 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A TRP* 1.3 89.5 - - - +
505A THR* 1.3 60.9 + - - +
506A LYS 3.1 28.7 - - - +
507A TRP* 4.4 5.5 - - + -
518A TYR* 3.8 12.3 - - + -
519A GLN 3.6 6.5 - - - +
520A LEU* 4.2 4.0 - - + -
586A GLY* 5.4 0.2 - - - -
614A MET* 3.7 25.1 - - + -
616A PHE* 3.6 38.4 - - + -
622A GLN* 2.8 28.8 + - - +
624A ASN* 4.9 2.1 + - - -
631A LYS* 5.4 0.9 - - - +
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Residues in contact with THR 505 (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 TRP* 3.5 34.3 + - + +
504A VAL* 1.3 74.0 - - - +
506A LYS* 1.3 66.3 + - - +
507A TRP* 5.6 0.7 - - - -
519A GLN* 3.1 34.9 + - - +
520A LEU 3.8 0.9 + - - +
521A SER* 4.0 22.7 - - - -
584A MET 3.7 1.2 - - - +
585A ASP* 3.6 21.9 + - - +
586A GLY* 2.8 27.0 + - - -
631A LYS* 6.3 0.2 - - - -
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Residues in contact with LYS 506 (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 VAL* 3.1 11.3 - - - +
505A THR* 1.3 87.9 + - - +
507A TRP* 1.3 69.3 + - - +
518A TYR* 3.2 0.2 - - - -
519A GLN* 3.0 42.7 + - + +
579A MET* 3.0 44.4 + - + +
580A GLU* 3.9 11.7 + - - +
583A LEU* 2.8 34.9 + - + +
584A MET* 3.5 17.2 - - - +
585A ASP* 3.5 20.0 - - - +
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Residues in contact with TRP 507 (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 VAL* 4.4 7.6 - - + -
505A THR 5.6 0.4 - - - -
506A LYS* 1.3 83.8 - - - +
508A VAL* 1.3 72.6 + - - +
509A ASP* 3.9 22.9 - - + -
516A PHE* 4.0 15.7 - + + -
517A GLY 3.2 11.7 - - - +
518A TYR* 3.9 5.2 - - + +
579A MET* 4.2 0.9 - - - -
583A LEU* 3.5 15.8 - - - +
607A LYS* 4.3 17.3 - - - -
612A LEU* 3.5 28.5 - - + -
614A MET* 4.8 0.7 - - + -
624A ASN* 3.6 29.5 - - + +
626A TYR* 4.5 9.9 - + - -
631A LYS* 5.8 1.0 - - - +
512B ASN* 4.0 41.6 - - + +
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Residues in contact with VAL 508 (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 TRP* 1.3 82.0 - - - +
509A ASP* 1.3 66.4 + - - +
510A TYR* 3.7 4.9 + - + +
516A PHE* 3.7 3.3 - - - -
517A GLY 2.7 46.9 + - - +
575A PHE* 3.3 33.8 - - + +
578A TYR* 4.3 24.7 - - + -
579A MET* 3.8 24.2 - - + -
583A LEU* 4.6 5.2 - - + -
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Residues in contact with ASP 509 (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 TRP* 3.9 14.8 - - + -
508A VAL* 1.3 73.1 - - - +
510A TYR* 1.3 60.9 + - - +
511A SER* 2.8 30.9 + - - -
512A ASN* 4.4 4.6 - - - +
515A GLY 4.5 0.2 - - - -
516A PHE* 4.0 18.3 - - + -
605A TRP* 4.1 1.0 - - - -
607A LYS* 3.0 28.2 + - - +
509B ASP 5.8 0.4 - - - +
607B LYS* 2.8 31.1 + - - -
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Residues in contact with TYR 510 (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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508A VAL* 3.7 5.8 + - + -
509A ASP* 1.3 73.8 - - - +
511A SER* 1.3 53.4 + - - +
512A ASN* 3.3 23.8 - - - -
513A LYS* 3.0 35.7 + - + +
514A TYR* 2.7 66.6 + + - -
515A GLY 2.8 15.2 + - - +
574A TYR* 4.2 26.3 + + - -
575A PHE* 3.8 17.9 - + + -
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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