Contacts of the strand formed by residues 611 - 616 (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 ALA 611 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A LYS* 3.3 0.7 - - - -
608A SER* 2.7 33.0 + - - -
610A LYS* 1.3 82.3 - - - +
612A LEU* 1.3 59.8 + - - +
623A VAL* 3.8 20.4 - - + -
624A ASN 3.3 13.2 - - - +
625A PHE* 3.9 13.0 - - + -
626A TYR* 3.1 14.2 + - - -
675A TYR* 4.0 6.1 - - + -
679A MET* 3.6 16.1 - - - +
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Residues in contact with LEU 612 (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* 3.5 48.5 - - + +
516A PHE* 3.9 26.5 - - + -
605A TRP* 4.3 5.4 - - + -
606A LEU 3.4 5.4 - - - +
607A LYS* 3.6 23.6 - - + -
611A ALA* 1.3 73.3 - - - +
613A MET* 1.3 75.0 + - - +
614A MET* 4.1 17.4 - - + +
622A GLN 3.9 0.5 - - - +
623A VAL* 3.1 6.7 - - - +
624A ASN* 2.8 40.7 + - + +
626A TYR* 3.7 10.7 + - + -
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Residues in contact with MET 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A GLN* 5.2 7.9 - - - +
605A TRP* 3.1 11.0 - - - +
606A LEU* 2.7 55.8 + - + +
612A LEU* 1.3 73.5 - - - +
614A MET* 1.3 69.5 + - - +
615A LEU* 4.9 9.0 - - - -
621A PHE* 3.6 26.7 - - + -
622A GLN 3.4 3.6 - - - -
623A VAL* 3.9 7.6 - - + -
679A MET* 2.9 56.3 - - + +
680A LEU* 3.5 16.8 - - + +
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Residues in contact with MET 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A VAL* 3.7 43.5 - - + -
507A TRP* 4.8 1.1 - - + -
516A PHE* 3.9 29.8 - - + -
518A TYR* 5.0 1.3 - - - -
602A LEU* 4.0 10.5 - - + -
604A GLN 3.7 4.3 - - - -
605A TRP* 4.4 5.4 - - + -
612A LEU* 4.1 23.3 - - + -
613A MET* 1.3 81.0 - - - +
615A LEU* 1.3 59.4 - - - +
616A PHE* 4.1 10.6 - - + -
620A THR 3.8 1.3 - - - +
621A PHE* 3.6 5.2 - - - -
622A GLN* 2.8 59.9 + - + +
624A ASN* 4.3 8.7 - - - +
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Residues in contact with LEU 615 (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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471A VAL* 4.1 10.8 - - + -
472A ALA* 3.6 37.5 - - + +
475A VAL* 4.3 7.6 - - + -
602A LEU* 3.3 5.9 - - - +
603A LEU* 2.7 38.5 + - + +
604A GLN* 3.1 34.4 + - + +
613A MET* 4.9 7.2 - - - -
614A MET* 1.3 74.3 - - - +
616A PHE* 1.3 62.2 + - - +
619A GLY 4.0 15.9 - - - +
620A THR 3.6 12.6 - - - +
621A PHE* 4.0 21.1 - - + -
680A LEU* 4.7 5.4 - - + -
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Residues in contact with PHE 616 (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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471A VAL* 3.8 8.3 - - - +
503A TRP* 6.2 0.7 - - - -
504A VAL* 3.6 33.2 - - + -
518A TYR* 3.5 32.1 - + - -
520A LEU* 4.2 9.0 - - + -
600A LEU* 4.0 21.3 - - + -
601A TYR* 3.5 18.6 - - - +
602A LEU* 3.5 20.4 - - + -
603A LEU* 3.8 3.8 - - - +
614A MET* 4.1 17.7 - - + -
615A LEU* 1.3 78.9 - - - +
617A ASN* 1.3 58.7 + - - +
618A ASP* 3.1 16.8 - - - +
619A GLY* 2.9 24.8 + - - -
620A THR* 3.0 28.8 + - + +
622A GLN* 5.5 2.0 - - + -
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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