Contacts of the strand formed by residues 614 - 623 (chain A) in PDB entry 1RS0
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 LYS 614 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ASP* 3.1 13.9 - - - +
610A GLU* 3.9 2.2 - - - -
611A GLU* 2.6 38.7 + - + +
612A GLU 2.8 13.2 + - - +
613A LYS* 1.3 74.6 - - + +
615A LEU* 1.3 62.7 + - - +
616A THR* 3.6 1.3 + - - -
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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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464A ASP* 2.8 47.6 + - + +
465A TYR* 4.7 14.4 - - + -
467A LYS* 6.2 0.2 - - - +
468A GLN* 3.8 27.4 + - + +
471A GLN* 4.0 23.1 - - + -
473A LYS* 6.2 0.7 - - + -
487A MET* 3.8 28.5 - - + -
608A VAL* 4.1 9.2 - - + -
609A SER 3.6 2.0 - - - -
610A GLU* 4.1 20.6 - - + +
613A LYS 5.2 1.8 - - - +
614A LYS* 1.3 75.1 - - - +
616A THR* 1.3 59.9 + - - +
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Residues in contact with THR 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLN* 5.2 0.7 - - - -
608A VAL* 3.4 6.5 - - - +
609A SER* 2.8 46.7 + - - +
611A GLU* 3.4 37.3 + - + -
614A LYS 3.6 1.5 + - - -
615A LEU* 1.3 73.9 - - - +
617A ARG* 1.3 71.9 + - - +
618A LYS* 3.5 16.5 + - + -
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Residues in contact with ARG 617 (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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456A VAL* 4.2 10.1 - - - +
458A GLU* 5.4 5.1 + - - +
467A LYS* 3.0 31.0 + - - +
468A GLN* 3.2 24.2 + - - +
470A TRP* 4.7 2.6 - - - -
606A LEU* 4.3 27.3 - - + +
607A PHE 3.7 4.0 - - - +
608A VAL* 4.4 4.9 - - + -
616A THR* 1.3 83.0 + - - +
618A LYS* 1.3 65.5 + - - +
619A GLU 3.9 2.9 + - - +
681A HIS* 6.1 0.6 - - - -
686A PHE* 3.8 34.6 - - - -
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Residues in contact with LYS 618 (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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606A LEU* 3.3 4.0 - - - -
607A PHE* 2.8 71.1 + - + +
609A SER* 4.2 13.6 + - - -
611A GLU* 2.5 33.0 + - - +
616A THR* 3.5 18.1 - - + +
617A ARG* 1.3 77.8 - - - +
619A GLU* 1.3 64.5 + - - +
620A VAL 3.6 0.5 + - - -
667A PRO* 3.8 22.5 - - + +
668A ASN 5.2 6.3 + - - -
670A CYS* 5.8 4.6 - - - -
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Residues in contact with GLU 619 (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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604A LYS* 3.5 32.5 - - + +
605A ALA 3.6 7.2 - - - +
606A LEU* 4.3 4.9 - - + +
617A ARG 3.9 4.2 + - - -
618A LYS* 1.3 70.1 - - - +
620A VAL* 1.3 62.6 + - - +
621A TYR* 3.1 28.0 + - + -
666A ASP* 4.5 1.0 - - - +
667A PRO* 2.8 27.7 - - - +
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Residues in contact with VAL 620 (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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604A LYS* 3.9 0.5 - - - -
605A ALA* 2.8 39.1 + - + +
606A LEU 4.5 0.2 - - - +
607A PHE* 3.9 17.0 - - + -
618A LYS 4.5 2.9 - - - +
619A GLU* 1.3 80.7 - - - +
621A TYR* 1.3 73.9 + - - +
658A THR* 4.0 28.5 - - + +
666A ASP* 3.3 15.5 - - + +
667A PRO* 3.5 33.7 - - + +
678A LEU* 4.2 16.8 - - + -
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Residues in contact with TYR 621 (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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602A ASP* 4.5 11.9 - - + -
603A ILE 3.2 5.8 - - - +
604A LYS* 2.6 53.9 + - + -
619A GLU* 3.1 21.7 + - + -
620A VAL* 1.3 83.4 - - - +
622A ILE* 1.3 63.0 + - - +
623A LYS* 2.9 27.5 + - - +
658A THR* 3.4 11.3 - - - -
663A PRO* 4.0 25.6 - - + -
664A TYR* 3.7 44.2 - + + -
666A ASP* 2.6 28.2 + - - +
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Residues in contact with ILE 622 (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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598A LEU* 4.3 19.1 - - + -
601A GLN 3.1 0.9 - - - +
602A ASP* 3.3 0.9 - - - -
603A ILE* 2.6 52.7 + - + +
605A ALA* 3.8 20.6 - - + -
621A TYR* 1.3 71.1 - - - +
623A LYS* 1.3 62.8 + - - +
624A ASN* 2.9 22.8 + - + +
656A LEU* 4.3 25.4 - - + -
657A CYS 3.6 10.3 - - - +
658A THR* 3.7 17.0 - - + -
678A LEU* 3.6 24.9 - - + -
680A VAL* 5.0 0.2 - - + -
689A VAL* 4.3 6.3 - - + -
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Residues in contact with LYS 623 (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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602A ASP* 3.8 18.6 - - - +
621A TYR* 2.9 23.4 + - - +
622A ILE* 1.3 71.1 - - - +
624A ASN* 1.3 58.4 + - - +
625A GLY 3.5 2.5 - - - -
627A LYS* 4.0 13.7 - - + +
628A LYS* 3.2 35.7 - - - +
631A CYS* 3.8 19.5 - - + -
657A CYS* 2.9 21.4 + - - +
659A GLY 2.5 31.3 + - - +
660A GLY* 4.8 0.4 - - - -
662A SER 2.9 31.6 - - - +
663A PRO* 3.9 6.3 - - + -
666A ASP* 3.2 14.5 + - - -
714A ARG* 3.9 5.2 - - - +
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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