Contacts of the strand formed by residues 658 - 667 (chain A) in PDB entry 1R4X
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 HIS 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A GLY 5.5 2.5 - - - -
626A LEU* 3.7 37.7 + - + +
654A THR* 4.1 0.9 - - - +
655A PHE* 2.9 34.0 + - + +
657A ASN* 1.3 98.8 + - + +
659A MET* 1.3 63.2 + - - +
690A LEU* 3.7 21.0 - - + +
709A LEU* 4.0 11.7 - - + -
710A VAL 3.2 17.0 - - - +
711A ALA* 3.7 13.2 - - - +
712A LEU* 3.5 10.6 - - - +
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Residues in contact with MET 659 (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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652A LYS* 4.5 11.4 - - - -
653A HIS 3.2 18.8 - - - +
654A THR* 4.4 15.9 - - + +
655A PHE* 4.6 0.4 - - - -
658A HIS* 1.3 74.3 - - - +
660A VAL* 1.3 66.2 + - - +
661A PHE* 3.4 36.6 - - + -
687A TYR* 4.0 13.2 - - + -
708A THR 3.9 0.7 - - - +
709A LEU* 3.7 2.9 - - - +
710A VAL* 2.9 42.9 + - + +
712A LEU* 3.9 19.3 - - + -
758A VAL* 4.0 19.5 - - + -
762A ASP* 4.8 3.1 - - + -
763A HIS* 4.5 8.7 - - + +
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Residues in contact with VAL 660 (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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617A LEU* 4.3 7.0 - - + -
623A PHE* 3.8 24.9 - - + -
626A LEU* 3.7 18.2 - - + -
652A LYS* 3.8 0.5 - - - -
653A HIS* 2.8 41.7 + - + +
655A PHE* 3.6 26.6 - - + -
659A MET* 1.3 76.3 - - - +
661A PHE* 1.3 65.3 + - - +
707A TYR* 3.6 31.0 - - + -
708A THR 3.4 5.6 - - - +
709A LEU* 3.8 10.3 - - + -
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Residues in contact with PHE 661 (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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650A CYS* 4.3 3.1 - - - -
651A THR 3.7 2.5 - - - -
652A LYS* 4.0 13.9 - - + -
659A MET* 3.4 36.8 - - + -
660A VAL* 1.3 72.4 - - - +
662A GLN* 1.3 61.3 + - - +
663A PHE* 3.6 25.0 - - + -
681A MET* 3.6 22.2 - - + -
707A TYR* 3.2 6.8 - - - +
708A THR 2.9 39.0 + - - +
710A VAL* 3.6 33.0 - - + -
724A PHE* 3.9 20.9 - + - -
756A LEU* 3.5 27.4 - - + -
758A VAL* 3.9 6.1 - - + -
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Residues in contact with GLN 662 (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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613A PHE* 3.8 19.9 - - - -
616A GLN* 4.7 6.6 + - - +
617A LEU* 4.7 1.6 - - - +
649A ARG 3.5 1.2 - - - +
650A CYS* 3.2 7.3 - - - -
651A THR* 2.9 43.6 + - - +
653A HIS* 2.9 29.9 + - + +
660A VAL 3.8 1.0 + - - -
661A PHE* 1.3 72.1 - - - +
663A PHE* 1.3 61.6 + - - +
664A ASP* 3.0 30.9 + - - +
705A THR* 3.7 12.7 + - + +
706A CYS 3.7 3.8 - - - -
707A TYR* 3.7 31.5 + - + -
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Residues in contact with PHE 663 (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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639A LEU* 3.6 21.8 - - + -
648A ILE* 4.0 13.2 - - + -
649A ARG 3.5 3.1 - - - -
650A CYS* 3.7 20.9 - - + -
661A PHE* 3.6 34.5 - - + -
662A GLN* 1.3 71.2 - - - +
664A ASP* 1.3 63.9 + - - +
665A CYS* 3.6 12.5 - - - -
679A VAL* 3.6 37.5 - - + -
681A MET* 3.8 14.1 - - + -
705A THR* 3.2 3.6 - - - -
706A CYS* 2.9 58.3 + - - -
708A THR* 3.6 20.2 - - - -
726A CYS* 5.0 2.0 - - - -
756A LEU* 5.3 0.4 - - + -
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Residues in contact with ASP 664 (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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647A VAL 3.5 4.5 - - - +
648A ILE* 3.6 0.3 - - - -
649A ARG* 2.9 53.3 + - + +
651A THR* 4.7 7.1 + - - -
662A GLN* 3.0 29.2 + - - +
663A PHE* 1.3 69.2 - - - +
665A CYS* 1.3 58.6 + - - +
666A THR* 5.3 1.1 + - - -
703A PRO* 5.6 5.6 - - + -
704A GLY 3.6 4.9 - - - +
705A THR* 2.7 27.0 + - - +
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Residues in contact with CYS 665 (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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647A VAL 3.3 4.3 - - - -
648A ILE* 3.6 25.4 - - + -
663A PHE* 3.6 30.5 - - - -
664A ASP* 1.3 74.1 - - - +
666A THR* 1.3 62.9 + - - +
667A ASN 4.2 0.7 - - - -
677A VAL* 5.0 5.6 - - - -
679A VAL* 4.9 2.9 - - - -
698A LEU* 3.7 26.0 - - + +
703A PRO* 3.2 3.8 - - - +
704A GLY 2.8 37.9 + - - +
706A CYS* 4.1 13.7 - - - -
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Residues in contact with THR 666 (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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646A TYR* 3.3 12.8 - - - +
647A VAL* 2.9 46.5 + - + +
648A ILE* 5.8 0.2 - - - -
664A ASP 5.3 0.9 + - - -
665A CYS* 1.3 76.5 + - - +
667A ASN* 1.3 71.2 + - - +
668A THR* 3.7 11.3 + - + +
698A LEU* 5.1 0.9 - - - -
701A ASN* 4.1 25.6 - - - +
702A GLN 4.6 1.1 - - - +
703A PRO* 3.7 22.4 - - + +
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Residues in contact with ASN 667 (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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646A TYR* 3.9 14.1 - - + -
665A CYS 4.2 1.0 + - - -
666A THR* 1.3 71.0 - - - +
668A THR* 1.3 58.0 + - - +
669A LEU* 3.1 18.6 + - - +
672A GLN* 2.9 57.9 + - - +
673A THR* 4.1 1.0 - - - +
674A LEU* 4.4 6.0 - - + +
698A LEU* 3.2 38.7 + - + +
699A PRO 4.2 3.3 + - - +
700A TYR* 3.4 9.3 - - - +
701A ASN* 2.9 27.4 + - - -
702A GLN 5.5 0.4 + - - -
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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