Contacts of the helix formed by residues 643 - 658 (chain A) in PDB entry 5P9I
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 THR 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A GLU* 3.7 13.7 - - - +
577A LYS* 3.9 15.5 - - - +
580A ILE* 3.7 5.8 - - - -
642A PRO* 1.3 76.9 - - - +
644A PHE* 1.3 58.7 + - - +
645A LYS* 3.4 9.7 + - - +
646A ILE* 3.1 35.4 + - + +
647A LEU* 2.9 27.7 + - - +
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Residues in contact with PHE 644 (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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506A CYS* 3.5 14.5 - - - +
509A MET* 3.5 51.1 - - + -
510A GLU* 3.6 25.5 - - + +
513A GLU* 2.9 38.1 + - + +
579A ASP* 3.7 29.6 - - + -
580A ILE* 3.5 24.4 - - + +
583A PHE* 3.6 28.5 - + + -
643A THR* 1.3 70.1 - - - +
645A LYS* 1.3 60.5 + - - +
647A LEU* 3.9 8.5 - - + -
648A LEU* 2.9 30.3 + - - +
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Residues in contact with LYS 645 (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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510A GLU* 3.7 32.1 - - + +
513A GLU* 4.4 1.4 + - - -
643A THR* 3.2 9.9 + - - +
644A PHE* 1.3 77.8 - - - +
646A ILE* 1.3 63.5 + - + +
648A LEU* 3.3 3.7 + - - +
649A SER* 3.1 21.8 + - - -
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Residues in contact with ILE 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A PRO* 3.8 18.4 - - + -
643A THR* 3.1 33.3 + - + +
645A LYS* 1.3 76.8 - - + +
647A LEU* 1.4 66.4 + - - +
649A SER* 2.6 26.4 + - - +
650A ASN* 2.9 27.1 + - - +
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Residues in contact with LEU 647 (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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506A CYS* 3.7 14.6 - - - -
580A ILE* 3.8 29.2 - - + -
583A PHE* 3.7 27.1 - - + -
629A ILE* 3.7 27.6 - - + -
632A SER* 4.0 4.3 - - - +
633A CYS* 3.8 18.6 - - - -
642A PRO* 3.7 21.8 - - + -
643A THR 2.9 13.3 + - - +
644A PHE* 3.7 7.0 - - + +
646A ILE* 1.4 76.4 - - - +
648A LEU* 1.3 56.7 + - - +
650A ASN* 3.1 9.4 + - - +
651A ILE* 2.8 33.2 + - + +
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Residues in contact with LEU 648 (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 LYS* 3.7 35.2 - - + +
506A CYS* 3.5 14.8 - - + +
507A GLU* 3.9 26.0 - - + +
510A GLU* 3.3 27.6 - - - +
644A PHE 2.9 17.1 + - - +
645A LYS* 3.6 6.1 - - + +
646A ILE 3.2 0.2 - - - -
647A LEU* 1.3 75.5 - - - +
649A SER* 1.3 57.6 + - - +
651A ILE* 3.2 3.4 + - + +
652A LEU* 2.9 48.2 + - + +
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Residues in contact with SER 649 (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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645A LYS 3.1 12.3 + - - -
646A ILE* 2.6 24.4 + - - +
648A LEU* 1.3 77.0 - - - +
650A ASN* 1.3 61.4 + - - +
652A LEU* 3.5 10.1 + - - +
653A ASP* 3.0 28.2 + - - +
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Residues in contact with ASN 650 (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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629A ILE* 3.7 25.0 - - + +
632A SER* 4.9 4.2 + - - -
642A PRO* 5.2 0.7 - - - +
646A ILE* 2.9 33.8 + - - +
647A LEU* 3.1 21.3 + - - +
649A SER* 1.3 78.9 + - - +
651A ILE* 1.3 65.7 + - - +
653A ASP* 3.3 8.0 + - - +
654A VAL* 3.1 27.9 + - - +
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Residues in contact with ILE 651 (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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499A LEU* 3.9 24.6 - - + +
502A CYS* 4.2 11.7 - - + +
503A LYS* 3.8 31.9 - - + -
506A CYS* 3.9 27.4 - - + -
583A PHE* 3.9 20.6 - - + -
587A MET* 4.7 3.6 - - + -
629A ILE* 4.2 21.3 - - + -
647A LEU 2.8 19.4 + - - +
648A LEU* 3.2 4.9 + - - +
650A ASN* 1.3 74.5 - - - +
652A LEU* 1.3 59.7 + - - +
654A VAL* 3.2 4.2 + - - +
655A MET* 2.9 28.1 + - + +
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Residues in contact with LEU 652 (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 LYS* 3.5 32.8 - - + +
507A GLU* 5.8 0.2 - - - +
648A LEU* 2.9 37.8 + - + +
649A SER* 3.8 7.9 - - - +
651A ILE* 1.3 75.7 - - - +
653A ASP* 1.3 57.8 + - - +
655A MET* 3.3 9.5 + - + +
656A ASP* 2.9 38.4 + - - +
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Residues in contact with ASP 653 (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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625A LYS* 5.3 6.4 - - - +
649A SER 3.0 14.5 + - - +
650A ASN* 3.5 13.5 - - - +
652A LEU* 1.3 76.3 - - - +
654A VAL* 1.3 64.3 + - - +
656A ASP* 3.3 9.1 + - - +
657A GLU* 3.0 29.8 + - - +
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Residues in contact with VAL 654 (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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499A LEU* 3.9 7.0 - - + -
625A LYS* 3.8 25.4 - - + -
626A VAL* 3.8 17.0 - - + -
629A ILE* 3.6 20.0 - - + -
650A ASN 3.1 17.0 + - - +
651A ILE 3.2 3.6 + - - +
653A ASP* 1.3 80.4 - - - +
655A MET* 1.3 57.1 + - - +
657A GLU* 3.2 5.4 + - - -
658A GLU* 2.8 66.6 + - + +
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Residues in contact with MET 655 (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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496A GLN 4.8 2.0 - - - +
499A LEU* 3.4 26.2 - - + +
500A GLU* 3.2 50.7 - - + +
503A LYS* 3.6 31.0 - - + -
651A ILE* 2.9 18.1 + - + +
652A LEU* 3.4 14.6 - - + +
654A VAL* 1.3 76.8 - - - +
656A ASP* 1.3 63.8 + - - +
658A GLU* 3.8 1.8 - - - -
659A SER* 3.1 26.2 + - - -
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Residues in contact with ASP 656 (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 LEU* 2.9 25.0 + - - +
653A ASP* 3.6 6.4 - - - +
655A MET* 1.3 81.9 - - - +
657A GLU* 1.3 60.8 + - - +
659A SER* 3.5 17.6 + - - +
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Residues in contact with GLU 657 (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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625A LYS* 5.0 15.9 - - + -
653A ASP* 3.0 21.4 + - - +
654A VAL* 3.7 7.2 - - - +
656A ASP* 1.3 76.3 - - - +
658A GLU* 1.4 61.9 + - + +
659A SER 3.5 3.6 + - - +
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Residues in contact with GLU 658 (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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495A THR* 4.9 9.9 + - - -
496A GLN* 5.7 5.0 - - - +
499A LEU* 4.6 6.7 - - + +
591A TYR* 5.4 0.7 + - - -
623A SER* 2.7 35.8 + - - -
625A LYS* 4.6 6.7 - - + +
626A VAL* 4.2 5.5 - - - +
654A VAL* 2.8 42.1 + - + +
655A MET* 3.8 3.6 - - - +
657A GLU* 1.4 75.5 - - + +
659A SER* 1.3 62.9 + - - +
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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