Contacts of the helix formed by residues 669 - 688 (chain G) in PDB entry 5ZRV
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 SER 669 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667G VAL 4.0 1.8 + - - -
668G SER* 1.3 77.6 - - - +
670G ASP* 1.3 65.9 + - - +
671G GLU 3.4 2.2 - - - -
672G ASP* 3.3 7.2 + - - +
673G ILE* 3.0 18.2 + - - -
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Residues in contact with ASP 670 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574G LEU 5.7 0.7 - - - +
669G SER* 1.3 67.9 - - - +
671G GLU* 1.3 60.5 + - - +
673G ILE 3.3 1.8 + - - +
674G GLN* 2.9 26.3 + - - -
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Residues in contact with GLU 671 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669G SER* 3.4 0.4 - - - +
670G ASP* 1.3 74.0 - - - +
672G ASP* 1.3 56.8 + - - +
674G GLN* 3.5 1.5 + - - +
675G PHE* 3.0 25.5 + - - -
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Residues in contact with ASP 672 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668G SER* 5.1 5.2 - - - +
669G SER* 3.3 15.2 + - - +
670G ASP 3.2 1.0 - - - -
671G GLU* 1.3 77.4 - - - +
673G ILE* 1.3 56.3 + - - +
675G PHE* 3.4 0.9 + - - -
676G ARG* 2.8 24.6 + - - -
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Residues in contact with ILE 673 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668G SER* 5.1 1.4 - - - +
669G SER 3.0 13.1 + - - -
670G ASP* 3.3 2.0 + - - +
672G ASP* 1.3 72.8 - - - +
674G GLN* 1.3 64.9 + - - +
676G ARG* 3.7 2.4 - - - +
677G LEU* 3.0 21.0 + - - -
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Residues in contact with GLN 674 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670G ASP 2.9 16.7 + - - -
671G GLU* 3.8 1.8 - - - +
673G ILE* 1.3 77.3 - - - +
675G PHE* 1.3 56.9 + - - +
677G LEU* 3.4 0.7 + - - -
678G VAL* 3.0 24.8 + - - -
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Residues in contact with PHE 675 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671G GLU 3.0 14.8 + - - -
672G ASP 3.7 2.9 - - - -
674G GLN* 1.3 76.3 - - - +
676G ARG* 1.3 57.2 + - - +
678G VAL* 4.4 1.6 - - - +
679G THR* 2.8 28.0 + - - +
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Residues in contact with ARG 676 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672G ASP 2.8 16.0 + - - -
673G ILE* 3.2 4.7 + - - +
674G GLN 3.2 0.6 - - - -
675G PHE* 1.3 76.4 - - - +
677G LEU* 1.3 56.9 + - - +
679G THR* 4.0 0.2 - - - -
680G ARG* 3.0 26.5 + - - -
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Residues in contact with LEU 677 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554G MET* 5.7 5.1 - - - +
673G ILE 3.0 14.8 + - - -
674G GLN 3.9 0.9 - - - -
676G ARG* 1.3 75.2 - - - +
678G VAL* 1.3 57.2 + - - +
680G ARG 3.9 0.5 - - - -
681G PHE* 3.0 24.4 + - - -
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Residues in contact with VAL 678 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674G GLN 3.0 16.1 + - - -
675G PHE* 4.0 1.1 - - - +
677G LEU* 1.3 78.2 - - - +
679G THR* 1.3 56.1 + - - +
681G PHE* 3.2 2.3 + - - +
682G VAL* 2.8 26.5 + - - -
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Residues in contact with THR 679 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675G PHE 2.8 22.7 + - - -
676G ARG 4.0 0.4 - - - -
678G VAL* 1.3 69.0 - - - +
680G ARG* 1.3 60.2 + - - +
682G VAL* 3.8 1.6 - - - +
683G ASN* 2.9 24.6 + - - -
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Residues in contact with ARG 680 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553G PRO 5.3 7.1 - - - -
676G ARG 3.0 16.2 + - - -
677G LEU* 4.0 1.3 - - - +
679G THR* 1.3 73.3 - - - +
681G PHE* 1.3 60.6 + - - +
683G ASN* 3.1 2.2 + - - +
684G GLU* 3.0 25.1 + - - -
744G PHE* 6.4 2.0 - - - +
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Residues in contact with PHE 681 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550G CYS* 5.5 8.2 - - - +
553G PRO 5.3 4.5 + - - -
554G MET* 5.9 3.8 - - - +
677G LEU 3.0 16.5 + - - -
678G VAL* 3.2 5.1 + - - +
680G ARG* 1.3 77.5 - - - +
682G VAL* 1.3 54.6 + - - +
684G GLU* 3.4 1.6 + - - -
685G ALA* 2.9 22.2 + - - -
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Residues in contact with VAL 682 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678G VAL 2.8 15.5 + - - -
679G THR* 3.8 2.0 - - - +
681G PHE* 1.3 73.5 - - - +
683G ASN* 1.3 60.3 + - - +
685G ALA* 3.6 4.4 - - - +
686G VAL* 2.8 25.1 + - - -
717G PRO* 4.8 21.3 - - - +
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Residues in contact with ASN 683 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G THR 2.9 16.6 + - - -
680G ARG* 3.1 4.9 + - - +
682G VAL* 1.3 76.3 - - - +
684G GLU* 1.3 57.2 + - - +
686G VAL* 3.5 1.4 + - - +
687G MET* 2.9 22.9 + - - -
746G PRO* 6.2 4.3 - - - -
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Residues in contact with GLU 684 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550G CYS* 6.1 7.2 - - - +
680G ARG 3.0 13.3 + - - -
681G PHE 3.8 2.5 - - - -
683G ASN* 1.3 78.1 - - - +
685G ALA* 1.3 56.7 + - - +
687G MET* 3.0 17.3 + - - +
688G CYS* 3.3 9.2 + - - -
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Residues in contact with ALA 685 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681G PHE 2.9 17.5 + - - -
682G VAL* 3.3 5.5 + - - +
684G GLU* 1.3 75.5 - - - +
686G VAL* 1.3 57.6 + - - +
688G CYS* 4.2 8.6 + - - +
717G PRO* 5.6 8.5 - - - -
718G PHE* 5.4 6.7 + - - -
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Residues in contact with VAL 686 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682G VAL 2.8 15.3 + - - -
683G ASN* 3.7 2.2 - - - +
685G ALA* 1.3 75.0 - - - +
687G MET* 1.3 65.3 + - - +
688G CYS 3.1 10.4 - - - +
690G GLN* 4.6 3.6 + - - -
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Residues in contact with MET 687 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683G ASN 2.9 15.9 + - - -
684G GLU* 3.0 7.7 + - - +
686G VAL* 1.3 77.3 - - - +
688G CYS* 1.3 60.8 + - - +
689G LEU 3.6 0.2 + - - -
690G GLN* 3.3 16.0 + - - +
691G GLU 4.1 3.3 + - - -
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Residues in contact with CYS 688 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684G GLU 3.3 10.4 + - - -
685G ALA* 4.2 5.8 - - - +
686G VAL* 3.1 16.9 - - - +
687G MET* 1.3 76.7 - - - +
689G LEU* 1.3 56.9 + - - +
690G GLN 3.1 5.0 + - - -
691G GLU 5.4 0.2 - - - +
693G ILE* 5.6 1.8 - - - +
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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