Contacts of the helix formed by residues 642 - 654 (chain G) in PDB entry 5O9Z
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 GLU 642 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641G SER* 1.3 72.8 - - - +
643G GLU* 1.3 56.3 + - - +
644G ILE 3.1 2.9 - - - -
645G TRP* 2.8 32.1 + - + +
646G LEU* 2.9 12.7 + - - +
671G SER* 6.0 4.5 - - - +
673G PRO* 3.6 35.0 - - + -
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Residues in contact with GLU 643 (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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608G GLU* 5.2 13.7 - - + -
641G SER* 3.3 10.2 - - - -
642G GLU* 1.3 77.4 - - - +
644G ILE* 1.3 57.7 + - - +
646G LEU* 3.2 10.2 + - - +
647G ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 644 (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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611G TRP* 6.3 3.1 - - + -
631G LEU* 4.8 9.4 - - + +
634G ALA* 4.9 11.4 - - + +
635G PHE* 4.6 25.6 - - + +
640G ASN* 5.8 5.6 - - + -
641G SER 4.1 10.3 + - - +
642G GLU 3.1 0.2 - - - -
643G GLU* 1.3 79.8 - - - +
645G TRP* 1.3 56.3 + - - +
647G ALA* 3.6 6.7 + - - +
648G ALA* 2.9 27.9 + - - +
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Residues in contact with TRP 645 (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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635G PHE* 5.1 7.2 - - + +
642G GLU* 2.8 24.5 + - + +
644G ILE* 1.3 74.6 - - - +
646G LEU* 1.3 59.1 + - - +
648G ALA* 3.3 8.5 + - - +
649G VAL* 2.9 26.0 + - - +
664G LEU* 6.0 0.7 - - - +
668G ALA* 4.4 26.3 - - + +
673G PRO* 5.8 1.8 - - + -
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Residues in contact with LEU 646 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642G GLU 2.9 10.5 + - - +
643G GLU* 3.2 12.8 + - - +
645G TRP* 1.3 74.8 - - - +
647G ALA* 1.3 61.1 + - - +
649G VAL* 3.0 11.1 + - - +
650G LYS* 2.9 26.0 + - - +
676G ARG* 6.1 5.6 - - + -
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Residues in contact with ALA 647 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615G ALA* 6.0 6.5 - - + -
631G LEU* 5.6 4.7 - - + -
643G GLU 2.9 16.1 + - - +
644G ILE* 3.9 7.0 - - - +
646G LEU* 1.3 76.9 - - - +
648G ALA* 1.3 56.8 + - - +
650G LYS* 3.7 8.3 - - - +
651G LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 648 (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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631G LEU* 4.6 18.3 - - + +
635G PHE* 5.7 3.6 - - + -
644G ILE 2.9 19.0 + - - +
645G TRP* 3.5 10.3 - - - +
646G LEU 3.2 0.2 - - - -
647G ALA* 1.3 75.8 - - - +
649G VAL* 1.3 58.3 + - - +
650G LYS 3.3 0.2 - - - -
651G LEU* 4.3 5.1 - - - +
652G GLU* 2.9 30.3 + - - +
664G LEU* 4.9 8.9 - - + +
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Residues in contact with VAL 649 (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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645G TRP 2.9 13.4 + - - +
646G LEU* 3.0 12.5 + - - +
648G ALA* 1.3 76.7 - - - +
650G LYS* 1.3 59.3 + - - +
652G GLU* 3.7 5.7 - - - +
653G SER* 2.9 28.9 + - - -
661G ALA* 5.2 7.3 - - + +
664G LEU* 5.4 7.9 - - + +
665G LEU* 6.1 5.8 - - + +
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Residues in contact with LYS 650 (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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646G LEU 2.9 11.5 + - - +
647G ALA* 3.3 11.2 + - - +
649G VAL* 1.3 75.5 - - - +
651G LEU* 1.3 60.2 + - - +
653G SER* 3.1 7.6 + - - -
654G GLU* 2.9 28.3 + - - +
931G ARG* 4.2 2.9 - - - +
932G LEU* 4.7 21.1 - - + +
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Residues in contact with LEU 651 (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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627G ALA* 5.8 8.1 - - + +
628G ARG* 5.9 8.3 - - + +
647G ALA 2.9 16.5 + - - +
648G ALA* 4.3 4.5 - - - +
650G LYS* 1.3 76.5 - - - +
652G GLU* 1.3 57.9 + - - +
654G GLU* 4.0 5.7 - - - +
655G ASN* 3.0 32.4 + - - +
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Residues in contact with GLU 652 (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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648G ALA 2.9 22.4 + - - +
649G VAL* 3.9 7.2 - - - +
650G LYS 3.2 0.2 - - - -
651G LEU* 1.3 76.5 - - - +
653G SER* 1.3 57.2 + - - +
655G ASN 2.8 19.0 - - - +
656G ASP* 4.2 5.2 - - + +
657G GLU 3.7 14.7 - - - +
660G ARG* 4.4 11.2 - - + +
661G ALA* 4.3 21.5 + - - +
664G LEU* 4.7 5.8 - - + -
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Residues in contact with SER 653 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649G VAL 2.9 18.7 + - - -
650G LYS* 3.1 6.9 + - - -
652G GLU* 1.3 77.7 - - - +
654G GLU* 1.3 64.2 + - - +
655G ASN 3.8 2.8 - - - +
657G GLU 5.5 1.5 - - - -
661G ALA* 4.9 9.4 - - - -
930G LEU 4.8 2.9 - - - +
931G ARG* 3.7 32.1 - - - +
932G LEU* 5.3 0.7 - - - -
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Residues in contact with GLU 654 (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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650G LYS 2.9 15.6 + - - +
651G LEU* 4.0 6.3 - - - +
653G SER* 1.3 80.4 - - - +
655G ASN* 1.3 60.1 + - + +
656G ASP 5.2 0.2 - - - +
930G LEU 5.7 0.2 - - - -
931G ARG* 3.5 15.8 - - + +
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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