Contacts of the helix formed by residues 638 - 656 (chain A) in PDB entry 6O81
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 ARG 638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A LYS* 1.3 84.1 + - + +
639A ALA* 1.3 62.3 + - - +
640A ALA* 3.3 10.1 - - + +
641A ASP* 3.4 10.5 + - + +
642A HIS* 3.0 25.6 + - - +
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Residues in contact with ALA 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ARG* 1.3 73.3 - - - +
640A ALA* 1.3 59.9 + - - +
642A HIS* 3.3 8.0 + - - +
643A LEU* 2.9 28.2 + - - +
680A THR* 5.3 5.1 - - - -
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Residues in contact with ALA 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS* 6.0 1.1 - - - +
638A ARG* 3.3 6.3 - - + +
639A ALA* 1.3 75.8 - - - +
641A ASP* 1.3 60.7 + - - +
643A LEU* 3.3 7.4 + - - +
644A GLU* 2.9 28.4 + - - +
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Residues in contact with ASP 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS* 6.1 4.7 - - - +
593A MET* 5.2 9.3 - - + +
635A TYR 4.5 3.6 - - - +
636A ILE* 3.8 13.7 - - - +
637A LYS 3.8 20.9 - - - +
638A ARG* 3.4 16.7 + - + +
639A ALA 3.3 0.4 - - - -
640A ALA* 1.3 77.5 - - - +
642A HIS* 1.3 56.8 + - - +
644A GLU* 3.4 5.7 + - - +
645A ALA* 2.9 29.1 + - - +
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Residues in contact with HIS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 4.7 5.3 - - + +
638A ARG 3.0 14.4 + - - +
639A ALA* 3.3 11.6 + - - +
641A ASP* 1.3 76.4 - - - +
643A LEU* 1.3 57.0 + - - +
645A ALA* 3.3 6.8 + - - +
646A LEU* 2.9 28.6 + - - +
675A ILE 4.8 12.8 - - - +
676A LEU* 4.9 9.8 - - - +
677A ALA* 5.1 2.5 - - + +
680A THR* 4.0 23.4 - - - -
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Residues in contact with LEU 643 (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 ALA 2.9 16.5 + - - +
640A ALA* 3.7 8.1 - - - +
641A ASP 3.3 0.2 - - - -
642A HIS* 1.3 74.8 - - - +
644A GLU* 1.3 58.4 + - - +
646A LEU* 3.3 7.0 + - - +
647A ALA* 2.9 28.8 + - - +
680A THR* 5.2 5.1 - - - -
684A TRP* 6.3 0.4 - - - -
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Residues in contact with GLU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS* 4.7 25.1 - - + +
593A MET* 5.5 4.3 - - + -
594A GLN* 5.3 7.4 - - + +
640A ALA 2.9 17.2 + - - +
641A ASP* 3.7 7.4 - - - +
643A LEU* 1.3 76.5 - - - +
645A ALA* 1.3 58.7 + - - +
647A ALA* 3.4 7.0 + - - +
648A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 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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593A MET* 5.7 7.1 - - + +
597A SER* 5.0 11.1 - - - -
636A ILE* 4.6 12.6 - - + -
641A ASP 2.9 17.8 + - - +
642A HIS* 3.7 7.6 - - - +
644A GLU* 1.3 74.7 - - - +
646A LEU* 1.3 58.7 + - - +
648A ALA* 3.4 6.7 + - - +
649A ILE* 2.9 29.3 + - - +
676A LEU* 6.2 3.6 - - + -
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Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A HIS 2.9 17.6 + - - +
643A LEU* 3.7 7.9 - - - +
644A GLU 3.3 0.2 - - - -
645A ALA* 1.3 76.5 - - - +
647A ALA* 1.3 56.5 + - - +
649A ILE* 3.3 6.8 + - - +
650A GLU* 2.9 28.9 + - - +
676A LEU* 5.9 5.2 - - + -
680A THR* 5.2 4.5 - - - +
681A ILE* 6.2 0.4 - - - -
684A TRP* 3.9 27.6 - - + -
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Residues in contact with ALA 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU 2.9 17.3 + - - +
644A GLU* 3.7 7.9 - - - +
645A ALA 3.3 0.2 - - - -
646A LEU* 1.3 76.3 - - - +
648A ALA* 1.3 57.6 + - - +
650A GLU* 3.3 7.1 + - - +
651A ASP* 2.9 28.9 + - - +
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Residues in contact with ALA 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLN* 4.4 18.8 - - + +
597A SER* 3.8 26.3 - - - -
598A HIS* 5.2 3.1 - - + +
644A GLU 2.9 18.1 + - - +
645A ALA 3.7 4.3 - - - +
646A LEU 3.3 0.2 - - - -
647A ALA* 1.3 73.2 - - - +
649A ILE* 1.3 60.5 + - - +
651A ASP* 3.4 6.8 + - - +
652A PHE* 2.9 29.3 + - - +
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Residues in contact with ILE 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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597A SER* 5.3 1.7 - - - -
645A ALA 2.9 17.7 + - - +
646A LEU* 3.7 7.4 - - - +
648A ALA* 1.3 75.2 - - - +
650A GLU* 1.3 59.6 + - - +
652A PHE* 3.4 6.3 + - - +
653A PHE* 2.9 29.1 + - - +
666A VAL* 6.1 5.2 - - + -
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Residues in contact with GLU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A LEU 2.9 17.6 + - - +
647A ALA* 3.7 8.1 - - - +
648A ALA 3.3 0.2 - - - -
649A ILE* 1.3 77.3 - - - +
651A ASP* 1.3 56.2 + - - +
653A PHE* 3.3 6.9 + - - +
654A LEU* 2.9 27.9 + - - +
694A GLY* 6.1 4.9 - - - -
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Residues in contact with ASP 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ALA 2.9 17.6 + - - +
648A ALA* 3.8 7.2 - - - +
650A GLU* 1.3 75.5 - - - +
652A PHE* 1.3 57.4 + - - +
654A LEU* 3.3 7.8 + - - +
655A GLU* 2.9 28.5 + - - +
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Residues in contact with PHE 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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597A SER 5.6 0.4 - - - +
598A HIS* 5.9 2.7 - - - -
601A LEU* 3.7 29.2 - - + -
648A ALA 2.9 17.8 + - - +
649A ILE* 3.8 7.6 - - - +
651A ASP* 1.3 73.0 - - - +
653A PHE* 1.3 61.0 + - - +
655A GLU* 3.3 6.6 + - - +
656A HIS* 2.8 33.1 + - - +
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Residues in contact with PHE 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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649A ILE 2.9 18.0 + - - +
650A GLU* 3.7 7.2 - - - +
652A PHE* 1.3 75.0 - - - +
654A LEU* 1.3 61.0 + - - +
656A HIS* 4.4 4.9 - - - +
657A GLU* 3.2 26.2 + - - +
660A GLY* 5.1 2.2 - - - -
663A MET* 3.8 29.4 - - + -
697A LEU* 6.4 1.8 - - + -
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Residues in contact with LEU 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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650A GLU 2.9 16.5 + - - +
651A ASP* 3.6 8.5 - - - +
652A PHE 3.3 0.2 - - - -
653A PHE* 1.3 79.7 - - - +
655A GLU* 1.3 59.4 + - - +
657A GLU* 4.1 10.5 + - - +
693A LYS* 6.5 0.9 - - + -
694A GLY* 6.3 2.9 - - - -
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Residues in contact with GLU 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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651A ASP 2.9 17.0 + - - +
652A PHE* 3.3 6.7 + - - +
654A LEU* 1.3 77.4 - - - +
656A HIS* 1.3 58.7 + - + +
657A GLU 3.7 0.8 + - - -
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Residues in contact with HIS 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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605A LEU* 5.7 8.7 - - + -
652A PHE 2.8 16.7 + - - +
653A PHE* 3.4 7.4 - - - +
655A GLU* 1.3 77.9 - - - +
657A GLU* 1.3 62.7 + - - +
658A ALA* 3.2 4.5 - - - -
659A LEU* 3.2 22.5 + - + +
660A GLY* 3.5 5.7 + - - -
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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