Contacts of the helix formed by residues 638 - 656 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B ILE 4.9 0.3 - - - -
637B LYS* 1.3 83.4 + - - +
639B ALA* 1.3 62.5 + - - +
640B ALA* 3.3 9.4 - - + +
641B ASP* 3.4 10.4 + - + +
642B HIS* 3.0 25.8 + - - +
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Residues in contact with ALA 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B ARG* 1.3 73.7 - - - +
640B ALA* 1.3 59.9 + - - +
642B HIS* 3.3 8.4 + - - +
643B LEU* 2.9 27.9 + - - +
680B THR* 5.3 4.6 - - - -
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Residues in contact with ALA 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LYS* 6.4 0.4 - - - -
638B ARG* 3.3 6.3 - - + +
639B ALA* 1.3 74.8 - - - +
641B ASP* 1.3 61.1 + - - +
643B LEU* 3.3 7.5 + - - +
644B GLU* 2.9 28.8 + - - +
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Residues in contact with ASP 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LYS* 6.1 4.5 - - - +
593B MET* 5.2 9.6 - - + +
635B TYR 4.5 3.8 - - - +
636B ILE* 3.8 12.4 - - + +
637B LYS 3.8 20.4 - - - +
638B ARG* 3.4 17.9 + - + +
639B ALA 3.3 0.4 - - - -
640B ALA* 1.3 77.7 - - - +
642B HIS* 1.3 56.7 + - - +
644B GLU* 3.4 7.3 + - - +
645B ALA* 2.9 28.9 + - - +
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Residues in contact with HIS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B ILE* 4.7 4.6 - - + +
638B ARG 3.0 14.9 + - - +
639B ALA* 3.3 11.4 + - - +
641B ASP* 1.3 76.2 - - - +
643B LEU* 1.3 57.9 + - - +
645B ALA* 3.4 7.6 + - - +
646B LEU* 2.9 28.4 + - - +
675B ILE 4.8 13.9 - - - +
676B LEU* 4.9 9.7 - - - +
677B ALA* 5.1 2.2 - - + +
680B THR* 4.0 24.1 - - - -
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Residues in contact with LEU 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B ALA 2.9 16.3 + - - +
640B ALA* 3.7 8.3 - - - +
642B HIS* 1.3 75.8 - - - +
644B GLU* 1.3 59.9 + - - +
646B LEU* 3.3 7.5 + - - +
647B ALA* 2.9 28.8 + - - +
680B THR* 5.2 4.5 - - - -
684B TRP* 6.3 0.2 - - - -
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Residues in contact with GLU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LYS* 4.7 25.8 - - + +
593B MET* 5.5 4.0 - - + -
594B GLN* 5.3 5.7 - - + +
640B ALA 2.9 16.3 + - - +
641B ASP* 3.7 7.6 - - - +
642B HIS 3.3 0.2 - - - -
643B LEU* 1.3 76.3 - - - +
645B ALA* 1.3 57.5 + - - +
647B ALA* 3.4 7.2 + - - +
648B ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B MET* 5.7 6.7 - - + +
597B SER* 4.9 11.3 - - - -
636B ILE* 4.6 12.8 - - + -
641B ASP 2.9 17.0 + - - +
642B HIS* 3.7 8.3 - - - +
644B GLU* 1.3 74.4 - - - +
646B LEU* 1.3 59.7 + - - +
648B ALA* 3.4 7.4 + - - +
649B ILE* 2.9 29.1 + - - +
676B LEU* 6.2 3.4 - - + -
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Residues in contact with LEU 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B HIS 2.9 17.4 + - - +
643B LEU* 3.7 7.6 - - - +
645B ALA* 1.3 78.2 - - - +
647B ALA* 1.3 56.8 + - - +
649B ILE* 3.3 7.0 + - - +
650B GLU* 2.9 28.6 + - - +
676B LEU* 5.9 5.4 - - + -
680B THR* 5.2 3.8 - - - +
681B ILE* 6.2 0.7 - - - -
684B TRP* 3.9 28.3 - - + -
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Residues in contact with ALA 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B LEU 2.9 16.8 + - - +
644B GLU* 3.7 7.4 - - - +
646B LEU* 1.3 76.1 - - - +
648B ALA* 1.3 58.6 + - - +
650B GLU* 3.3 6.7 + - - +
651B ASP* 2.9 28.6 + - - +
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Residues in contact with ALA 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B GLN* 4.4 19.5 - - + +
597B SER* 3.8 26.3 - - - -
598B HIS* 5.2 2.5 - - + +
644B GLU 2.9 16.7 + - - +
645B ALA* 3.7 4.9 - - - +
647B ALA* 1.3 73.6 - - - +
649B ILE* 1.3 60.4 + - - +
651B ASP* 3.4 6.4 + - - +
652B PHE* 2.9 30.0 + - - +
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Residues in contact with ILE 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B SER* 5.3 1.5 - - - -
645B ALA 2.9 18.0 + - - +
646B LEU* 3.7 7.6 - - - +
648B ALA* 1.3 73.9 - - - +
650B GLU* 1.3 58.6 + - - +
652B PHE* 3.4 6.1 + - - +
653B PHE* 2.9 28.6 + - - +
666B VAL* 6.1 5.4 - - + -
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Residues in contact with GLU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU 2.9 17.0 + - - +
647B ALA* 3.7 7.9 - - - +
649B ILE* 1.3 78.3 - - - +
651B ASP* 1.3 56.7 + - - +
653B PHE* 3.3 6.3 + - - +
654B LEU* 2.9 28.1 + - - +
694B GLY* 6.1 4.9 - - - -
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Residues in contact with ASP 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B ALA 2.9 16.9 + - - +
648B ALA* 3.8 7.9 - - - +
649B ILE 3.3 0.2 - - - -
650B GLU* 1.3 77.0 - - - +
652B PHE* 1.3 58.2 + - - +
654B LEU* 3.3 7.5 + - - +
655B GLU* 2.9 28.2 + - - +
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Residues in contact with PHE 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B SER 5.6 0.7 - - - +
598B HIS* 5.9 2.2 - - - -
601B LEU* 3.7 29.4 - - + -
648B ALA 2.9 18.2 + - - +
649B ILE* 3.8 7.2 - - - +
651B ASP* 1.3 73.0 - - - +
653B PHE* 1.3 60.0 + - - +
655B GLU* 3.3 6.1 + - - +
656B HIS* 2.8 33.4 + - - +
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Residues in contact with PHE 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B ILE 2.9 18.5 + - - +
650B GLU* 3.7 7.4 - - - +
651B ASP 3.3 0.2 - - - -
652B PHE* 1.3 75.5 - - - +
654B LEU* 1.3 62.5 + - - +
656B HIS* 3.4 5.3 - - - +
657B GLU* 3.2 26.0 + - - +
660B GLY* 5.1 2.0 - - - -
663B MET* 3.8 29.8 - - + -
697B LEU* 6.4 1.6 - - + -
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Residues in contact with LEU 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B GLU 2.9 18.3 + - - +
651B ASP* 3.6 8.3 - - - +
652B PHE 3.3 0.2 - - - -
653B PHE* 1.3 78.0 - - - +
655B GLU* 1.3 58.3 + - - +
656B HIS 3.7 0.2 + - - -
657B GLU* 4.1 11.3 + - - +
693B LYS* 6.5 0.9 - - + -
694B GLY* 6.3 2.7 - - - -
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Residues in contact with GLU 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B ASP 2.9 17.5 + - - +
652B PHE* 3.9 7.2 - - - +
653B PHE 3.3 0.2 - - - -
654B LEU* 1.3 76.9 - - - +
656B HIS* 1.3 59.2 + - + +
657B GLU 3.7 0.8 + - - -
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Residues in contact with HIS 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LEU* 5.7 8.7 - - + -
652B PHE 2.8 17.1 + - - +
653B PHE* 3.4 7.6 - - - +
655B GLU* 1.3 77.1 - - - +
657B GLU* 1.3 62.4 + - - +
658B ALA* 3.2 5.2 - - - +
659B LEU* 3.2 21.6 + - + +
660B GLY* 3.5 6.1 + - - -
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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
------------------------------------------------------------
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