Contacts of the helix formed by residues 662 - 671 (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 SER 662 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614B SER* 3.4 30.4 - - - -
617B TYR* 4.8 2.5 - - - -
618B CYS* 4.1 18.6 - - - -
659B LEU* 2.9 16.0 + - - -
661B ILE* 1.3 76.3 - - - +
663B MET* 1.3 57.8 + - - +
664B ALA 3.2 1.3 - - - -
665B LYS* 2.9 23.0 + - - +
666B VAL* 3.0 15.6 + - - +
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Residues in contact with MET 663 (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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653B PHE* 3.8 29.4 - - + -
659B LEU 3.6 1.8 + - - -
660B GLY* 2.9 25.0 + - - +
662B SER* 1.3 78.4 - - - +
664B ALA* 1.3 59.0 + - - +
666B VAL* 3.8 7.0 + - - +
667B LEU* 3.6 15.8 + - - +
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Residues in contact with ALA 664 (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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660B GLY 4.1 1.6 + - - -
661B ILE 4.1 4.1 + - - +
662B SER 3.2 0.4 - - - -
663B MET* 1.3 76.1 - - - +
665B LYS* 1.3 59.6 + - - +
666B VAL 3.2 0.7 - - - -
667B LEU* 2.9 22.0 + - - +
668B MET* 3.0 14.7 + - - +
702B GLN* 3.5 42.8 - - + +
703B LEU* 3.8 14.1 - - + +
706B PHE* 4.0 9.8 - - + +
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Residues in contact with LYS 665 (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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618B CYS* 4.6 13.7 - - + -
661B ILE 4.2 3.2 + - - +
662B SER* 2.9 26.6 + - - +
664B ALA* 1.3 76.8 - - - +
666B VAL* 1.3 61.7 + - - +
668B MET* 3.6 8.1 + - - +
669B ALA* 3.3 19.6 + - - +
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Residues in contact with VAL 666 (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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621B LEU* 5.9 7.6 - - + -
649B ILE* 6.1 5.6 - - + -
662B SER 3.0 12.9 + - - +
663B MET* 4.1 7.4 - - - +
664B ALA 3.2 0.2 - - - -
665B LYS* 1.3 76.6 - - - +
667B LEU* 1.3 58.7 + - - +
669B ALA* 3.4 7.4 - - + +
670B PHE* 2.9 32.7 + - - +
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Residues in contact with LEU 667 (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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663B MET 3.6 7.4 + - - +
664B ALA* 2.9 19.9 + - + +
666B VAL* 1.3 80.1 - - - +
668B MET* 1.3 56.9 + - - +
669B ALA 3.6 0.2 + - - -
670B PHE* 4.8 3.7 - - - +
671B TYR* 3.9 19.1 + - - +
703B LEU* 6.5 0.2 - - - -
706B PHE* 5.0 7.9 - - + -
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Residues in contact with MET 668 (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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664B ALA 3.0 12.9 + - - +
665B LYS* 3.9 8.5 - - - +
666B VAL 3.2 0.4 - - - -
667B LEU* 1.3 75.5 - - - +
669B ALA* 1.3 57.4 + - - +
671B TYR* 4.3 5.5 - - - +
672B GLN* 3.4 21.1 + - - +
706B PHE* 5.1 10.7 - - + +
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Residues in contact with ALA 669 (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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621B LEU 5.9 0.7 - - - +
622B LEU* 5.9 7.4 - - + -
625B LEU* 5.4 11.9 - - + -
665B LYS 3.3 12.8 + - - +
666B VAL* 2.9 13.3 + - - +
668B MET* 1.3 76.1 - - - +
670B PHE* 1.3 60.4 + - - +
671B TYR 3.2 2.0 - - - -
672B GLN* 2.9 6.8 + - - +
673B LEU* 2.9 31.9 + - - +
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Residues in contact with PHE 670 (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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666B VAL 2.9 14.7 + - - +
667B LEU* 4.8 3.6 - - - +
668B MET 3.7 0.2 - - - -
669B ALA* 1.3 77.1 - - - +
671B TYR* 1.3 59.6 + - - +
673B LEU* 4.7 0.9 - - - +
674B GLU 3.5 0.7 + - - -
675B ILE* 2.8 41.1 + - + -
676B LEU* 2.9 31.7 + - + +
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Residues in contact with TYR 671 (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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667B LEU 3.9 16.2 + - - +
668B MET* 4.4 4.9 - - - +
669B ALA 3.2 0.8 - - - -
670B PHE* 1.3 77.5 - - - +
672B GLN* 1.3 59.6 + - - +
674B GLU* 4.2 5.7 + - - +
676B LEU* 3.4 14.3 + - - +
677B ALA 5.4 4.9 - - - +
678B GLY* 5.5 4.3 - - - +
710B LEU* 5.8 8.7 - - + -
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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