Contacts of the helix formed by residues 700 - 715 (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 ASN 700 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696B GLN 4.2 3.0 + - - +
697B LEU* 3.8 15.2 + - - +
698B ARG 3.3 3.4 - - - -
699B LYS* 1.3 81.6 - - - +
701B GLN* 1.3 65.3 + - - +
702B GLN* 3.4 9.0 - - + +
703B LEU* 4.1 5.8 - - + +
704B GLN* 3.2 23.2 + - - +
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Residues in contact with GLN 701 (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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700B ASN* 1.3 72.9 - - - +
702B GLN* 1.3 60.9 + - - +
704B GLN* 3.8 4.9 - - - +
705B ARG* 2.9 29.5 + - - +
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Residues in contact with GLN 702 (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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661B ILE* 4.7 17.9 - - + +
664B ALA* 3.5 16.3 - - + +
700B ASN* 3.4 5.0 - - + +
701B GLN* 1.3 77.2 - - - +
703B LEU* 1.3 59.8 + - - +
705B ARG* 3.4 5.9 + - - +
706B PHE* 2.9 29.3 + - - +
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Residues in contact with LEU 703 (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* 3.8 15.0 - - + +
697B LEU 4.8 2.9 - - - +
698B ARG* 3.4 33.0 - - + +
700B ASN* 3.8 8.2 + - + +
702B GLN* 1.3 79.3 - - - +
704B GLN* 1.3 58.4 + - - +
706B PHE* 3.4 2.6 + - - +
707B ILE* 2.9 29.6 + - - +
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Residues in contact with GLN 704 (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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698B ARG 4.8 1.7 + - - +
699B LYS* 5.6 1.6 - - - -
700B ASN 3.2 20.1 + - - +
701B GLN* 3.9 5.4 - - - +
703B LEU* 1.3 77.4 - - - +
705B ARG* 1.3 57.2 + - - +
707B ILE* 3.4 5.9 + - - +
708B GLN* 2.9 29.5 + - - +
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Residues in contact with ARG 705 (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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701B GLN 2.9 19.4 + - - +
702B GLN* 3.7 6.7 - - - +
704B GLN* 1.3 77.7 - - - +
706B PHE* 1.3 56.8 + - - +
708B GLN* 3.4 6.5 + - - +
709B TRP* 2.9 29.1 + - - +
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Residues in contact with PHE 706 (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* 4.0 25.6 - - + +
667B LEU* 5.0 7.4 - - + -
668B MET* 5.1 11.4 - - + +
702B GLN 2.9 17.0 + - - +
703B LEU* 3.7 4.7 - - - +
705B ARG* 1.3 75.4 - - - +
707B ILE* 1.3 58.9 + - - +
709B TRP* 3.4 6.4 + - - +
710B LEU* 2.9 28.9 + - - +
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Residues in contact with ILE 707 (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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685B PHE* 5.6 10.3 - - + -
703B LEU 2.9 17.4 + - - +
704B GLN* 3.8 7.0 - - - +
705B ARG 3.3 0.2 - - - -
706B PHE* 1.3 76.2 - - - +
708B GLN* 1.3 57.7 + - - +
710B LEU* 3.4 6.6 + - - +
711B LYS* 2.9 29.5 + - - +
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Residues in contact with GLN 708 (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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704B GLN 2.9 17.6 + - - +
705B ARG* 3.8 7.2 - - - +
707B ILE* 1.3 77.3 - - - +
709B TRP* 1.3 55.4 + - - +
711B LYS* 3.4 6.2 + - - +
712B GLU* 2.9 29.5 + - - +
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Residues in contact with TRP 709 (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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705B ARG 2.9 18.3 + - - +
706B PHE* 3.7 7.4 - - - +
708B GLN* 1.3 77.6 - - - +
710B LEU* 1.3 57.8 + - - +
712B GLU* 3.4 5.8 + - - +
713B ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 710 (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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671B TYR* 5.8 8.7 - - + -
678B GLY* 6.4 2.7 - - - -
706B PHE 2.9 17.6 + - - +
707B ILE* 3.7 7.2 - - - +
708B GLN 3.3 0.2 - - - -
709B TRP* 1.3 78.2 - - - +
711B LYS* 1.3 56.8 + - - +
713B ALA* 3.8 4.5 - - - +
714B GLU* 2.9 32.4 + - - +
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Residues in contact with LYS 711 (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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707B ILE 2.9 17.9 + - - +
708B GLN* 3.8 7.0 - - - +
710B LEU* 1.3 78.2 - - - +
712B GLU* 1.3 60.7 + - - +
714B GLU* 4.6 3.6 - - - -
715B GLU 3.1 27.6 + - - +
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Residues in contact with GLU 712 (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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708B GLN 2.9 18.1 + - - +
709B TRP* 3.8 6.7 - - - +
710B LEU 3.3 0.2 - - - -
711B LYS* 1.3 78.0 - - - +
713B ALA* 1.3 61.2 + - - +
715B GLU* 3.9 7.7 + - - +
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Residues in contact with ALA 713 (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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709B TRP 2.9 18.3 + - - +
710B LEU* 4.1 4.5 - - - +
712B GLU* 1.3 74.8 - - - +
714B GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 714 (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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678B GLY* 6.6 0.2 - - - -
710B LEU 2.9 19.3 + - - +
711B LYS* 4.3 4.9 - - - +
713B ALA* 1.3 80.2 - - - +
715B GLU* 1.3 59.2 + - - +
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Residues in contact with GLU 715 (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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711B LYS* 3.1 19.1 + - - +
712B GLU 3.9 5.8 + - - -
713B ALA 3.5 1.4 - - - -
714B GLU* 1.3 82.0 - - - +
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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