Contacts of the helix formed by residues 700 - 715 (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 ASN 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A GLN 4.2 2.4 + - - +
697A LEU* 3.8 15.6 + - - +
698A ARG 3.3 3.2 - - - -
699A LYS* 1.3 82.2 - - - +
701A GLN* 1.3 65.6 + - - +
702A GLN* 3.4 8.5 - - + +
703A LEU* 4.1 6.7 - - + +
704A GLN* 3.2 23.0 + - - +
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Residues in contact with GLN 701 (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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700A ASN* 1.3 74.2 - - - +
702A GLN* 1.3 59.9 + - - +
704A GLN* 3.8 4.6 - - - +
705A ARG* 2.9 30.5 + - - +
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Residues in contact with GLN 702 (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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661A ILE* 4.7 17.0 - - + +
664A ALA* 3.5 15.9 - - + +
700A ASN* 3.4 4.8 - - + +
701A GLN* 1.3 76.2 - - - +
703A LEU* 1.3 60.3 + - - +
705A ARG* 3.4 5.6 + - - +
706A PHE* 2.9 29.8 + - - +
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Residues in contact with LEU 703 (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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664A ALA* 3.8 14.9 - - + +
697A LEU 4.8 2.7 - - - +
698A ARG* 3.4 33.2 - - + +
700A ASN* 3.8 7.7 + - + +
701A GLN 3.4 0.4 - - - -
702A GLN* 1.3 78.3 - - - +
704A GLN* 1.3 57.6 + - - +
706A PHE* 3.4 3.0 + - - +
707A ILE* 2.9 28.9 + - - +
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Residues in contact with GLN 704 (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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698A ARG 4.8 1.7 + - - +
699A LYS* 5.6 1.3 - - - -
700A ASN 3.2 20.2 + - - +
701A GLN* 3.9 5.6 - - - +
703A LEU* 1.3 77.9 - - - +
705A ARG* 1.3 58.0 + - - +
707A ILE* 3.4 5.6 + - - +
708A GLN* 2.9 29.6 + - - +
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Residues in contact with ARG 705 (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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701A GLN 2.9 19.0 + - - +
702A GLN* 3.7 6.7 - - - +
704A GLN* 1.3 76.9 - - - +
706A PHE* 1.3 56.2 + - - +
708A GLN* 3.4 7.0 + - - +
709A TRP* 2.9 29.3 + - - +
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Residues in contact with PHE 706 (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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664A ALA* 4.0 25.8 - - + +
667A LEU* 5.0 8.1 - - + -
668A MET* 5.1 10.2 - - + +
702A GLN 2.9 18.3 + - - +
703A LEU* 3.7 4.7 - - - +
704A GLN 3.3 0.2 - - - -
705A ARG* 1.3 74.3 - - - +
707A ILE* 1.3 58.2 + - - +
709A TRP* 3.4 6.8 + - - +
710A LEU* 2.9 30.0 + - - +
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Residues in contact with ILE 707 (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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685A PHE* 5.6 10.1 - - + -
703A LEU 2.9 18.3 + - - +
704A GLN* 3.8 7.2 - - - +
705A ARG 3.3 0.2 - - - -
706A PHE* 1.3 75.7 - - - +
708A GLN* 1.3 58.0 + - - +
710A LEU* 3.4 6.4 + - - +
711A LYS* 2.9 29.6 + - - +
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Residues in contact with GLN 708 (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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704A GLN 2.9 17.7 + - - +
705A ARG* 3.8 7.2 - - - +
706A PHE 3.3 0.2 - - - -
707A ILE* 1.3 78.7 - - - +
709A TRP* 1.3 58.1 + - - +
711A LYS* 3.4 6.4 + - - +
712A GLU* 2.9 29.3 + - - +
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Residues in contact with TRP 709 (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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705A ARG 2.9 18.4 + - - +
706A PHE* 3.7 8.1 - - - +
708A GLN* 1.3 74.4 - - - +
710A LEU* 1.3 58.3 + - - +
712A GLU* 3.4 6.4 + - - +
713A ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 710 (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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671A TYR* 5.8 8.7 - - + -
678A GLY* 6.4 2.5 - - - -
706A PHE 2.9 18.1 + - - +
707A ILE* 3.7 7.0 - - - +
709A TRP* 1.3 77.7 - - - +
711A LYS* 1.3 56.6 + - - +
713A ALA* 3.8 4.5 - - - +
714A GLU* 2.9 31.9 + - - +
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Residues in contact with LYS 711 (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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707A ILE 2.9 19.3 + - - +
708A GLN* 3.8 6.5 - - - +
710A LEU* 1.3 76.4 - - - +
712A GLU* 1.3 61.0 + - - +
714A GLU* 4.6 4.0 - - - -
715A GLU 3.1 27.5 + - - +
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Residues in contact with GLU 712 (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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708A GLN 2.9 18.1 + - - +
709A TRP* 3.8 6.7 - - - +
711A LYS* 1.3 77.8 - - - +
713A ALA* 1.3 60.3 + - - +
714A GLU 3.6 0.2 + - - -
715A GLU* 3.9 8.0 + - - -
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Residues in contact with ALA 713 (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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709A TRP 2.9 17.7 + - - +
710A LEU* 4.1 4.5 - - - +
712A GLU* 1.3 74.4 - - - +
714A GLU* 1.3 64.2 + - - +
715A GLU* 4.7 0.2 - - - -
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Residues in contact with GLU 714 (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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678A GLY* 6.6 0.4 - - - -
710A LEU 2.9 19.1 + - - +
711A LYS* 4.3 5.4 - - - +
712A GLU 3.4 0.2 - - - -
713A ALA* 1.3 81.0 - - - +
715A GLU* 1.3 58.7 + - - +
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Residues in contact with GLU 715 (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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711A LYS* 3.1 19.0 + - - +
712A GLU* 3.9 6.7 + - - -
713A ALA 3.5 1.6 - - - -
714A GLU* 1.3 81.3 - - - +
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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