Contacts of the helix formed by residues 677 - 687 (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 ALA 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642A HIS* 5.1 2.5 - - + +
671A TYR* 5.4 1.5 - - - +
674A GLU* 6.4 0.2 - - - +
675A ILE 4.1 1.4 + - - -
676A LEU* 1.3 78.1 - - - +
678A GLY* 1.3 61.4 + - - +
679A GLU* 3.4 9.0 - - + +
680A THR* 3.8 14.5 - - - +
681A ILE* 3.0 27.4 + - - +
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Residues in contact with GLY 678 (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* 5.5 6.1 - - - +
677A ALA* 1.3 73.1 - - - +
679A GLU* 1.3 60.0 + - - +
681A ILE* 3.4 6.2 + - - +
682A LEU* 2.9 28.8 + - - +
710A LEU* 6.4 2.2 - - - -
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Residues in contact with GLU 679 (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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677A ALA* 3.4 5.0 - - + +
678A GLY* 1.3 72.8 - - - +
680A THR* 1.3 61.2 + - - +
682A LEU* 3.3 6.7 + - - +
683A SER* 2.9 28.6 + - - -
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Residues in contact with THR 680 (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* 5.3 4.5 - - - -
642A HIS* 4.0 31.6 - - - -
643A LEU* 5.2 3.6 - - - -
646A LEU* 5.2 1.4 - - - +
676A LEU* 5.0 3.6 - - - -
677A ALA* 3.5 20.7 + - - +
678A GLY 3.3 0.2 - - - -
679A GLU* 1.3 75.8 - - - +
681A ILE* 1.3 60.2 + - - +
683A SER* 3.4 6.7 + - - -
684A TRP* 2.9 29.3 + - - +
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Residues in contact with ILE 681 (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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667A LEU* 5.8 5.8 - - + +
671A TYR* 5.9 5.2 - - + -
676A LEU* 5.4 7.8 - - + +
677A ALA 3.0 18.1 + - - +
678A GLY* 3.7 7.6 - - - +
679A GLU 3.3 0.2 - - - -
680A THR* 1.3 77.2 - - - +
682A LEU* 1.3 57.8 + - - +
684A TRP* 3.4 6.3 + - - +
685A PHE* 2.9 29.7 + - - +
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Residues in contact with LEU 682 (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 2.9 17.4 + - - +
679A GLU* 3.7 7.2 - - - +
680A THR 3.3 0.2 - - - -
681A ILE* 1.3 77.9 - - - +
683A SER* 1.3 55.8 + - - +
685A PHE* 3.8 5.5 - - - +
686A SER* 2.9 31.0 + - - -
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Residues in contact with SER 683 (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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679A GLU 2.9 17.6 + - - -
680A THR* 3.8 7.2 - - - -
681A ILE 3.3 0.2 - - - -
682A LEU* 1.3 75.7 - - - +
684A TRP* 1.3 59.8 + - - +
686A SER* 4.0 5.5 - - - -
687A GLN* 3.1 28.9 + - - +
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Residues in contact with TRP 684 (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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643A LEU* 6.3 0.2 - - - -
646A LEU* 3.9 26.2 - - + -
680A THR 2.9 16.5 + - - +
681A ILE* 3.8 7.0 - - - +
682A LEU 3.3 0.2 - - - -
683A SER* 1.3 77.0 - - - +
685A PHE* 1.3 61.4 + - - +
687A GLN* 3.2 21.3 + - - +
698A ARG* 5.7 2.1 - - - +
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Residues in contact with PHE 685 (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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681A ILE 2.9 17.0 + - - +
682A LEU* 3.9 5.8 - - - +
683A SER 3.4 0.2 - - - -
684A TRP* 1.3 76.8 - - - +
686A SER* 1.3 62.0 + - - +
687A GLN 4.1 3.5 - - - +
698A ARG* 5.5 12.5 - - + +
707A ILE* 5.6 11.0 - - + -
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Residues in contact with SER 686 (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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682A LEU 2.9 18.2 + - - -
683A SER* 4.1 5.8 - - - -
684A TRP 3.3 0.2 - - - -
685A PHE* 1.3 75.4 - - - +
687A GLN* 1.3 63.2 + - - +
688A ARG* 3.5 3.5 + - - +
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Residues in contact with GLN 687 (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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683A SER 3.1 18.3 + - - +
684A TRP* 3.2 18.4 + - - +
685A PHE 3.3 3.6 - - - +
686A SER* 1.3 76.4 - - - +
688A ARG* 1.3 65.5 + - - +
695A GLN* 5.2 2.1 - - - +
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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
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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