Contacts of the helix formed by residues 681 - 693 (chain A) in PDB entry 2WKP
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 THR 681 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A ARG* 3.6 9.9 - - - +
679A PRO* 4.0 7.9 - - + +
680A ILE* 1.3 79.1 - - - +
682A TYR* 1.3 64.9 + - - +
683A PRO* 3.5 13.1 - - - +
684A GLN* 2.9 42.4 + - - +
685A GLY* 3.0 19.6 + - - -
697A TYR* 4.3 0.2 + - - -
699A GLU* 4.2 1.0 - - - +
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Residues in contact with TYR 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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663A ARG* 3.4 11.0 - - - +
681A THR* 1.3 70.9 - - - +
683A PRO* 1.3 73.4 - - + +
685A GLY 3.2 1.4 + - - -
686A LEU* 2.9 54.5 + - + +
697A TYR* 3.6 38.6 + + - -
698A LEU* 5.8 0.2 - - - -
699A GLU* 3.3 32.5 - - + +
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Residues in contact with PRO 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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681A THR* 3.5 14.1 - - - +
682A TYR* 1.3 104.7 - - + +
684A GLN* 1.3 56.8 + - + +
686A LEU* 3.5 7.3 + - + +
687A ALA* 3.0 28.4 + - - +
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Residues in contact with GLN 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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633A PHE* 3.4 17.7 - - + -
678A THR* 5.7 3.2 + - - -
679A PRO 3.8 2.6 - - - +
680A ILE* 3.5 21.6 - - + +
681A THR* 2.9 42.6 + - - +
683A PRO* 1.3 76.6 - - + +
685A GLY* 1.3 65.3 + - - +
687A ALA* 3.3 7.2 + - - +
688A MET 3.1 18.0 + - - -
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Residues in contact with GLY 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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633A PHE* 4.0 15.0 - - - -
655A LEU* 3.6 6.8 - - - +
680A ILE* 4.0 2.6 - - - +
681A THR 3.0 11.8 + - - -
684A GLN* 1.3 75.3 - - - +
686A LEU* 1.3 57.7 + - - +
688A MET* 3.3 4.3 + - - +
689A ALA* 2.9 25.1 + - - +
697A TYR* 3.5 30.5 - - - -
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Residues in contact with LEU 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 TYR* 2.9 42.8 + - + +
683A PRO* 3.8 7.6 - - + +
685A GLY* 1.3 76.4 - - - +
687A ALA* 1.3 61.9 + - - +
689A ALA* 3.2 4.9 + - + +
690A LYS* 3.0 56.0 + - + +
697A TYR* 3.5 28.9 - - + +
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Residues in contact with ALA 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 PRO 3.0 17.7 + - - +
684A GLN* 3.6 7.2 - - - +
685A GLY 3.3 0.2 - - - -
686A LEU* 1.3 76.6 - - - +
688A MET* 1.3 57.2 + - - +
690A LYS* 3.3 12.5 + - - +
691A GLU* 2.9 28.8 + - - +
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Residues in contact with MET 688 (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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633A PHE* 3.5 61.0 - - + +
636A VAL* 4.1 10.3 - - + -
637A ARG* 3.5 59.2 - - + +
655A LEU* 3.7 15.5 - - + -
684A GLN 3.1 5.9 + - - -
685A GLY 3.5 4.3 - - - +
687A ALA* 1.3 74.0 - - - +
689A ALA* 1.3 65.6 + - - +
691A GLU* 3.1 13.2 + - - +
692A ILE* 3.0 31.4 + - + +
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Residues in contact with ALA 689 (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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655A LEU* 3.5 14.2 - - + +
685A GLY 2.9 8.8 + - - +
686A LEU* 3.2 11.6 + - + +
688A MET* 1.3 76.7 - - - +
690A LYS* 1.3 61.2 + - + +
692A ILE* 3.3 1.6 + - - +
693A GLY 3.0 4.5 + - - -
694A ALA* 2.9 47.6 + - + +
696A LYS 4.7 0.4 - - - -
697A TYR* 3.6 31.2 - - + +
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Residues in contact with LYS 690 (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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686A LEU* 3.0 49.8 + - + +
687A ALA* 3.6 11.0 - - - +
689A ALA* 1.3 77.2 - - + +
691A GLU* 1.3 64.0 + - - +
693A GLY* 3.3 12.7 + - - -
694A ALA 5.4 1.8 - - - -
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Residues in contact with GLU 691 (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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637A ARG* 2.7 54.8 + - - +
641A TYR* 4.8 5.1 + - + -
687A ALA 2.9 13.9 + - - +
688A MET* 3.1 18.7 + - - +
690A LYS* 1.3 78.7 - - - +
692A ILE* 1.3 61.2 + - + +
693A GLY 3.3 0.4 + - - -
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Residues in contact with ILE 692 (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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623A ILE* 4.6 2.5 - - + -
636A VAL* 4.0 22.2 - - + -
637A ARG* 4.8 5.2 - - + -
641A TYR* 3.1 65.0 + - + -
645A ARG* 5.0 2.1 + - - -
653A ILE* 4.3 20.8 - - + +
655A LEU* 4.4 11.4 - - + -
688A MET* 3.0 32.2 + - - +
689A ALA* 3.5 9.4 - - - +
691A GLU* 1.3 82.0 - - + +
693A GLY* 1.3 59.3 + - - +
694A ALA* 3.9 15.7 - - + +
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Residues in contact with GLY 693 (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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645A ARG* 4.6 10.8 + - - -
653A ILE* 5.3 0.7 + - - +
689A ALA 3.0 4.1 + - - -
690A LYS* 3.3 11.8 + - - -
691A GLU 3.3 1.4 + - - -
692A ILE* 1.3 80.5 - - - +
694A ALA* 1.3 64.3 + - - +
695A VAL* 3.6 6.6 + - - +
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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