Contacts of the helix formed by residues 678 - 686 (chain A) in PDB entry 2P0C
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 ASP 678 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ANP 3.7 24.3 + - - +
676A TYR 4.4 1.7 - - - +
677A GLY* 1.3 76.1 - - - +
679A LEU* 1.3 62.9 + - - +
680A HIS* 3.1 17.3 + - - +
681A THR* 2.6 44.2 + - - -
682A TYR* 3.4 18.0 + - - +
727A ARG* 3.2 30.7 - - - +
729A CYS 3.3 7.2 - - - +
730A MET* 3.7 6.5 - - + -
731A LEU* 4.1 1.2 - - - +
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Residues in contact with LEU 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 GLY 4.1 0.2 + - - -
678A ASP* 1.3 70.0 - - - +
680A HIS* 1.3 60.3 + - - +
682A TYR* 3.3 9.7 + - + +
683A LEU* 2.9 46.3 + - + +
703A PHE* 3.8 37.7 - - + -
707A ILE* 4.0 16.6 - - + -
726A ALA* 3.5 14.3 + - + +
729A CYS* 2.8 19.8 + - + +
730A MET* 4.7 0.4 - - - +
731A LEU* 4.2 20.1 - - + +
737A VAL* 4.4 7.4 - - + -
793A ILE* 3.7 33.4 - - + -
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Residues in contact with HIS 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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678A ASP* 3.1 11.8 + - - +
679A LEU* 1.3 79.7 - - - +
681A THR* 1.3 63.7 + - - +
683A LEU* 3.2 6.3 + - + +
684A LEU* 3.2 40.8 + - + +
726A ALA* 3.3 12.0 + - + -
727A ARG* 3.7 23.3 - - + +
766A TRP* 6.3 0.4 - + - -
792A GLU* 3.3 27.1 + - + -
797A GLY* 3.1 36.8 + - - -
798A MET 4.5 2.4 + - - -
799A THR* 5.7 4.2 - - - -
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Residues in contact with THR 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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678A ASP* 2.6 34.2 + - - -
679A LEU 3.4 0.2 - - - -
680A HIS* 1.3 75.1 + - - +
682A TYR* 1.3 58.7 + - - +
684A LEU* 3.2 11.0 + - - +
685A TYR* 2.9 67.6 + - + +
802B PRO* 4.7 1.1 - - + -
803B GLY* 4.1 19.4 + - - +
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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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676A TYR* 5.1 5.1 + - + +
678A ASP 3.4 5.4 + - - +
679A LEU* 3.3 12.3 + - + +
681A THR* 1.3 79.2 - - - +
683A LEU* 1.3 64.2 + - - +
685A TYR* 3.3 9.8 + + - +
686A SER* 3.0 24.1 + - - -
692A PRO* 3.4 38.4 - - + +
695A ILE* 3.4 32.5 - - + +
699A THR* 5.9 1.2 - - - +
703A PHE* 4.0 19.7 - + - -
731A LEU* 3.5 29.6 - - + -
735A MET* 3.7 32.5 - - + +
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LEU* 2.9 42.1 + - + +
680A HIS* 3.2 14.3 + - - +
682A TYR* 1.3 71.8 - - - +
684A LEU* 1.3 60.8 + - - +
686A SER* 2.6 26.3 + - - -
687A ARG* 3.8 4.7 + - - +
695A ILE* 4.0 12.6 - - + -
700A LEU* 4.0 26.9 - - + -
703A PHE* 4.5 1.3 - - + -
726A ALA* 4.5 5.2 - - + -
792A GLU 3.7 24.0 - - - +
793A ILE* 3.7 24.7 - - + +
796A ARG* 3.7 24.6 - - - +
797A GLY* 4.1 3.8 - - - +
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Residues in contact with LEU 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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680A HIS* 3.2 37.3 + - + +
681A THR* 3.2 8.5 + - + +
683A LEU* 1.3 70.7 - - - +
685A TYR* 1.3 67.1 + - - +
686A SER 3.1 1.6 - - - -
687A ARG* 3.2 24.1 + - - +
688A LEU* 3.8 3.0 - - - +
796A ARG 3.8 5.4 - - - +
797A GLY* 3.5 33.7 - - - +
798B MET* 3.5 32.5 - - + +
799B THR 6.3 0.2 - - - +
802B PRO* 4.0 28.7 - - + -
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Residues in contact with TYR 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 THR* 2.9 45.4 + - + +
682A TYR* 3.7 8.5 - + - +
684A LEU* 1.3 76.0 - - - +
686A SER* 1.3 57.4 + - - +
687A ARG 3.1 0.4 - - - -
688A LEU* 2.8 36.3 + - + +
691A GLY* 3.6 10.1 - - - -
692A PRO* 3.7 18.4 - - + -
802B PRO* 3.4 33.5 + - + -
803B GLY* 3.8 8.1 + - - -
804B VAL* 6.0 0.2 - - - +
820B LYS* 3.4 29.5 + - - -
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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 TYR 3.0 12.9 + - - -
683A LEU 2.6 20.6 + - - -
684A LEU 3.1 0.6 - - - -
685A TYR* 1.3 76.3 - - - +
687A ARG* 1.3 61.0 + - - +
688A LEU 3.2 2.4 + - - +
692A PRO* 3.4 23.2 - - - +
693A LYS 3.8 15.9 - - - +
694A HIS* 4.2 4.3 + - - +
695A ILE* 3.7 27.3 + - - +
796A ARG* 4.5 8.0 - - - -
823B GLU* 3.8 15.1 - - - +
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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