Contacts of the helix formed by residues 687 - 697 (chain A) in PDB entry 4K6J
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 MET 687 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A GLU* 5.9 2.5 - - - +
683A THR 4.5 0.4 + - - +
684A LYS* 3.1 19.5 + - + +
685A CYS 2.9 3.8 - - - +
686A ALA* 1.3 78.2 - - - +
688A PRO* 1.3 61.5 - - + +
689A SER* 3.1 10.1 - - - +
690A PHE* 2.8 50.1 + - + +
691A ARG 3.1 10.0 + - - -
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Residues in contact with PRO 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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643A ASN 4.7 11.4 - - - +
644A ASP* 3.9 24.7 - - + +
645A VAL 5.3 4.5 - - - +
646A VAL* 4.1 14.6 - - + -
686A ALA 3.3 11.4 - - - +
687A MET* 1.3 85.3 - - + +
689A SER* 1.3 62.0 + - - +
691A ARG* 3.5 28.6 + - + +
692A MET* 3.0 26.7 + - + +
695A ARG* 5.3 0.9 + - - -
730A ASP* 5.4 0.2 - - - +
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Residues in contact with SER 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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645A VAL 4.5 5.3 + - - -
646A VAL* 4.0 15.0 - - - +
647A GLU* 3.3 39.3 + - - +
687A MET* 3.0 10.2 + - - +
688A PRO* 1.3 76.6 - - - +
690A PHE* 1.3 64.5 + - - +
692A MET* 3.4 4.9 + - - +
693A HIS* 3.1 34.9 + - - -
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Residues in contact with PHE 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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653A GLU* 6.0 0.9 - - - -
654A PHE* 3.5 29.5 - + + -
657A ASP* 4.6 11.2 - - + -
658A ILE* 3.6 25.8 - - + -
661A LEU* 4.8 1.8 - - + -
681A LEU* 3.7 22.9 - - + -
684A LYS* 3.1 62.6 - - + +
685A CYS* 3.8 13.5 - - - -
687A MET* 2.8 22.8 + - + +
689A SER* 1.3 76.9 - - - +
691A ARG* 1.3 64.8 + - - +
693A HIS* 3.0 8.0 + - - +
694A LEU* 2.8 25.2 + - + +
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Residues in contact with ARG 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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644A ASP* 5.5 2.2 + - - -
685A CYS* 2.6 34.5 + - + +
686A ALA* 3.8 15.2 + - - +
687A MET 3.1 3.4 + - - +
688A PRO* 3.7 35.2 - - - +
690A PHE* 1.3 79.2 - - - +
692A MET* 1.3 57.0 + - - +
694A LEU* 3.2 8.0 + - - +
695A ARG* 2.9 39.1 + - - +
726A ILE* 4.2 12.7 + - - +
727A LEU* 3.9 26.9 - - + +
729A ARG* 4.0 15.4 - - - +
730A ASP* 2.8 50.0 + - - +
779A VAL* 4.0 18.4 + - - +
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Residues in contact with MET 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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646A VAL* 3.3 47.6 - - + -
647A GLU 5.1 3.6 - - - +
648A PHE* 4.7 21.1 - - + -
688A PRO* 3.0 12.5 + - + +
689A SER 3.5 6.3 - - - +
690A PHE 3.1 0.2 - - - -
691A ARG* 1.3 79.3 - - - +
693A HIS* 1.3 60.9 + - + +
695A ARG* 3.8 21.4 + - - +
696A ALA* 2.8 34.7 + - + +
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Residues in contact with HIS 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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647A GLU 3.1 26.0 + - - -
648A PHE* 3.7 7.9 + - - -
649A GLY 3.0 28.5 + - - -
650A GLU* 3.7 22.8 + - - -
651A ASN* 4.0 8.0 + - + +
654A PHE* 3.5 30.0 - + + -
689A SER* 3.1 27.7 + - - +
690A PHE* 3.0 8.5 + - - +
692A MET* 1.3 79.4 - - + +
694A LEU* 1.3 65.7 + - - +
696A ALA* 4.2 5.5 - - - +
697A HIS* 3.0 37.0 + - - +
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Residues in contact with LEU 694 (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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654A PHE* 3.7 7.0 - - + -
658A ILE* 3.4 34.1 - - + -
681A LEU* 4.7 7.2 - - + -
685A CYS* 3.8 26.7 - - - -
690A PHE* 2.8 14.1 + - + +
691A ARG* 3.2 9.4 + - - +
693A HIS* 1.3 78.7 - - - +
695A ARG* 1.3 58.6 + - + +
697A HIS 3.6 0.3 + - - -
698A GLY 3.5 2.1 + - - -
699A MET* 3.2 46.8 + - + +
700A VAL* 4.3 15.3 + - + +
703A VAL* 4.7 14.1 - - + -
727A LEU* 3.9 20.6 - - + -
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Residues in contact with ARG 695 (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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688A PRO 5.3 0.6 + - - -
691A ARG* 2.9 20.2 + - - +
692A MET* 4.1 26.0 + - - +
694A LEU* 1.3 74.3 - - + +
696A ALA* 1.3 64.9 + - - +
697A HIS 3.1 2.7 - - - -
698A GLY* 3.1 11.5 + - - +
700A VAL* 3.8 15.5 - - + -
727A LEU* 5.3 5.8 + - + -
730A ASP* 2.9 41.3 + - - +
731A ARG 4.7 5.6 + - - -
732A LEU* 3.6 21.3 - - - -
735A ASP* 3.1 44.8 + - - +
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Residues in contact with ALA 696 (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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692A MET* 2.8 24.9 + - + +
693A HIS* 3.9 7.6 - - + +
694A LEU 3.4 0.4 - - - -
695A ARG* 1.3 76.6 - - - +
697A HIS* 1.3 63.4 + - + +
698A GLY 3.3 0.8 + - - -
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Residues in contact with HIS 697 (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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650A GLU* 3.1 41.0 + - - -
654A PHE* 3.3 20.9 - + - -
655A THR* 4.6 6.1 + - + +
693A HIS* 3.0 30.1 + - - +
695A ARG 3.1 0.8 - - - -
696A ALA* 1.3 81.2 - - + +
698A GLY* 1.3 64.5 + - - +
699A MET* 3.3 32.7 - - + +
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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