Contacts of the helix formed by residues 686 - 697 (chain A) in PDB entry 4IQJ
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 ARG 686 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A LEU 5.3 1.1 - - - +
651A ASP* 6.2 1.3 - - + +
656A PHE* 3.2 17.8 - - - -
685A ARG* 1.3 82.8 - - - +
687A LEU* 1.3 64.3 + - - +
688A GLU* 3.8 32.3 + - + +
689A ASP* 3.0 43.8 + - - +
690A ILE 4.0 1.6 + - - -
712A HIS* 5.8 1.3 - - - -
735A ASP 5.0 1.4 + - - -
736A GLU* 3.5 40.4 + - - +
738A TYR* 4.8 11.4 + - - -
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Residues in contact with LEU 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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441A ILE* 5.5 0.9 - - + -
446A PHE* 3.6 28.3 - - + -
650A LEU* 4.5 31.3 + - + +
656A PHE* 3.4 6.9 - - - -
686A ARG* 1.3 75.7 - - - +
688A GLU* 1.3 68.5 + - - +
690A ILE* 3.2 21.9 + - + +
691A ILE* 3.2 20.3 + - + +
819A ALA 5.0 3.6 - - - +
822A SER* 3.8 14.1 - - - +
823A LEU* 4.9 19.1 - - + +
826A TYR* 3.7 38.1 - - + -
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Residues in contact with GLU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ARG* 5.5 5.9 + - - +
446A PHE* 3.4 29.7 - - + -
650A LEU* 5.9 2.3 - - - +
686A ARG* 3.2 38.2 + - + +
687A LEU* 1.3 86.2 + - - +
689A ASP* 1.3 57.1 + - - +
690A ILE 3.3 0.2 - - - -
691A ILE* 3.5 10.9 + - + +
692A ALA* 3.0 28.9 + - - +
708A TYR* 4.1 2.0 + - - -
736A GLU* 3.4 38.6 - - + +
743A TYR* 3.9 3.4 + - - +
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Residues in contact with ASP 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A LEU* 4.2 11.8 - - + +
684A PRO* 3.8 16.6 - - + -
685A ARG* 3.0 10.8 + - - -
686A ARG* 3.0 44.8 + - - +
687A LEU 3.1 0.6 - - - -
688A GLU* 1.3 76.5 - - - +
690A ILE* 1.3 59.6 + - - +
692A ALA* 3.6 2.3 + - - +
693A LEU* 2.9 29.3 + - - +
708A TYR* 3.3 20.4 + - - +
712A HIS* 3.3 29.4 + - - -
736A GLU 5.7 0.2 - - - +
738A TYR* 4.4 2.1 - - - -
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Residues in contact with ILE 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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656A PHE* 4.2 13.5 - - + -
659A LEU* 3.4 33.4 - - + -
670A LEU* 4.8 14.6 - - + -
679A VAL* 6.5 0.4 - - + -
684A PRO* 4.7 9.2 - - + -
686A ARG 4.6 4.9 - - - +
687A LEU* 3.2 19.6 + - + +
689A ASP* 1.3 73.0 - - - +
691A ILE* 1.3 68.6 + - - +
693A LEU* 3.0 9.1 + - + -
694A VAL* 2.8 39.2 + - + +
822A SER* 3.6 24.0 - - - +
825A SER* 4.7 11.9 - - - -
826A TYR* 5.1 8.3 - - + +
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Residues in contact with ILE 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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446A PHE* 4.1 26.2 - - + -
687A LEU* 3.2 17.5 + - + +
688A GLU* 3.6 12.1 - - + +
689A ASP 3.4 0.2 - - - -
690A ILE* 1.3 76.8 - - - +
692A ALA* 1.3 58.9 + - - +
694A VAL* 3.0 20.5 - - - +
695A SER* 3.0 16.3 + - - -
743A TYR* 2.8 33.0 - - + +
815A LYS* 4.3 10.3 - - + -
818A ALA* 3.8 17.3 - - + -
819A ALA* 3.7 25.4 - - + +
822A SER* 3.2 26.9 - - - +
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Residues in contact with ALA 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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688A GLU 3.0 15.6 + - - +
689A ASP 3.7 2.2 - - - +
691A ILE* 1.3 76.8 - - - +
693A LEU* 1.3 56.6 + - - +
695A SER* 3.5 2.4 + - - -
696A LEU* 3.1 37.5 + - + +
708A TYR* 3.4 36.1 - - + +
736A GLU 6.1 0.2 - - - +
737A THR* 4.5 8.1 - - - +
742A VAL* 4.7 1.8 - - + -
743A TYR* 3.0 18.3 + - + +
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Residues in contact with LEU 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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670A LEU* 5.0 3.4 - - + -
675A MET* 3.8 15.7 - - + -
678A THR* 4.3 19.7 - - - +
679A VAL* 3.4 38.8 - - + +
682A LEU* 3.9 27.1 - - + -
684A PRO* 6.1 1.8 - - + -
689A ASP 2.9 17.7 + - - +
690A ILE* 3.0 9.6 + - + +
692A ALA* 1.3 74.5 - - - +
694A VAL* 1.3 60.9 + - + +
696A LEU* 4.7 4.0 - - - -
697A TYR* 2.9 34.5 + - - +
705A ILE* 4.5 23.1 - - + -
708A TYR* 6.3 0.9 - - - -
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Residues in contact with VAL 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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669A GLN* 4.4 34.5 - - + +
670A LEU* 5.4 2.0 - - + -
675A MET* 4.1 20.6 - - + -
690A ILE* 2.8 31.2 + - + +
691A ILE* 3.0 26.5 - - - +
693A LEU* 1.3 77.1 - - - +
695A SER* 1.3 65.5 + - - +
696A LEU 3.6 0.2 + - - -
697A TYR* 3.9 10.3 + - - +
698A ARG* 3.7 15.1 + - - -
813A PHE* 5.8 2.0 - - + -
818A ALA* 4.3 11.4 - - + +
822A SER* 4.0 7.2 - - - +
825A SER* 5.5 0.2 - - - +
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Residues in contact with SER 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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691A ILE 3.0 17.5 + - - -
692A ALA 3.8 0.4 - - - -
693A LEU 3.2 0.2 - - - -
694A VAL* 1.3 81.3 - - - +
696A LEU* 1.3 57.1 + - - +
698A ARG* 3.1 26.2 + - - +
701A PRO* 4.2 3.1 - - - +
742A VAL* 3.7 24.0 - - - +
743A TYR* 3.4 10.7 - - - -
811A TYR 5.2 1.4 - - - +
813A PHE* 3.3 39.7 - - - +
818A ALA* 3.4 5.9 - - - +
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Residues in contact with LEU 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ALA 3.1 23.9 + - - +
693A LEU* 3.3 3.6 + - - +
695A SER* 1.3 77.0 - - - +
697A TYR* 1.3 59.5 + - - +
698A ARG 2.9 10.0 + - - -
701A PRO* 3.4 30.8 - - + +
702A MET* 3.3 22.2 + - - -
704A HIS* 4.3 17.5 - - + +
705A ILE* 4.0 21.5 - - + -
708A TYR* 4.3 27.4 - - + -
740A ILE* 5.0 1.6 - - + -
742A VAL* 3.7 41.7 - - + +
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Residues in contact with TYR 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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672A SER* 5.3 6.0 - - - -
674A GLY* 3.3 23.3 - - - -
675A MET* 3.4 43.8 + - + -
678A THR* 4.0 22.4 - - + -
693A LEU* 2.9 19.2 + - + +
694A VAL 3.9 9.0 + - - +
695A SER 3.5 0.8 - - - -
696A LEU* 1.3 71.4 - - - +
698A ARG* 1.3 68.2 + - - +
702A MET* 4.2 25.3 - - + +
705A ILE* 4.0 21.1 - - + +
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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