Contacts of the helix formed by residues 694 - 707 (chain F) in PDB entry 1SOJ
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 694 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688F MET* 4.0 4.7 - - + -
691F LYS* 3.2 25.6 + - + +
692F SER 3.0 1.8 - - - -
693F GLY* 1.3 84.5 - - - +
695F ILE* 1.3 60.0 + - - +
697F SER* 3.6 7.9 - - - +
698F GLN* 3.0 34.6 + - + +
725F ARG* 3.4 53.3 - - - +
728F GLU* 2.8 16.4 - - - +
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Residues in contact with ILE 695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681F ILE* 5.1 5.2 - - + -
684F LEU* 4.7 13.7 - - + -
685F VAL* 3.4 42.6 - - + +
688F MET* 3.8 17.9 - - - -
692F SER* 2.9 20.3 + - - +
693F GLY 3.5 1.4 - - - -
694F ARG* 1.3 76.1 - - - +
696F LEU* 1.3 59.3 + - - +
698F GLN* 3.2 3.1 + - - +
699F VAL* 2.8 36.4 + - + +
728F GLU* 3.2 0.2 + - - -
739F ARG* 5.3 6.2 - - - +
740F ILE* 3.9 20.0 - - + -
743F THR* 3.7 27.1 - - + +
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Residues in contact with LEU 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695F ILE* 1.3 79.8 - - - +
697F SER* 1.3 58.4 + - - +
699F VAL* 3.2 0.3 + - - -
700F MET* 2.8 40.1 + - + +
724F PHE* 5.2 2.5 - - + +
727F LEU* 4.2 11.2 - - + -
728F GLU* 2.9 23.4 + - + +
731F TYR* 4.1 18.2 - - + -
739F ARG* 4.5 7.9 + - + +
742F ALA* 4.2 8.5 - - + -
743F THR* 3.3 36.0 + - - +
746F LEU* 4.2 16.2 - - + -
819F ALA* 3.5 31.9 - - + +
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Residues in contact with SER 697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694F ARG* 3.4 13.0 + - - +
696F LEU* 1.3 73.9 - - - +
698F GLN* 1.3 65.0 + - - +
700F MET* 3.9 1.8 - - - +
701F TYR* 3.2 23.7 + - - +
720F PHE* 4.8 0.5 - - - -
721F MET* 3.6 18.0 - - - +
724F PHE* 4.0 29.2 - - - -
725F ARG* 3.6 14.8 + - - -
728F GLU* 2.6 32.9 + - - +
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Residues in contact with GLN 698 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670F LEU* 4.9 7.2 - - + -
688F MET* 3.9 19.7 - - + -
694F ARG* 3.0 31.6 + - + +
695F ILE* 3.7 2.9 - - - +
697F SER* 1.3 81.5 + - - +
699F VAL* 1.3 65.8 + - + +
701F TYR* 3.5 6.6 + - - +
702F THR* 2.9 29.8 + - - +
721F MET* 3.5 28.0 - - - +
725F ARG* 4.2 11.1 - - - +
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Residues in contact with VAL 699 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670F LEU* 4.6 7.6 - - + -
674F MET* 3.3 34.1 - - + -
679F PHE* 5.3 0.4 - - + -
684F LEU* 4.5 16.2 - - + -
695F ILE* 2.8 26.5 + - + +
696F LEU 3.9 2.2 - - - +
698F GLN* 1.3 74.6 - - + +
700F MET* 1.3 61.2 + - - +
702F THR* 3.1 6.3 + - - -
703F LEU* 2.8 41.6 + - + +
743F THR* 3.7 25.8 - - + +
746F LEU* 4.0 10.3 - - + -
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Residues in contact with MET 700 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696F LEU* 2.8 24.5 + - + +
697F SER* 3.9 7.0 - - - +
699F VAL* 1.3 77.4 - - - +
701F TYR* 1.3 57.0 + - - +
703F LEU* 3.3 2.1 + - + -
704F PHE* 2.9 63.5 + - + +
720F PHE* 4.0 11.2 - - + -
724F PHE* 3.9 26.7 - - + -
746F LEU* 2.9 45.8 - - + -
815F TYR* 4.0 8.7 - - + +
816F VAL* 4.9 0.9 - - - -
819F ALA* 3.7 23.1 - - + -
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Residues in contact with TYR 701 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F LEU* 6.0 6.1 - - + -
667F TYR* 5.9 0.4 - + - -
697F SER 3.2 16.1 + - - +
698F GLN* 3.8 7.0 - - - +
700F MET* 1.3 80.0 - - - +
702F THR* 1.3 69.5 + - - +
704F PHE* 3.4 7.7 + - - +
705F GLN* 3.0 51.6 + - + +
710F LEU* 3.9 17.4 - - + +
717F THR* 3.6 34.9 + - + +
720F PHE* 3.6 17.6 - + - -
721F MET* 3.9 25.6 - - + -
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Residues in contact with THR 702 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667F TYR* 3.7 24.6 - - + -
670F LEU* 3.5 29.1 - - + +
671F ILE* 3.4 29.4 - - + -
674F MET* 4.8 6.3 - - - -
698F GLN* 2.9 21.8 + - - +
699F VAL* 3.5 4.7 - - - -
701F TYR* 1.3 83.2 - - - +
703F LEU* 1.3 64.2 + - - +
705F GLN* 3.0 14.6 + - - +
706F ASP* 3.1 10.4 + - - +
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Residues in contact with LEU 703 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671F ILE* 5.0 5.2 - - + -
674F MET* 4.0 24.7 - - + -
699F VAL* 2.8 32.6 + - + +
700F MET* 4.0 4.5 - - + +
702F THR* 1.3 73.7 - - - +
704F PHE* 1.3 62.9 + - + +
705F GLN 3.1 0.2 - - - -
706F ASP* 3.3 2.8 + - - +
707F THR* 2.9 36.2 + - + +
746F LEU* 3.7 33.4 - - + +
747F HIS* 4.5 1.1 - - - -
750F TRP* 3.4 57.7 - - + -
815F TYR* 6.0 2.7 - - + -
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Residues in contact with PHE 704 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700F MET* 2.9 46.3 + - + +
701F TYR 3.9 3.6 - - - +
702F THR 3.2 0.4 - - - -
703F LEU* 1.3 79.6 - - + +
705F GLN* 1.3 59.1 + - - +
707F THR* 3.6 5.6 - - - -
708F GLY 3.5 1.2 + - - -
709F LEU* 3.3 33.7 + - + -
710F LEU* 3.2 37.7 + - + +
715F ILE* 4.2 11.4 - - + -
720F PHE* 3.5 32.1 - + + -
812F MET* 4.0 29.6 - - + -
815F TYR* 4.1 11.7 - + + -
816F VAL* 3.8 26.2 - - + -
870F PHE* 4.9 1.6 - + - -
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Residues in contact with GLN 705 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F LEU* 6.2 0.5 - - - +
667F TYR* 3.5 31.9 - - + +
701F TYR* 3.0 51.5 + - - +
702F THR 3.0 6.7 + - - +
704F PHE* 1.3 76.4 - - - +
706F ASP* 1.3 67.6 + - - +
707F THR 3.0 2.5 + - - -
708F GLY* 3.3 4.1 + - - +
710F LEU* 3.5 18.1 - - + +
790F LYS* 2.9 29.4 + - - +
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Residues in contact with ASP 706 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667F TYR* 3.4 15.4 + - - +
671F ILE* 3.8 13.2 - - + +
702F THR 3.1 12.2 + - - +
703F LEU* 3.8 7.9 - - - +
705F GLN* 1.3 79.1 - - - +
707F THR* 1.3 55.7 + - - +
750F TRP* 3.3 22.3 + - + -
788F SER 3.5 0.7 - - - +
789F SER* 2.5 25.2 + - - -
790F LYS* 2.9 38.4 + - - +
791F SER* 2.9 37.9 + - - -
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Residues in contact with THR 707 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703F LEU 2.9 19.6 + - - +
704F PHE* 3.6 2.6 - - - -
706F ASP* 1.3 81.2 - - - +
708F GLY* 1.3 58.7 + - - +
709F LEU* 3.3 25.7 + - - +
712F ILE* 4.8 1.0 - - - +
750F TRP* 3.7 29.4 - - + +
754F THR* 5.1 2.5 - - - +
787F ILE* 3.4 46.8 - - + +
788F SER 3.6 16.7 + - - +
789F SER* 5.2 1.8 - - - -
790F LYS* 5.0 0.9 - - - -
815F TYR* 4.1 7.2 - - + -
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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