Contacts of the helix formed by residues 694 - 707 (chain A) in PDB entry 1SO2
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688A MET* 4.1 2.2 - - + -
691A LYS* 3.1 33.2 + - + +
692A SER 3.1 1.4 - - - -
693A GLY* 1.3 83.6 - - - +
695A ILE* 1.3 53.5 + - - +
697A SER* 3.1 6.9 + - - +
698A GLN* 2.8 47.0 + - + +
725A ARG* 3.6 38.3 - - - +
728A GLU* 2.7 23.5 - - - +
865C ARG* 5.0 12.1 - - - +
866C PRO* 3.7 30.7 - - - +
867C GLU* 4.1 14.7 + - - -
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Residues in contact with ILE 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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681A ILE* 4.1 17.7 - - + -
684A LEU* 3.8 31.4 - - + -
685A VAL* 3.8 26.7 - - + -
688A MET* 3.8 16.3 - - - +
692A SER* 3.5 18.7 + - - +
693A GLY 5.0 0.2 - - - -
694A ARG* 1.3 78.8 - - - +
696A LEU* 1.3 60.9 + - - +
698A GLN* 3.9 1.2 - - - +
699A VAL* 2.9 38.7 + - + +
728A GLU* 3.1 0.4 + - - -
739A ARG* 4.3 21.3 - - + +
740A ILE* 4.7 7.9 - - + -
743A THR* 3.9 15.9 - - + +
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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
----------------------------------------------------------
695A ILE* 1.3 78.5 - - - +
697A SER* 1.3 57.0 + - - +
699A VAL* 3.9 1.3 - - - +
700A MET* 3.0 35.4 + - + +
724A PHE* 5.3 2.9 - - + +
727A LEU* 4.6 6.7 - - + -
728A GLU* 2.8 29.7 + - + -
731A TYR* 4.0 20.0 - - + -
739A ARG* 4.3 8.7 - - + +
742A ALA* 4.0 10.8 - - + +
743A THR* 3.3 37.2 - - - +
746A LEU* 4.1 15.0 - - + -
819A ALA* 3.8 33.7 - - + +
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Residues in contact with SER 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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694A ARG* 3.1 12.5 + - - +
696A LEU* 1.3 71.1 - - - +
698A GLN* 1.3 68.8 + - - +
700A MET* 3.4 2.9 + - - +
701A TYR* 3.1 23.0 + - - +
720A PHE* 4.9 0.3 - - - -
721A MET* 3.8 13.5 - - - +
724A PHE* 3.9 30.5 - - - -
725A ARG* 3.9 14.8 - - - +
728A GLU* 2.7 39.1 + - - +
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Residues in contact with GLN 698 (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 6.3 - - + -
688A MET* 4.0 17.3 - - + -
691A LYS* 5.7 5.2 - - - +
694A ARG* 2.8 41.5 + - + +
695A ILE* 3.9 5.8 - - - +
697A SER* 1.3 84.3 + - - +
699A VAL* 1.3 63.2 + - + +
701A TYR* 3.4 7.2 + - - +
702A THR* 3.0 26.6 + - - -
721A MET* 3.4 28.9 - - - +
725A ARG* 4.6 8.3 - - - +
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Residues in contact with VAL 699 (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* 4.6 6.7 - - + -
674A MET* 3.9 26.9 - - - -
679A PHE* 5.4 0.7 - - + -
684A LEU* 4.4 13.0 - - + -
695A ILE* 2.9 30.6 + - + +
696A LEU 4.0 3.1 - - - +
698A GLN* 1.3 76.6 - - + +
700A MET* 1.3 62.9 - - - +
702A THR* 3.5 6.8 + - - -
703A LEU* 3.0 29.4 + - + +
743A THR* 3.6 27.1 - - + +
746A LEU* 4.0 18.8 - - + -
747A HIS* 5.5 2.0 - - + -
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Residues in contact with MET 700 (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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696A LEU* 3.0 26.9 + - + +
697A SER* 3.6 7.4 - - - +
698A GLN 3.2 0.2 - - - -
699A VAL* 1.3 74.3 - - - +
701A TYR* 1.3 66.8 + - - +
703A LEU* 3.2 5.9 + - + -
704A PHE* 2.8 58.2 + - + +
720A PHE* 4.1 14.1 - - + -
724A PHE* 4.3 25.4 - - + -
746A LEU* 3.0 45.8 - - + -
815A TYR* 4.4 4.9 - - + +
819A ALA* 3.9 21.8 - - + -
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Residues in contact with TYR 701 (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 LEU* 6.1 4.3 - - + +
667A TYR* 5.3 7.4 - + - -
697A SER 3.1 14.8 + - - +
698A GLN* 3.4 6.5 + - - +
700A MET* 1.3 79.2 - - - +
702A THR* 1.3 68.6 + - - +
704A PHE* 3.4 2.2 + - - +
705A GLN* 3.1 47.5 + - + +
710A LEU* 4.0 19.3 - - + +
717A THR* 4.1 26.7 + - + +
720A PHE* 3.8 14.5 - + - -
721A MET* 3.8 28.9 - - + -
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Residues in contact with THR 702 (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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667A TYR* 3.4 36.5 - - + +
670A LEU* 3.4 18.8 - - + +
671A ILE* 3.6 15.3 - - + -
674A MET* 3.6 26.0 - - + -
698A GLN 3.0 13.8 + - - -
699A VAL 3.6 8.1 - - - -
701A TYR* 1.3 83.0 - - - +
703A LEU* 1.3 58.2 + - - +
705A GLN 3.4 0.7 + - - -
706A ASP* 2.9 23.9 + - - +
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Residues in contact with LEU 703 (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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671A ILE* 4.8 0.9 - - + -
674A MET* 3.8 20.2 - - + -
699A VAL* 3.0 29.5 + - + +
700A MET* 3.8 7.4 - - + +
702A THR* 1.3 74.9 - - - +
704A PHE* 1.3 63.8 + - + +
705A GLN 2.9 4.9 - - - -
706A ASP* 3.0 3.9 + - + +
707A THR* 2.9 30.0 + - - +
746A LEU* 3.9 28.0 - - + +
747A HIS* 4.6 4.0 - - - -
750A TRP* 3.3 67.3 - - + +
815A TYR* 6.2 2.5 - - + -
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Residues in contact with PHE 704 (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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700A MET* 2.8 51.4 + - + +
701A TYR 4.1 1.8 - - - +
703A LEU* 1.3 75.8 - - + +
705A GLN* 1.3 55.8 + - - +
707A THR* 3.6 5.4 - - - -
708A GLY 3.2 1.2 + - - -
709A LEU* 2.7 51.5 + - + -
710A LEU* 3.4 26.3 + - + -
715A ILE* 4.2 5.4 - - + -
720A PHE* 3.4 29.2 - + + -
812A MET* 3.7 39.7 - - + -
815A TYR* 3.9 16.6 - + + -
816A VAL* 3.8 19.5 - - + -
870A PHE* 5.1 1.8 - + - -
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Residues in contact with GLN 705 (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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667A TYR* 3.7 20.5 + - + +
701A TYR* 3.1 35.4 + - + +
702A THR 3.5 5.4 - - - +
703A LEU 2.9 0.2 - - - -
704A PHE* 1.3 78.6 - - - +
706A ASP* 1.3 63.9 + - - +
707A THR 3.2 0.2 - - - -
708A GLY* 3.4 7.3 + - - -
710A LEU* 3.0 31.0 - - + +
711A GLU* 5.9 5.7 - - - +
790A LYS* 3.0 39.4 + - - +
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Residues in contact with ASP 706 (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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667A TYR* 3.3 14.2 + - - +
671A ILE* 3.9 10.8 - - + +
702A THR 2.9 17.2 + - - +
703A LEU* 3.0 7.6 + - - +
705A GLN* 1.3 77.1 - - - +
707A THR* 1.3 57.7 + - - +
750A TRP* 2.9 25.9 + - - -
788A SER 3.7 0.5 - - - +
789A SER* 2.6 23.4 + - - -
790A LYS* 3.2 34.6 + - - +
791A SER* 2.6 37.0 + - - -
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Residues in contact with THR 707 (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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703A LEU 2.9 17.3 + - - +
704A PHE* 3.4 2.9 + - - -
706A ASP* 1.3 89.9 - - - +
708A GLY* 1.3 61.6 + - - +
709A LEU* 3.3 23.7 + - - +
712A ILE* 4.4 1.0 - - - +
750A TRP* 3.5 20.9 - - + +
754A THR* 4.7 2.9 - - + -
787A ILE* 3.3 49.2 - - + +
788A SER 4.0 13.1 + - - +
789A SER* 4.9 1.3 - - - -
790A LYS* 5.3 0.4 - - - -
815A TYR* 4.5 5.1 - - + -
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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