Contacts of the helix formed by residues 694 - 708 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C LEU* 2.8 41.7 - - - +
688C MET* 3.8 7.4 - - + +
691C LYS* 3.1 32.6 + - + +
692C SER 3.1 1.2 - - - -
693C GLY* 1.3 80.7 - - - +
695C ILE* 1.3 56.6 + - - +
697C SER* 3.3 8.6 + - - +
698C GLN* 3.1 34.3 - - + +
725C ARG* 3.3 40.0 - - - +
728C GLU* 2.9 17.7 - - - +
729C ASN* 5.9 1.3 - - - +
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Residues in contact with ILE 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C ILE* 4.5 13.0 - - + -
684C LEU* 3.7 31.0 - - + -
685C VAL* 3.7 32.1 - - + +
688C MET* 4.0 15.5 - - - -
692C SER* 3.3 18.8 + - - +
693C GLY 3.4 0.6 - - - -
694C ARG* 1.3 77.3 - - - +
696C LEU* 1.3 65.1 + - - +
698C GLN* 3.8 1.8 + - + +
699C VAL* 2.9 36.0 + - + +
728C GLU* 3.0 1.0 + - - -
739C ARG* 4.3 20.4 - - + -
740C ILE* 4.7 8.3 - - + +
743C THR* 3.9 15.7 - - + +
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Residues in contact with LEU 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C ILE* 1.3 77.7 - - + +
697C SER* 1.3 58.7 + - - +
699C VAL* 3.5 1.4 + - - +
700C MET* 3.0 37.4 + - + +
724C PHE* 5.1 3.4 - - + +
727C LEU* 4.8 4.9 - - + -
728C GLU* 2.8 33.6 + - + +
731C TYR* 4.4 10.3 - - + -
739C ARG* 4.4 6.5 - - + +
742C ALA* 3.9 14.6 - - + +
743C THR* 3.4 42.6 - - - +
746C LEU* 4.1 13.2 - - + -
819C ALA* 3.8 31.4 - - + +
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Residues in contact with SER 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694C ARG* 3.3 10.6 + - - +
696C LEU* 1.3 74.3 - - - +
698C GLN* 1.3 63.2 + - - +
700C MET* 3.6 2.2 + - - +
701C TYR* 3.1 18.0 + - - +
720C PHE* 4.9 0.2 - - - -
721C MET* 3.4 30.4 - - - +
724C PHE* 3.9 24.2 - - - -
725C ARG* 3.8 14.1 - - - +
728C GLU* 2.6 36.0 + - - -
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Residues in contact with GLN 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659C LEU 4.3 7.5 + - - +
660C ASP* 5.4 0.6 - - - -
663C LEU* 4.0 28.8 - - - +
666C GLU* 4.8 4.7 - - - +
670C LEU* 4.9 10.8 - - + -
688C MET* 4.3 16.4 - - + -
694C ARG* 3.1 34.1 + - + +
695C ILE 4.3 2.9 - - - +
696C LEU 3.4 0.4 - - - -
697C SER* 1.3 77.2 + - - +
699C VAL* 1.3 61.1 + - + +
701C TYR* 3.6 5.4 + - - +
702C THR* 2.7 33.4 + - - -
721C MET* 3.8 22.0 - - - +
725C ARG* 3.9 13.5 - - - +
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Residues in contact with VAL 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C LEU* 4.9 8.3 - - + -
674C MET* 3.4 33.4 - - + -
679C PHE* 5.6 0.2 - - + -
684C LEU* 4.3 21.1 - - + -
695C ILE 2.9 24.3 + - - +
696C LEU 3.9 3.6 - - - +
697C SER 3.3 0.4 - - - -
698C GLN* 1.3 78.7 - - + +
700C MET* 1.3 55.0 + - - +
702C THR* 3.0 5.8 + - - -
703C LEU* 2.7 38.5 + - + +
743C THR* 3.7 21.8 - - + +
746C LEU* 3.9 17.0 - - + -
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Residues in contact with MET 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696C LEU* 3.0 24.7 + - + +
697C SER* 3.7 7.0 - - - +
698C GLN 3.4 0.2 - - - -
699C VAL* 1.3 77.2 - - - +
701C TYR* 1.3 57.5 + - - +
703C LEU* 3.8 2.9 - - + +
704C PHE* 2.8 64.6 + - + +
720C PHE* 4.1 11.4 - - + -
724C PHE* 4.1 28.5 - - + -
746C LEU* 3.1 46.4 - - + -
815C TYR* 4.3 7.9 - - + +
816C VAL* 5.0 2.2 - - - -
819C ALA* 3.9 20.0 - - + -
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Residues in contact with TYR 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C LEU* 3.5 40.9 - - + +
667C TYR* 5.3 4.5 - + + -
697C SER 3.1 14.3 + - - +
698C GLN* 3.8 6.1 - - - +
700C MET* 1.3 81.0 - - - +
702C THR* 1.3 66.2 + - - +
704C PHE* 3.8 2.1 - - - +
705C GLN* 3.1 45.5 + - + +
710C LEU* 3.9 21.0 - - + +
717C THR* 4.0 28.7 + - + +
720C PHE* 3.7 14.5 - + - -
721C MET* 3.6 24.0 - - + -
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Residues in contact with THR 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C LEU* 5.0 5.7 - - - +
667C TYR* 3.4 32.8 - - + -
670C LEU* 3.5 41.5 - - + +
671C ILE* 4.0 18.4 - - + -
674C MET* 4.8 1.1 - - - -
698C GLN 2.7 18.6 + - - -
699C VAL 3.0 7.7 + - - -
701C TYR* 1.3 78.9 - - - +
703C LEU* 1.3 66.7 + - - +
704C PHE 3.0 1.3 - - - -
705C GLN 3.1 1.9 + - - -
706C ASP* 3.0 19.9 + - - +
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Residues in contact with LEU 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C ILE* 4.2 4.9 - - + -
674C MET* 4.0 21.8 - - + -
699C VAL* 2.7 31.5 + - + +
700C MET* 4.2 2.9 - - - +
702C THR* 1.3 74.1 - - - +
704C PHE* 1.3 63.9 + - + +
706C ASP* 3.8 3.4 - - - +
707C THR* 2.8 30.8 + - - +
709C LEU* 5.3 0.2 - - - +
746C LEU* 3.8 33.9 - - + +
747C HIS* 4.3 2.7 - - - -
750C TRP* 3.2 64.8 + - + -
815C TYR* 5.6 3.3 - - + -
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Residues in contact with PHE 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C MET* 2.8 50.1 + - + +
701C TYR 3.8 3.1 - - - +
702C THR 3.0 0.2 - - - -
703C LEU* 1.3 81.9 - - + +
705C GLN* 1.3 60.5 + - - +
707C THR* 3.2 12.4 + - - -
708C GLY* 3.2 0.5 + - - -
709C LEU* 3.2 35.9 + - + -
710C LEU* 3.6 21.6 + - + -
715C ILE* 3.7 24.7 - - + -
720C PHE* 3.3 32.1 - + + -
812C MET* 3.9 30.3 - - + -
815C TYR* 4.3 12.6 - + + -
816C VAL* 4.1 15.0 - - + -
870C PHE* 5.2 2.0 - + - -
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Residues in contact with GLN 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667C TYR* 3.2 29.9 + - + -
701C TYR* 3.1 33.5 + - + +
702C THR 3.1 2.5 + - - +
704C PHE* 1.3 74.6 - - - +
706C ASP* 1.3 64.0 - - - +
708C GLY* 3.1 8.8 + - - -
710C LEU* 3.7 24.9 - - + +
790C LYS* 2.9 38.1 + - - +
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Residues in contact with ASP 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667C TYR* 3.2 16.7 + - - +
671C ILE* 3.7 13.1 - - + +
702C THR 3.0 11.7 + - - +
703C LEU* 3.8 5.8 - - - +
704C PHE 3.5 0.2 - - - -
705C GLN* 1.3 81.0 - - - +
707C THR* 1.3 57.0 + - - +
750C TRP* 3.2 22.7 + - - -
788C SER 3.0 5.0 - - - +
789C SER* 2.7 22.8 + - - -
790C LYS* 3.0 35.9 + - - +
791C SER* 2.8 40.1 + - - -
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Residues in contact with THR 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703C LEU 2.8 19.3 + - - +
704C PHE 3.2 9.0 + - - -
706C ASP* 1.3 78.4 - - - +
708C GLY* 1.3 60.4 + - - +
709C LEU* 3.4 19.7 - - - +
712C ILE* 4.5 1.2 - - - +
750C TRP* 3.8 26.2 - - + +
754C THR* 4.7 4.3 - - + -
787C ILE* 3.5 36.0 - - + +
788C SER 3.5 26.0 + - - +
789C SER* 5.0 1.8 - - - -
790C LYS* 5.0 0.7 - - - -
815C TYR* 4.2 6.3 - - + +
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Residues in contact with GLY 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704C PHE 3.2 2.9 + - - -
705C GLN* 3.1 15.8 + - - -
707C THR* 1.3 78.9 - - - +
709C LEU* 1.3 63.8 + - - +
710C LEU* 3.1 3.6 - - - -
711C GLU* 3.1 12.1 + - - +
712C ILE* 3.0 28.9 + - - +
790C LYS* 4.7 8.7 - - - -
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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
------------------------------------------------------------
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