Contacts of the helix formed by residues 662 - 675 (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 ILE 662 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660C ASP 3.6 0.4 + - - -
661C LEU* 1.3 74.2 - - + +
663C LEU* 1.3 54.5 + - - +
664C VAL* 2.8 16.7 + - - +
665C GLU* 2.9 38.8 + - - +
666C GLU* 3.1 13.9 + - + +
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Residues in contact with LEU 663 (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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659C LEU 5.2 0.2 - - - +
660C ASP* 2.9 41.8 + - + +
661C LEU 2.9 2.8 + - - -
662C ILE* 1.3 76.0 - - - +
664C VAL* 1.3 62.2 + - - +
665C GLU 3.2 0.2 - - - -
666C GLU* 3.0 31.2 - - + +
667C TYR* 2.9 36.6 + - + +
670C LEU* 5.7 2.7 - - + -
698C GLN* 4.0 17.3 - - - +
701C TYR* 3.5 41.3 - - + +
702C THR* 5.0 6.3 - - - +
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Residues in contact with VAL 664 (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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662C ILE* 2.8 5.1 + - - +
663C LEU* 1.3 82.9 - - - +
665C GLU* 1.3 64.2 + - + +
667C TYR* 3.8 2.4 - - - +
668C ASP* 3.0 32.4 + - - +
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Residues in contact with GLU 665 (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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662C ILE* 2.9 30.8 + - - +
664C VAL* 1.3 83.5 - - + +
666C GLU* 1.3 69.8 + - + +
668C ASP* 3.1 15.4 + - - +
669C SER* 3.2 13.6 + - - -
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Residues in contact with GLU 666 (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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660C ASP* 4.2 3.8 - - - +
661C LEU 3.2 15.5 - - - +
662C ILE* 3.1 12.5 + - + +
663C LEU* 3.0 43.5 - - + +
665C GLU* 1.3 78.3 - - + +
667C TYR* 1.3 55.7 + - - +
669C SER* 3.1 5.2 + - - -
670C LEU* 2.7 43.3 + - + +
698C GLN* 4.8 5.0 - - - +
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Residues in contact with TYR 667 (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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663C LEU* 2.9 26.3 + - + +
664C VAL* 3.8 4.5 - - - +
666C GLU* 1.3 77.0 - - - +
668C ASP* 1.3 70.3 + - - +
670C LEU* 4.0 5.6 - - - +
671C ILE* 3.0 47.9 + - + +
701C TYR* 5.3 4.7 - + + -
702C THR* 3.4 34.1 - - + -
705C GLN* 3.2 36.9 + - + -
706C ASP* 3.2 32.5 + - + +
790C LYS* 4.5 9.9 - - + +
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Residues in contact with ASP 668 (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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664C VAL* 3.0 20.9 + - - +
665C GLU* 3.1 10.3 + - - +
667C TYR* 1.3 88.6 - - - +
669C SER* 1.3 63.4 + - - +
671C ILE* 3.3 9.1 - - - +
672C GLU* 3.1 22.9 + - - +
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Residues in contact with SER 669 (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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665C GLU 3.2 7.4 + - - -
666C GLU* 3.1 8.6 + - - -
668C ASP* 1.3 78.8 - - - +
670C LEU* 1.3 65.6 + - - +
672C GLU* 3.3 7.7 + - - +
673C LYS* 3.1 51.8 + - - +
687C LYS* 4.4 5.7 + - - -
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Residues in contact with LEU 670 (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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663C LEU* 5.7 2.2 - - + -
666C GLU* 2.7 29.9 + - + +
667C TYR* 4.0 3.6 - - - +
669C SER* 1.3 74.3 + - - +
671C ILE* 1.3 65.9 + - - +
673C LYS* 3.0 12.4 + - + +
674C MET* 2.9 65.5 + - + +
679C PHE* 5.7 2.0 - - + -
684C LEU* 5.0 20.4 - - + -
698C GLN* 4.6 15.9 - - + +
699C VAL* 4.9 9.2 - - + -
702C THR* 3.5 33.0 - - + +
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Residues in contact with ILE 671 (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* 3.0 38.7 + - + +
668C ASP* 3.3 11.9 - - - +
670C LEU* 1.3 78.3 - - - +
672C GLU* 1.3 57.0 + - - +
674C MET* 3.4 3.8 + - - -
675C SER* 2.6 38.4 + - - +
702C THR* 4.0 18.2 - - + -
703C LEU* 4.2 8.1 - - + -
706C ASP* 3.7 32.5 - - + +
750C TRP* 4.1 14.8 - - + -
791C SER* 3.8 23.6 - - - -
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Residues in contact with GLU 672 (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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668C ASP 3.1 14.5 + - - +
669C SER* 3.4 8.9 - - - +
670C LEU 3.0 0.6 - - - -
671C ILE* 1.3 84.4 - - + +
673C LYS* 1.3 70.9 + - - +
675C SER* 3.1 21.0 + - - -
676C ASN* 4.1 2.9 + - - +
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Residues in contact with LYS 673 (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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669C SER* 3.1 35.4 + - - +
670C LEU* 3.0 9.9 + - - +
672C GLU* 1.3 84.9 + - - +
674C MET* 1.3 62.2 + - - +
676C ASN* 3.4 18.0 + - - +
679C PHE* 3.5 31.0 - - + +
680C PRO* 4.1 15.7 - - + +
684C LEU* 5.4 15.1 - - + +
687C LYS* 3.3 31.3 - - - +
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Residues in contact with MET 674 (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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670C LEU* 2.9 47.5 + - + +
671C ILE* 3.9 5.8 - - - +
673C LYS* 1.3 72.0 - - - +
675C SER* 1.3 59.4 + - - +
676C ASN 2.8 12.5 + - - +
679C PHE* 3.7 32.1 - - + -
699C VAL* 3.4 29.8 - - + -
702C THR* 4.8 1.6 - - - -
703C LEU* 4.0 20.2 - - + -
743C THR* 5.6 0.2 - - + -
747C HIS* 2.8 52.4 + - + -
750C TRP* 3.5 14.5 - - + -
751C TYR* 4.2 0.7 - - - -
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Residues in contact with SER 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C ILE* 2.6 21.4 + - - +
672C GLU* 3.1 15.5 + - - -
674C MET* 1.3 76.3 - - - +
676C ASN* 1.3 56.4 + - - +
750C TRP* 4.6 1.7 - - - -
751C TYR* 3.5 16.4 + - - -
755C ARG* 4.2 18.4 + - - +
791C SER* 3.7 25.2 + - - -
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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