Contacts of the helix formed by residues 661 - 675 (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 LEU 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659A LEU 3.2 2.0 + - - -
660A ASP* 1.3 77.6 - - + +
662A ILE* 1.3 61.6 + - - +
663A LEU 3.3 2.5 - - - -
664A VAL* 3.8 11.5 + - - +
665A GLU* 3.6 30.3 + - - +
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Residues in contact with ILE 662 (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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659A LEU* 3.8 27.0 + - + +
660A ASP 3.4 0.6 - - - -
661A LEU* 1.3 75.2 - - - +
663A LEU* 1.3 62.9 + - - +
664A VAL 3.2 2.2 - - - -
665A GLU* 3.8 13.5 - - + +
666A GLU* 3.1 32.5 + - - +
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Residues in contact with LEU 663 (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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659A LEU 4.0 12.0 - - - +
660A ASP 3.9 13.7 + - - +
661A LEU 3.3 0.2 - - - -
662A ILE* 1.3 80.5 - - - +
664A VAL* 1.3 62.9 + - + +
666A GLU* 3.9 12.8 - - + +
667A TYR* 3.4 21.0 + - - +
701A TYR* 6.1 4.3 - - + +
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Residues in contact with VAL 664 (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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660A ASP 4.6 9.9 - - - +
661A LEU* 4.0 11.0 - - - +
662A ILE 3.2 0.6 - - - -
663A LEU* 1.3 79.3 - - + +
665A GLU* 1.3 58.8 + - + +
666A GLU 3.2 1.6 - - - -
667A TYR* 3.2 6.5 + - + +
668A ASP* 2.7 61.7 + - - +
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Residues in contact with GLU 665 (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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661A LEU* 3.6 23.4 + - - +
662A ILE* 3.5 13.2 + - + +
664A VAL* 1.3 78.3 - - + +
666A GLU* 1.3 62.2 + - - +
668A ASP* 4.3 4.1 - - - +
669A SER* 3.2 27.4 + - - -
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Residues in contact with GLU 666 (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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659A LEU 5.6 2.1 + - - -
662A ILE* 3.1 24.4 + - - +
663A LEU* 3.9 14.1 - - + +
664A VAL 3.2 0.2 - - - -
665A GLU* 1.3 77.8 - - - +
667A TYR* 1.3 61.8 + - - +
669A SER* 4.0 3.2 - - - -
670A LEU* 3.2 25.3 + - - +
673A LYS* 4.9 0.9 + - - -
691A LYS* 5.2 7.1 + - - -
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Residues in contact with TYR 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LEU 3.4 12.3 + - - +
664A VAL* 3.2 10.4 + - + +
666A GLU* 1.3 80.7 - - - +
668A ASP* 1.3 79.8 + - - +
669A SER 3.1 0.3 + - - -
670A LEU* 3.8 3.4 - - - +
671A ILE* 3.0 43.2 + - + +
701A TYR* 5.3 8.3 - + - -
702A THR* 3.4 43.1 - - + -
705A GLN* 3.7 19.5 + - + +
706A ASP* 3.3 33.1 + - - +
790A LYS* 5.1 5.4 + - - +
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Residues in contact with ASP 668 (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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664A VAL* 2.7 49.1 + - - +
665A GLU* 4.3 4.5 - - - +
667A TYR* 1.3 87.7 - - - +
669A SER* 1.3 56.3 + - - +
671A ILE* 3.7 6.8 + - - +
672A GLU* 3.1 25.5 + - - +
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Residues in contact with SER 669 (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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665A GLU 3.2 19.7 + - - -
666A GLU* 4.0 3.8 - - - -
667A TYR 3.2 0.8 - - - -
668A ASP* 1.3 75.4 - - - +
670A LEU* 1.3 61.1 + - - +
672A GLU* 2.8 32.8 + - - +
673A LYS* 2.9 39.2 + - - +
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Residues in contact with LEU 670 (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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666A GLU 3.2 15.5 + - - +
667A TYR* 3.8 3.1 - - - +
669A SER* 1.3 77.4 - - - +
671A ILE* 1.3 57.6 + - - +
673A LYS* 3.2 13.3 + - + +
674A MET* 2.8 64.3 + - + +
679A PHE* 4.1 6.5 - - + -
684A LEU* 3.9 36.3 - - + -
698A GLN* 4.8 6.3 - - + +
699A VAL* 4.6 14.1 - - + +
702A THR* 3.4 25.4 - - + +
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Residues in contact with ILE 671 (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* 3.0 42.8 + - + +
668A ASP* 3.8 9.0 - - - +
670A LEU* 1.3 75.8 - - - +
672A GLU* 1.3 62.8 + - - +
674A MET* 3.9 9.6 - - + +
675A SER* 2.8 30.7 + - - +
702A THR* 3.6 20.9 - - + -
703A LEU* 4.8 3.6 - - + -
706A ASP* 3.9 29.6 - - + +
750A TRP* 5.0 4.3 - - + -
791A SER* 3.6 25.6 - - - +
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Residues in contact with GLU 672 (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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668A ASP 3.1 15.2 + - - +
669A SER* 2.8 24.3 + - - +
671A ILE* 1.3 80.8 - - - +
673A LYS* 1.3 76.5 + - - +
675A SER* 3.3 18.6 + - - -
676A ASN* 3.7 10.0 + - - -
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Residues in contact with LYS 673 (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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666A GLU 4.9 0.6 + - - -
669A SER* 2.9 36.6 + - - +
670A LEU* 3.2 34.4 - - + +
672A GLU* 1.3 91.9 - - - +
674A MET* 1.3 61.4 + - - +
676A ASN* 3.3 24.5 + - - +
679A PHE* 3.4 28.4 - - + -
680A PRO* 3.9 16.9 - - + +
684A LEU* 5.0 13.2 - - + +
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Residues in contact with MET 674 (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* 2.8 55.1 + - + +
671A ILE* 4.1 6.5 - - + +
673A LYS* 1.3 71.7 - - - +
675A SER* 1.3 57.9 + - - +
676A ASN 2.8 12.6 + - - +
679A PHE* 3.7 26.2 - - + -
699A VAL* 3.9 22.7 - - + -
702A THR* 3.6 25.8 - - + -
703A LEU* 3.8 21.8 - - + -
747A HIS* 2.9 36.9 + - + -
750A TRP* 3.6 14.9 - - + -
751A TYR* 4.2 0.7 - - - -
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Residues in contact with SER 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ILE* 2.8 19.9 + - - +
672A GLU* 3.5 13.7 - - - -
673A LYS 3.2 1.2 - - - -
674A MET* 1.3 75.2 - - - +
676A ASN* 1.3 60.0 + - - +
677A TRP 4.0 0.2 + - - -
750A TRP* 4.6 1.2 - - - -
751A TYR* 3.5 16.1 + - - -
755A ARG* 3.9 26.6 + - - +
791A SER* 3.9 17.3 + - - -
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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