Contacts of the helix formed by residues 663 - 675 (chain B) 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 663 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660B ASP* 3.4 42.8 - - + +
661B LEU 2.8 4.9 + - - +
662B ILE* 1.3 80.6 - - - +
664B VAL* 1.3 70.4 + - + +
665B GLU 3.2 3.7 - - - +
666B GLU* 3.2 27.9 + - - +
667B TYR* 3.2 20.0 + - - +
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Residues in contact with VAL 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B ASP 5.8 2.2 - - - +
661B LEU* 3.7 8.8 + - - +
663B LEU* 1.3 76.7 - - + +
665B GLU* 1.3 64.5 + - - +
667B TYR* 4.1 10.1 - - + -
668B ASP* 2.6 62.2 + - - +
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Residues in contact with GLU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B LEU 4.5 3.8 + - - +
662B ILE* 4.7 13.2 - - - +
663B LEU 3.2 5.5 - - - +
664B VAL* 1.3 77.7 - - - +
666B GLU* 1.3 69.4 + - + +
668B ASP* 4.0 4.6 - - - +
669B SER* 3.1 21.2 + - - -
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Residues in contact with GLU 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B ILE* 3.9 10.1 - - + +
663B LEU* 3.2 38.0 - - - +
665B GLU* 1.3 77.3 - - + +
667B TYR* 1.3 56.4 + - - +
669B SER* 2.7 35.2 + - - -
670B LEU* 3.0 10.7 + - - +
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Residues in contact with TYR 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B LEU 3.2 8.5 + - - +
664B VAL* 3.4 15.7 + - + +
666B GLU* 1.3 78.7 - - - +
668B ASP* 1.3 80.4 + - - +
670B LEU* 3.4 4.7 + - - +
671B ILE* 3.0 42.0 + - + +
701B TYR* 5.9 4.7 - + - -
702B THR* 3.6 31.6 - - + +
705B GLN* 3.5 32.7 + - + +
706B ASP* 3.2 31.5 + - - +
790B LYS* 4.8 7.5 + - + +
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Residues in contact with ASP 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B VAL* 2.6 42.0 + - - +
665B GLU* 4.1 4.2 - - - +
667B TYR* 1.3 89.6 - - - +
669B SER* 1.3 65.0 + - - +
671B ILE* 4.0 5.6 - - - +
672B GLU* 3.2 20.6 + - - +
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Residues in contact with SER 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B GLU 3.1 13.6 + - - -
666B GLU* 2.7 20.4 + - - -
668B ASP* 1.3 68.8 - - - +
670B LEU* 1.3 57.9 - - - -
672B GLU* 2.8 40.3 + - - +
673B LYS* 3.0 28.4 + - - -
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Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B GLU 3.0 10.2 + - - +
667B TYR* 3.9 3.8 - - - +
669B SER* 1.3 79.7 - - - +
671B ILE* 1.3 57.8 + - - +
673B LYS* 3.1 15.4 + - - +
674B MET* 2.8 60.9 + - + +
679B PHE* 4.1 8.1 - - + -
684B LEU* 4.0 33.4 - - + -
698B GLN* 5.0 4.5 - - + +
699B VAL* 4.7 11.2 - - + +
702B THR* 3.6 30.3 - - + +
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Residues in contact with ILE 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B TYR* 3.0 38.9 + - + +
668B ASP* 4.0 6.7 - - - +
670B LEU* 1.3 76.4 - - - +
672B GLU* 1.3 58.1 + - - +
674B MET* 3.8 4.4 - - - +
675B SER* 2.7 35.3 + - - +
702B THR* 3.4 28.0 - - + +
703B LEU* 4.8 8.1 - - + -
706B ASP* 3.8 30.5 - - + +
750B TRP* 5.0 4.1 - - + -
791B SER* 3.5 27.3 + - - +
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Residues in contact with GLU 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B ASP 3.2 12.9 + - - +
669B SER* 2.8 22.3 + - - +
671B ILE* 1.3 84.5 - - - +
673B LYS* 1.3 73.7 + - - +
675B SER* 3.5 15.8 + - - -
676B ASN* 4.4 3.1 + - - +
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Residues in contact with LYS 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669B SER* 3.0 32.8 + - - -
670B LEU* 3.1 34.0 + - - +
672B GLU* 1.3 88.2 - - - +
674B MET* 1.3 62.9 + - - +
676B ASN* 3.4 19.2 + - - +
679B PHE* 3.7 26.4 - - + -
680B PRO* 4.0 20.5 - - + +
683B GLU* 5.5 4.7 - - + +
684B LEU* 5.8 7.0 - - + +
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Residues in contact with MET 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670B LEU* 2.8 47.1 + - + +
671B ILE* 4.0 5.2 - - - +
673B LYS* 1.3 68.9 - - - +
675B SER* 1.3 53.2 + - - +
676B ASN 2.7 16.5 + - - +
679B PHE* 3.7 34.8 - - + -
699B VAL* 3.2 39.5 - - + -
702B THR* 4.7 5.6 - - - -
703B LEU* 4.1 21.3 - - + -
743B THR* 5.2 0.2 - - + -
747B HIS* 2.9 41.3 + - + -
750B TRP* 3.5 15.5 - - + -
751B TYR* 4.0 1.4 - - - -
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Residues in contact with SER 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671B ILE* 2.7 22.6 + - - +
672B GLU* 3.6 11.5 - - - -
673B LYS 3.2 1.2 - - - -
674B MET* 1.3 75.4 - - - +
676B ASN* 1.3 56.7 + - - +
750B TRP* 4.4 0.4 - - - -
751B TYR* 3.5 17.2 + - - -
755B ARG* 3.5 27.8 + - - +
791B SER* 3.8 19.4 + - - -
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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