Contacts of the helix formed by residues 746 - 751 (chain B) in PDB entry 5KJH
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 CYS 746 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B CYS* 3.9 8.3 - - - -
729B CYS* 3.5 23.8 - - - -
736B CYS* 3.7 35.9 - - - -
737B LEU 4.6 1.0 + - - +
740B GLN* 3.8 9.4 + - + +
745B PRO* 1.3 70.1 - - - +
747B ILE* 1.4 66.2 + - - +
748B CYS* 3.7 23.3 - - - -
749B VAL* 3.0 22.2 + - + +
750B GLN* 3.0 24.0 + - - +
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Residues in contact with ILE 747 (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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656B TYR* 3.5 38.4 - - + -
661B LYS* 3.6 13.9 + - - +
662B GLN* 3.8 16.4 - - - +
663B LEU* 3.7 26.7 - - + +
724B PHE* 4.2 10.3 - - + -
726B GLY 3.6 25.6 - - - +
727B CYS* 3.7 14.2 - - - +
745B PRO 3.5 6.4 + - - +
746B CYS* 1.4 68.8 - - - +
748B CYS* 1.4 54.3 + - - +
750B GLN* 3.2 13.6 + - - +
751B LEU* 2.8 50.0 + - + +
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Residues in contact with CYS 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B PHE* 3.7 21.8 - - - -
727B CYS* 3.7 14.4 - - - -
746B CYS* 3.2 7.2 - - - -
747B ILE* 1.4 73.5 - - - +
749B VAL* 1.4 59.4 + - - +
751B LEU 3.2 6.2 + - - -
753B ARG* 3.0 47.4 + - + +
754B GLU 4.6 0.9 - - - +
755B CYS* 3.9 7.6 - - - -
756B ASP 5.2 0.2 - - - -
760B CYS* 3.6 31.2 - - - -
786B ASN* 3.6 17.9 - - - +
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Residues in contact with VAL 749 (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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736B CYS 3.5 33.7 - - - +
737B LEU 3.9 6.3 - - - +
738B GLN* 3.3 51.6 - - + +
746B CYS* 3.0 17.5 + - + +
748B CYS* 1.4 74.3 - - - +
750B GLN* 1.3 63.0 + - + +
752B ASN* 3.2 20.8 + - - +
753B ARG 4.4 2.9 - - - +
786B ASN* 3.8 18.8 - - - +
890B LYS* 4.7 1.0 + - - -
892B MET* 6.0 1.7 - - - +
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Residues in contact with GLN 750 (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 GLN* 5.8 0.9 - - - +
663B LEU* 3.9 28.7 + - + +
667B TRP* 3.5 41.3 - - + +
674B HIS* 3.8 7.3 - - - +
745B PRO* 4.0 31.2 - - + +
746B CYS 3.0 12.6 + - - +
747B ILE* 3.2 24.0 + - - +
749B VAL* 1.3 78.2 - - + +
751B LEU* 1.3 58.8 + - - +
752B ASN* 3.3 6.0 + - - +
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Residues in contact with LEU 751 (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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655B TRP* 6.2 0.4 - - + -
663B LEU* 3.9 24.9 - - + -
667B TRP* 4.3 6.7 - - + -
671B THR* 5.2 2.0 - - + -
673B THR* 4.0 24.5 - - + +
674B HIS* 3.3 28.3 - - + +
676B HIS* 3.9 4.9 - - - -
708B LEU* 3.8 27.6 - - + -
724B PHE* 4.1 6.5 - - + -
747B ILE* 2.8 32.6 + - + +
748B CYS 3.2 0.8 + - - -
750B GLN* 1.3 74.8 - - - +
752B ASN* 1.4 68.8 + - - +
753B ARG* 3.4 33.8 + - - +
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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