Contacts of the helix formed by residues 839 - 847 (chain A) in PDB entry 1KEK
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 GLY 839 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837A ALA 3.4 1.6 + - - -
838A THR* 1.3 78.9 - - - +
840A CYS* 1.3 68.3 + - - -
841A SER* 2.9 5.8 + - - -
842A SER* 2.9 11.4 + - - -
843A ILE* 3.1 14.0 + - - +
962A GLY 6.1 0.9 - - - -
996A ASN* 3.9 6.3 - - - -
2236A HTL 3.7 30.5 - - - -
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Residues in contact with CYS 840 (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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459A LYS* 3.2 21.9 - - - +
817A GLU* 3.5 14.4 - - - +
839A GLY* 1.3 69.5 - - - -
841A SER* 1.3 55.6 - - - +
843A ILE* 3.0 3.3 + - - +
844A TRP* 2.7 42.2 + - + -
995A SER* 3.9 0.4 - - - -
996A ASN* 3.4 31.1 - - - +
2235A SF4 2.3 37.9 - - - -
2236A HTL 2.8 20.6 + - - +
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Residues in contact with SER 841 (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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817A GLU* 3.7 0.6 + - - -
836A ASN* 2.6 31.6 + - - +
837A ALA 4.0 3.8 + - - -
839A GLY* 3.0 2.8 - - - -
840A CYS* 1.3 80.2 - - - +
842A SER* 1.3 56.3 + - - +
844A TRP* 3.5 22.6 - - - -
845A GLY* 2.9 25.5 + - - -
864A TRP* 4.2 3.3 + - - -
960A PHE* 4.9 1.3 - - - -
961A GLY* 4.3 9.9 + - - -
962A GLY 4.9 0.9 + - - -
989A MET* 3.2 33.4 - - - +
2236A HTL 4.4 1.7 + - - -
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Residues in contact with SER 842 (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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836A ASN* 3.6 2.0 + - - -
837A ALA 3.7 14.4 - - - -
838A THR* 3.3 16.0 - - - +
839A GLY 2.9 22.2 + - - -
841A SER* 1.3 79.8 + - - +
843A ILE* 1.3 68.7 + - - +
845A GLY 3.7 0.7 - - - -
846A ALA* 2.9 28.1 + - - +
864A TRP* 3.9 21.0 - - - -
866A ASN* 4.2 12.2 + - - -
217B GLY 5.6 0.6 - - - +
219B ALA* 5.3 2.1 - - - +
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Residues in contact with ILE 843 (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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121A LEU* 5.0 2.7 - - + -
457A SER* 4.7 10.6 - - - +
459A LYS* 3.9 13.9 - - + -
838A THR* 5.1 0.2 - - + -
839A GLY 3.3 13.0 - - - +
840A CYS* 3.0 6.4 + - - +
842A SER* 1.3 83.6 - - - +
844A TRP* 1.3 65.2 + - - +
847A SER* 2.6 37.4 + - - +
996A ASN* 3.5 30.3 - - - +
2236A HTL 3.9 22.0 - - + -
219B ALA* 4.2 22.7 - - + -
1202B MET* 4.3 19.1 - - + -
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Residues in contact with TRP 844 (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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459A LYS* 4.9 2.7 - - + +
806A MET* 3.8 21.8 - - + -
809A SER* 3.5 18.9 - - - +
810A GLY* 3.9 10.7 + - - +
811A ALA* 3.4 42.4 - - + +
815A CYS* 4.5 0.4 - - - -
817A GLU* 2.9 34.4 + - + +
818A THR* 3.7 15.1 - - + +
821A VAL* 3.4 28.0 - - + -
836A ASN* 5.8 0.2 - - - -
840A CYS 2.7 27.1 + - - -
841A SER* 3.5 26.1 - - - +
843A ILE* 1.3 74.9 - - - +
845A GLY* 1.3 86.1 + - - +
846A ALA* 3.7 0.5 + - - -
847A SER 4.9 0.5 + - - -
850A SER 4.9 0.9 - - - +
852A PRO* 3.3 18.2 - - - +
853A TYR* 3.9 17.3 - - - -
960A PHE* 5.8 0.4 - + - -
989A MET* 4.5 2.7 - - + -
2235A SF4 3.9 12.8 - - - -
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Residues in contact with GLY 845 (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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841A SER 2.9 23.5 + - - -
842A SER 3.8 0.2 - - - -
844A TRP* 1.3 94.1 - - - +
846A ALA* 1.3 62.7 + - - +
851A MET* 4.7 1.4 - - - +
852A PRO* 3.2 23.0 - - - +
853A TYR* 4.0 16.6 - - - -
864A TRP* 4.4 5.8 - - - -
215B VAL* 5.3 0.7 - - - +
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Residues in contact with ALA 846 (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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842A SER 2.9 15.9 + - - +
845A GLY* 1.3 78.4 - - - +
847A SER* 1.4 63.8 + - - +
850A SER 4.3 1.1 - - - -
851A MET* 3.7 10.3 - - - -
864A TRP* 3.5 31.2 - - + -
215B VAL* 3.8 19.5 - - + -
217B GLY 4.6 0.2 - - - +
218B THR* 3.2 10.4 - - - -
219B ALA 2.9 21.8 + - - -
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Residues in contact with SER 847 (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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457A SER* 3.9 29.4 + - - -
843A ILE* 2.6 39.9 + - - +
844A TRP 4.9 0.6 + - - -
846A ALA* 1.4 74.4 - - - +
848A ALA* 1.4 65.5 + - - +
850A SER* 3.0 26.7 + - - +
851A MET* 3.8 0.4 - - - -
219B ALA* 3.6 16.0 - - - +
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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