Contacts of the helix formed by residues 839 - 847 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837B ALA 3.4 1.9 + - - -
838B THR* 1.3 79.8 - - - +
840B CYS* 1.3 67.2 + - - -
841B SER* 3.1 4.0 - - - -
842B SER* 2.9 18.4 + - - -
843B ILE* 3.1 9.2 + - - +
996B ASN* 3.8 6.7 - - - -
3236B HTL 3.6 29.6 - - - -
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Residues in contact with CYS 840 (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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459B LYS* 3.4 19.5 - - - +
817B GLU* 3.4 13.7 - - - +
839B GLY* 1.3 69.4 - - - -
841B SER* 1.3 57.8 + - - +
843B ILE* 3.1 1.6 + - - -
844B TRP* 2.8 40.1 + - + -
995B SER* 3.9 0.4 - - - -
996B ASN* 3.4 36.6 - - - +
3235B SF4 2.3 37.9 - - - -
3236B HTL 2.7 20.7 + - - +
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Residues in contact with SER 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B GLU* 3.6 7.0 + - - -
836B ASN* 3.0 34.5 + - - -
837B ALA 4.1 3.6 + - - -
839B GLY* 4.8 1.6 - - - -
840B CYS* 1.3 80.4 - - - +
842B SER* 1.3 58.1 + - - +
844B TRP* 3.5 30.7 - - - -
845B GLY* 3.2 21.1 + - - -
864B TRP* 4.0 0.5 + - - -
960B PHE* 4.9 1.3 - - - -
961B GLY* 4.3 16.8 + - - -
962B GLY 4.8 1.2 + - - -
989B MET* 4.3 13.3 - - - -
3236B HTL 4.4 2.5 + - - -
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Residues in contact with SER 842 (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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217A GLY 5.6 1.0 - - - +
219A ALA* 5.2 2.4 + - - +
121B LEU* 5.8 0.2 - - - +
836B ASN* 3.7 1.3 + - - -
837B ALA 3.6 15.5 - - - -
838B THR* 3.3 14.6 - - - +
839B GLY 2.9 25.7 + - - +
841B SER* 1.3 81.1 + - - +
843B ILE* 1.3 64.7 + - - +
845B GLY 3.7 0.2 - - - -
846B ALA* 2.8 31.2 + - - +
864B TRP* 3.9 20.4 - - - -
866B ASN* 4.1 12.8 + - - -
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Residues in contact with ILE 843 (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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219A ALA* 4.0 26.0 - - + -
1200A THR* 5.4 0.4 - - - +
1202A MET* 4.5 16.2 - - + -
121B LEU* 5.1 2.2 - - + -
123B ILE* 6.0 0.2 - - + -
457B SER* 4.7 11.2 - - - +
459B LYS* 3.9 13.9 - - + -
838B THR* 5.4 0.2 - - + -
839B GLY 3.4 10.3 - - - +
840B CYS* 3.1 6.6 + - - +
842B SER* 1.3 82.2 - - - +
844B TRP* 1.3 64.1 + - - +
845B GLY 3.1 0.7 - - - -
847B SER* 2.6 38.0 + - - +
996B ASN* 3.4 34.1 - - - +
3236B HTL 3.8 22.2 - - + -
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Residues in contact with TRP 844 (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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459B LYS* 4.8 2.4 - - + +
806B MET* 3.9 20.2 - - + -
809B SER* 3.6 13.9 - - - +
810B GLY* 3.9 10.2 + - - +
811B ALA* 3.4 40.8 - - + +
815B CYS* 4.5 0.6 - - - -
817B GLU* 3.0 32.6 + - + +
818B THR* 3.6 21.6 - - + +
821B VAL* 3.6 34.5 - - + -
836B ASN* 5.7 0.4 - - - -
840B CYS 2.8 27.2 + - - -
841B SER* 3.5 23.8 - - - -
843B ILE* 1.3 75.1 - - - +
845B GLY* 1.3 85.8 + - - +
846B ALA 3.6 0.2 + - - -
847B SER 4.9 0.3 + - - -
850B SER 4.8 1.6 - - - +
852B PRO* 3.3 18.4 - - - +
853B TYR* 3.9 15.3 - - - -
960B PHE* 5.7 0.2 - + - -
989B MET* 4.3 0.2 - - + -
3235B SF4 3.9 13.0 - - - -
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Residues in contact with GLY 845 (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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215A VAL* 5.3 1.0 - - - +
841B SER 3.2 22.8 + - - -
843B ILE 3.1 0.8 - - - -
844B TRP* 1.3 92.0 - - - +
846B ALA* 1.3 63.1 + - - +
851B MET* 4.6 2.4 - - - +
852B PRO* 3.2 23.0 - - - +
853B TYR* 3.9 17.1 - - - -
864B TRP* 4.4 4.8 - - - -
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Residues in contact with ALA 846 (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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215A VAL* 3.8 17.9 - - + -
217A GLY 4.5 0.2 - - - +
218A THR* 3.2 11.3 - - - -
219A ALA* 2.9 21.7 + - - -
842B SER 2.8 12.7 + - - +
844B TRP 3.5 0.2 - - - -
845B GLY* 1.3 81.9 - - - +
847B SER* 1.3 63.3 + - - +
850B SER 4.3 1.3 - - - -
851B MET* 3.9 10.1 - - - -
864B TRP* 3.4 33.2 - - + -
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Residues in contact with SER 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA* 3.5 15.9 - - - +
457B SER* 3.8 30.5 + - - -
843B ILE* 2.6 40.0 + - - +
844B TRP 4.9 0.4 + - - -
846B ALA* 1.3 74.7 - - - +
848B ALA* 1.3 64.3 + - - +
849B PRO* 4.3 0.3 - - - +
850B SER* 3.0 27.1 + - - +
851B MET* 3.9 0.2 - - - -
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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