Contacts of the strand formed by residues 832 - 836 (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 MET 832 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PRO* 3.4 10.9 - - - +
824B ILE* 3.7 26.9 - - + +
825B THR* 4.4 10.1 - - + -
828B PHE* 3.8 8.7 - - - +
829B GLY* 3.6 36.3 + - - +
831B ARG* 1.3 81.2 - - - +
833B PHE* 1.3 61.5 + - - +
834B ILE* 3.7 22.9 - - + -
862B PRO* 3.6 13.6 - - + +
863B ALA* 3.1 22.2 + - - +
956B SER* 3.0 14.1 - - - +
958B TRP* 3.5 32.5 - - + +
960B PHE* 4.0 5.2 - - + -
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Residues in contact with PHE 833 (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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77A ALA* 4.3 11.2 - - + -
208A MET* 3.2 49.1 - - + -
209A ASN* 4.0 4.0 - - - -
210A PRO* 3.7 20.6 - - + -
832B MET* 1.3 78.4 - - - +
834B ILE* 1.3 65.6 + - - +
863B ALA* 3.4 7.6 - - + -
879B MET* 3.9 27.6 - - + -
883B MET* 4.0 24.0 - - + -
955B LYS* 3.7 26.5 - - + -
956B SER 3.0 5.7 + - - +
957B VAL* 4.0 25.4 - - + -
958B TRP* 2.9 26.9 + - - +
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Residues in contact with ILE 834 (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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208A MET* 4.2 3.1 - - - +
825B THR* 5.5 0.4 - - + -
832B MET* 3.7 23.6 - - + -
833B PHE* 1.3 80.3 - - - +
835B ALA* 1.3 64.5 + - - +
836B ASN* 3.9 7.4 - - - +
853B TYR* 3.6 31.4 - - + -
862B PRO* 3.7 18.6 - - + -
863B ALA 2.8 11.9 + - - +
864B TRP* 3.5 20.3 - - + +
865B GLY* 2.9 28.6 + - - +
879B MET* 4.6 3.8 - - - -
958B TRP* 3.3 4.5 - - + +
960B PHE* 3.7 40.2 - - + -
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Residues in contact with ALA 835 (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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833B PHE 4.2 0.2 - - - -
834B ILE* 1.3 70.4 - - - +
836B ASN* 1.3 59.1 + - - +
837B ALA 3.9 0.2 + - - -
865B GLY 3.6 4.3 - - - -
872B ALA* 3.6 11.0 - - - +
875B TYR* 3.7 17.3 - - + -
876B GLY* 3.5 37.9 - - - +
879B MET* 3.9 5.1 - - + -
958B TRP 2.9 10.6 + - - +
959B ILE* 3.3 6.9 - - + +
960B PHE 2.9 23.8 + - - +
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Residues in contact with ASN 836 (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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834B ILE* 3.8 2.2 - - + +
835B ALA* 1.3 72.8 - - - +
837B ALA* 1.4 82.8 + - - +
841B SER* 3.0 29.1 + - - -
842B SER 3.7 2.3 + - - -
853B TYR* 4.2 2.4 + - - -
864B TRP* 3.2 50.3 - - + +
865B GLY 2.8 12.1 + - - +
866B ASN* 2.9 26.7 - - + +
867B SER 4.2 2.8 + - - -
868B LEU 4.4 0.5 - - - +
872B ALA* 4.1 2.0 - - - +
875B TYR* 4.7 0.6 - - - -
960B PHE* 3.5 31.5 - - - +
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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