Contacts of the helix formed by residues 770 - 782 (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 GLN 770 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681B VAL* 3.8 29.6 - - + -
682B PRO 4.5 2.3 - - - +
683B GLN* 2.8 51.5 + - - +
742B THR* 4.0 9.4 - - + -
765B GLN* 3.8 10.8 - - + +
766B PRO 3.9 3.8 - - - +
767B LEU 2.8 5.7 + - - +
769B THR* 1.3 112.3 + - - +
771B ARG* 1.3 61.0 + - - +
772B ASP 3.4 2.9 - - - -
773B ALA* 3.4 6.9 + - - +
774B GLN* 2.9 43.0 + - + +
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Residues in contact with ARG 771 (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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676B GLY* 5.1 4.4 + - - -
742B THR* 3.8 18.8 - - - +
743B LEU* 3.7 23.2 - - + +
767B LEU* 3.1 42.2 + - + +
768B ASP* 4.2 17.5 - - - +
770B GLN* 1.3 74.5 - - - +
772B ASP* 1.3 78.4 + - - +
775B VAL* 3.0 35.9 + - + +
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Residues in contact with ASP 772 (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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768B ASP 4.9 7.1 + - - +
769B THR 5.4 0.6 - - - -
770B GLN 3.4 1.4 - - - +
771B ARG* 1.3 87.5 + - - +
773B ALA* 1.3 57.6 + - - +
776B PRO* 3.2 24.3 - - - +
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Residues in contact with ALA 773 (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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720B ASN* 3.5 24.7 + - - +
769B THR 5.8 1.3 - - - +
770B GLN* 3.4 6.9 + - - +
772B ASP* 1.3 78.6 - - - +
774B GLN* 1.3 79.0 + - - +
776B PRO* 3.4 5.2 - - - +
777B ASN* 3.2 25.8 + - - +
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Residues in contact with GLN 774 (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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682B PRO 6.1 0.7 - - - +
683B GLN* 6.1 0.5 - - - +
720B ASN* 5.4 1.4 - - - +
737B ARG* 3.1 16.4 + - - +
739B GLN* 2.9 28.9 + - - +
740B ILE* 4.0 8.4 - - + +
742B THR* 3.6 27.8 - - + +
770B GLN* 2.9 36.4 + - + +
773B ALA* 1.3 87.6 - - + +
775B VAL* 1.3 58.1 + - - +
777B ASN* 3.1 22.6 + - - +
778B LEU* 2.8 32.6 + - - +
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Residues in contact with VAL 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B THR* 3.9 9.2 - - - +
743B LEU* 3.7 43.1 - - + -
771B ARG* 3.0 22.8 + - + +
774B GLN* 1.3 72.5 - - - +
776B PRO* 1.3 75.9 - - + +
777B ASN 3.2 0.2 + - - -
778B LEU* 3.2 4.5 + - - +
779B GLU* 2.9 42.5 + - + +
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Residues in contact with PRO 776 (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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718B PRO* 4.5 8.8 - - + +
772B ASP 3.2 25.1 - - - +
773B ALA* 3.4 8.3 - - - +
775B VAL* 1.3 98.5 - - + +
777B ASN* 1.3 61.7 + - - +
779B GLU* 3.3 10.5 + - + +
780B TYR* 3.0 23.0 + - - +
783B ARG* 4.4 0.7 + - - -
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Residues in contact with ASN 777 (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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718B PRO* 3.2 29.4 - - - +
720B ASN* 3.2 30.3 + - - +
721B PHE* 3.3 25.1 - - + +
737B ARG* 3.6 6.9 + - - -
739B GLN* 3.2 19.7 - - - +
773B ALA 3.2 11.3 + - - +
774B GLN* 3.1 28.2 + - - +
776B PRO* 1.3 79.0 - - - +
778B LEU* 1.3 56.8 + - - +
780B TYR* 3.3 0.9 + - - +
781B ALA* 2.9 24.4 + - - +
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Residues in contact with LEU 778 (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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674B LYS* 4.6 12.6 - - - +
705B LEU* 4.3 21.5 - - + -
739B GLN* 3.8 24.0 - - + -
740B ILE 4.3 2.9 - - - +
741B ASN* 3.8 46.4 - - + +
742B THR 5.7 0.4 - - - +
774B GLN 2.8 16.2 + - - +
775B VAL* 3.7 5.4 - - - +
777B ASN* 1.3 73.7 - - - +
779B GLU* 1.3 80.5 + - - +
781B ALA* 3.7 0.9 - - - +
782B ALA* 2.8 34.3 + - + +
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Residues in contact with GLU 779 (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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674B LYS* 5.2 9.1 - - - -
775B VAL* 2.9 40.5 + - + +
776B PRO* 3.4 13.0 - - + +
777B ASN 3.3 0.2 - - - -
778B LEU* 1.3 92.1 - - - +
780B TYR* 1.3 60.8 + - - +
782B ALA* 3.5 11.4 + - - +
783B ARG* 2.7 34.9 + - - +
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Residues in contact with TYR 780 (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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713B GLU 2.7 27.7 + - - -
714B LEU* 3.5 8.2 - - - -
716B GLY* 3.6 13.3 + - - -
717B ALA* 3.3 41.3 + - + -
718B PRO* 3.8 17.9 - - + -
721B PHE* 4.0 18.4 - + + -
776B PRO 3.0 14.5 + - - +
777B ASN 3.7 3.6 - - - +
779B GLU* 1.3 75.2 - - - +
781B ALA* 1.3 59.0 + - - +
783B ARG* 2.8 55.9 + - + +
784B ILE* 3.6 17.3 + - + +
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Residues in contact with ALA 781 (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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705B LEU* 3.7 17.3 - - + +
707B VAL* 3.7 26.1 - - + +
721B PHE* 3.9 5.4 - - + -
739B GLN* 3.9 13.0 - - + -
777B ASN 2.9 17.4 + - - +
778B LEU 3.2 4.2 + - - +
780B TYR* 1.3 76.7 - - - +
782B ALA* 1.3 62.6 + - - +
784B ILE* 3.1 34.6 + - - +
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Residues in contact with ALA 782 (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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705B LEU* 4.0 11.6 - - + +
778B LEU* 2.8 24.8 + - + +
779B GLU* 3.7 9.0 - - - +
780B TYR 3.1 0.4 - - - -
781B ALA* 1.3 78.4 - - - +
783B ARG* 1.3 57.9 + - + +
784B ILE 3.3 4.3 + - - +
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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