Contacts of the helix formed by residues 685 - 693 (chain F) in PDB entry 1KKQ
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 LEU 685 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 4.0 23.6 - - + -
310B LYS* 4.4 20.4 - - + +
313B VAL* 3.9 24.5 - - + -
314B TYR* 4.5 18.8 - - + +
776B 471 4.0 25.4 - - + +
683F MET 3.0 23.8 + - - +
684F GLY* 1.3 74.2 - - - +
686F GLU* 1.3 55.6 - - - +
687F ALA* 2.7 20.3 + - - -
688F ILE* 2.9 21.4 + - + +
689F ILE* 3.5 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 686 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 4.0 19.7 - - + +
310B LYS* 3.7 36.1 + - + +
684F GLY* 3.7 2.8 - - - -
685F LEU* 1.3 78.6 - - - +
687F ALA* 1.3 57.3 + - + +
688F ILE 3.4 0.4 - - - -
689F ILE* 3.9 11.9 - - - +
690F ARG* 2.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 687 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685F LEU* 2.7 6.3 + - - +
686F GLU* 1.3 77.5 - - + +
688F ILE* 1.3 72.3 + - + +
689F ILE 3.5 0.2 - - - -
690F ARG* 3.9 5.8 + - - +
691F LYS* 3.7 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 688 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 4.0 30.1 - - + -
284B VAL* 4.2 19.3 - - + -
285B THR* 4.5 9.1 + - - +
460B LEU* 6.1 4.3 - - + -
464B TYR* 6.1 6.5 - - + -
776B 471 4.9 14.6 - - + -
685F LEU* 2.9 14.2 + - + +
687F ALA* 1.3 84.3 - - + +
689F ILE* 1.3 64.4 + - - +
691F LYS* 3.3 7.3 + - - +
692F ALA* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 689 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 4.2 15.9 - - + -
288B THR* 3.9 14.3 - - - +
306B VAL* 3.3 42.6 - - + +
309B LEU* 3.4 25.8 - - + -
310B LYS* 3.9 8.3 - - + +
313B VAL* 6.1 1.8 - - + -
685F LEU* 3.5 24.9 - - + +
686F GLU* 3.9 8.7 - - - +
688F ILE* 1.3 70.3 - - - +
690F ARG* 1.3 60.7 + - - +
691F LYS 3.0 4.5 - - - -
692F ALA* 2.8 11.1 + - - +
693F LEU* 2.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 690 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 5.0 9.7 - - + +
303B ASN* 3.5 28.9 + - - +
306B VAL* 3.9 28.1 - - + +
686F GLU* 2.3 53.5 + - - +
687F ALA* 4.0 8.5 - - - +
688F ILE 3.3 0.6 - - - -
689F ILE* 1.3 84.6 - - - +
691F LYS* 1.3 52.0 - - - +
693F LEU* 4.0 5.2 - - - -
694F MET* 2.6 38.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 691 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B TYR* 6.3 1.4 - - - +
468B TYR* 3.5 43.2 - - - +
687F ALA 3.7 10.2 + - - +
688F ILE* 3.3 8.6 + - - +
689F ILE 3.0 0.8 - - - -
690F ARG* 1.3 76.0 - - - +
692F ALA* 1.3 66.6 + - - +
693F LEU 3.1 1.6 - - - -
694F MET* 3.3 24.5 + - + +
695F GLY* 5.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 692 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B THR* 3.8 28.3 - - + +
288B THR* 3.5 28.6 - - + +
289B GLU* 3.8 12.0 - - - +
292B LYS* 3.3 12.6 + - - -
688F ILE 3.3 11.9 + - - +
689F ILE* 2.8 9.4 + - - +
691F LYS* 1.3 79.0 - - - +
693F LEU* 1.3 62.2 + - - +
694F MET 3.3 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 693 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR* 3.5 20.9 - - + +
292B LYS* 3.2 25.8 + - + +
297B PHE* 5.0 4.7 - - + -
302B LEU* 5.3 6.5 - - + +
305B GLN* 4.0 28.7 - - + +
306B VAL* 3.5 26.2 - - + +
309B LEU* 4.5 5.4 - - + -
689F ILE* 2.8 42.4 + - + +
690F ARG* 3.8 0.7 - - - +
692F ALA* 1.3 79.9 - - - +
694F MET* 1.3 76.7 + - + +
696F LYS* 5.1 0.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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