Contacts of the helix formed by residues 668 - 673 (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 668 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 1.3 71.2 - - - +
669A THR* 1.3 64.2 + - - +
670A SER* 3.1 3.4 - - - -
671A GLN* 3.2 26.1 + - - +
672A PHE* 4.0 7.6 - - - -
851A MET 3.3 7.1 + - - -
852A PRO 5.1 0.7 - - - -
853A TYR 2.6 18.5 + - - -
854A LYS* 3.9 17.5 - - - -
855A THR 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ASN* 6.1 2.7 - - - +
638A PHE* 3.8 33.0 - - + -
639A PHE* 3.7 19.7 - - - -
643A VAL* 3.9 12.4 - - + +
666A PRO* 4.0 19.5 - - + +
667A LEU 3.4 1.3 - - - +
668A GLY* 1.3 74.5 - - - +
670A SER* 1.3 61.3 + - - +
671A GLN 3.2 1.0 + - - -
672A PHE* 3.6 14.4 + - - -
673A GLU* 4.3 2.4 + - - +
849A PRO 2.6 27.8 + - - +
850A SER* 3.5 2.0 - - - -
851A MET* 2.7 22.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A GLY 3.1 1.2 - - - -
669A THR* 1.3 74.5 + - - +
671A GLN* 1.3 61.4 + - - +
672A PHE 2.9 12.1 + - - -
673A GLU* 3.1 37.2 + - - +
674A LYS 4.5 1.6 + - - -
744A ASP* 4.9 0.2 - - - +
807A GLU 2.8 23.5 + - - -
808A PHE* 3.7 29.8 - - - +
850A SER* 4.0 3.4 - - - -
851A MET 3.1 13.4 + - - -
852A PRO* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A GLY* 3.2 23.8 - - - +
669A THR 3.2 0.4 - - - -
670A SER* 1.3 80.6 + - - +
672A PHE* 1.3 74.3 + - + +
673A GLU 3.6 0.2 - - - -
674A LYS* 2.9 27.9 + - - +
807A GLU* 2.9 32.3 + - - +
808A PHE* 3.5 22.3 - - - -
852A PRO 5.2 0.6 + - - -
854A LYS* 3.2 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A MET 4.3 7.2 - - - -
635A THR* 3.2 33.7 - - - +
636A ASN* 3.5 38.8 - - + -
639A PHE* 3.4 42.7 - + + -
668A GLY 4.0 14.8 - - - -
669A THR* 3.8 9.9 - - - -
670A SER 2.9 0.8 - - - -
671A GLN* 1.3 91.8 - - + +
673A GLU* 1.3 63.7 + - - +
674A LYS* 3.5 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LYS* 2.6 33.3 + - - -
639A PHE* 4.3 5.2 - - + -
643A VAL* 5.3 0.7 - - + -
647A LEU* 3.6 32.5 - - + +
669A THR 4.3 7.6 - - - +
670A SER* 3.1 25.0 + - - +
672A PHE* 1.3 79.8 - - - +
674A LYS* 1.3 68.6 + - - +
675A ARG* 2.9 20.3 + - + +
744A ASP* 5.4 1.3 - - - +
808A PHE* 4.4 4.5 - - + +
850A SER* 2.6 30.9 + - - -
----------------------------------------------------------
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