Contacts of the helix formed by residues 564 - 571 (chain D) in PDB entry 1CX2
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 ILE 564 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D MET* 4.9 5.6 - - + -
201D PHE* 3.9 12.8 - - + -
301D TYR* 4.1 11.7 - - + +
343D ILE* 3.7 5.5 - - + +
347D ASP* 2.7 20.5 + - + +
563D SER* 1.3 72.5 - - - +
565D GLN* 1.3 68.0 + - + +
567D LEU* 3.2 13.0 + - + +
568D ILE* 3.1 44.5 + - + +
578D THR* 4.9 3.1 + - - -
579D SER* 4.5 19.3 - - - +
580D PHE* 3.2 47.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 565 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D SER* 3.7 12.5 - - - +
564D ILE* 1.3 85.3 - - + +
566D SER* 1.3 60.1 + - - +
568D ILE* 3.6 2.3 + - - +
569D CYS* 3.1 31.8 + - + +
576D PRO 3.6 20.6 + - - -
577D PHE* 3.8 16.0 - - - +
578D THR* 3.5 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 566 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561D THR 4.2 9.8 + - - -
562D ALA* 5.3 1.3 - - - -
563D SER* 2.5 29.2 + - - -
565D GLN* 1.3 76.7 - - - +
567D LEU* 1.3 59.2 + - - +
568D ILE 2.9 2.4 + - - -
569D CYS* 2.9 6.9 + - - +
570D ASN* 2.7 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PHE* 4.7 4.5 - - + -
301D TYR* 5.1 2.0 - - + -
304D ILE* 3.8 21.3 - - + +
305D TRP* 3.6 49.1 - - + +
308D GLU* 3.9 28.9 - - + +
339D GLU* 4.7 4.3 - - - +
343D ILE* 4.1 11.4 - - + -
563D SER 2.8 17.7 + - - +
564D ILE* 3.4 20.2 - - + +
566D SER* 1.3 76.4 - - - +
568D ILE* 1.3 58.6 + - + +
570D ASN* 4.9 1.6 - - - -
571D ASN* 3.1 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 568 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D MET* 4.3 12.3 - - + -
301D TYR* 4.6 7.6 - - + -
304D ILE* 4.4 17.0 - - + -
423D VAL* 4.0 15.7 - - + -
564D ILE* 3.1 38.0 + - + +
565D GLN 4.1 1.3 - - - +
566D SER 3.0 0.8 - - - -
567D LEU* 1.3 77.1 - - + +
569D CYS* 1.3 61.4 + - - +
570D ASN 3.0 4.0 - - - -
571D ASN 2.9 0.7 + - - -
572D VAL* 2.6 50.7 + - + +
576D PRO* 3.4 34.1 - - + +
578D THR* 3.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 569 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D GLN* 3.1 31.1 + - + +
566D SER* 2.9 7.9 + - - +
568D ILE* 1.3 76.2 - - - +
570D ASN* 1.3 61.9 + - - +
572D VAL 4.7 1.4 - - - +
574D GLY 4.6 3.1 - - - +
575D CYS* 2.0 73.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 570 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D GLU* 4.6 3.5 + - - +
311D ARG* 3.8 45.2 + - - +
566D SER* 2.7 31.1 + - - +
567D LEU* 4.9 1.1 - - - +
569D CYS* 1.3 82.2 - - - +
571D ASN* 1.3 69.0 + - - +
572D VAL 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 571 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D ILE* 3.9 18.0 + - + +
307D ARG* 3.1 59.5 + - + +
308D GLU* 2.9 43.5 + - - +
311D ARG* 4.6 3.8 - - - +
419D LEU* 6.0 0.3 - - - +
567D LEU* 3.1 25.3 + - - +
568D ILE 2.9 3.8 + - - -
570D ASN* 1.3 85.9 - - - +
572D VAL* 1.3 60.4 + - + +
573D LYS 3.9 0.9 + - - -
----------------------------------------------------------
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