Contacts of the helix formed by residues 379 - 385 (chain C) 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 SER 379 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 5.0 2.6 - - - +
148C TYR* 3.6 24.8 + - - +
149C THR 2.9 9.7 + - - -
150C ARG* 3.0 28.3 + - - +
219C GLY* 4.9 0.4 - - - -
378C ALA* 1.3 70.1 - - - +
380C GLU* 1.3 59.3 + - - +
382C ASN* 3.1 8.2 + - - +
383C THR* 2.8 26.5 + - - -
458C MET* 3.9 21.8 - - - +
460C TYR* 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ARG* 3.3 27.2 - - - +
151C ALA* 3.4 20.4 + - + +
152C LEU 3.4 0.5 + - - -
378C ALA* 4.1 2.9 - - + -
379C SER* 1.3 75.7 - - - +
381C PHE* 1.3 56.2 + - - +
382C ASN 3.0 0.2 + - - -
383C THR* 3.0 1.1 + - - -
384C LEU* 2.7 41.2 + - + +
460C TYR* 3.0 30.3 + - - -
466C TYR* 2.5 35.1 + - + -
503C LEU* 4.6 13.0 - - + -
525C LEU* 5.2 2.7 - - + -
529C PHE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 4.0 18.4 - + - -
210C PHE* 3.3 32.5 - + + -
377C ILE* 5.4 8.1 - - + -
378C ALA 3.8 16.3 + - - +
379C SER 3.3 0.4 - - - -
380C GLU* 1.3 78.6 - - - +
382C ASN* 1.3 61.8 + - - +
384C LEU* 3.9 5.9 - - + +
385C TYR* 3.1 50.5 + + - +
526C GLY* 3.4 23.1 - - - -
529C PHE* 2.9 48.2 - + + -
530C SER* 3.4 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C TYR* 3.7 15.7 + - + -
210C PHE* 3.0 35.8 - - + +
212C THR* 4.3 3.9 + - - -
378C ALA 3.6 5.9 + - - +
379C SER* 3.1 15.4 + - - +
380C GLU 3.0 0.4 - - - -
381C PHE* 1.3 76.5 - - - +
383C THR* 1.3 74.6 + - - +
385C TYR* 3.0 11.3 + - - +
386C HIS* 2.8 27.4 + - - -
682C HEM 3.1 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C SER 2.8 18.2 + - - -
380C GLU 3.7 3.1 - - - +
382C ASN* 1.3 76.3 + - - +
384C LEU* 1.3 57.9 + - + +
385C TYR 2.7 13.5 + - - -
386C HIS* 2.8 36.9 + - - +
451C SER* 4.9 1.4 + - - -
455C SER* 2.8 26.7 + - - +
458C MET* 4.5 4.3 - - - +
460C TYR* 3.6 21.4 + - + -
503C LEU* 4.7 7.6 - - + -
504C TYR* 4.1 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C GLU* 2.7 29.4 + - + +
381C PHE* 3.9 12.1 - - + +
383C THR* 1.3 75.7 - - + +
385C TYR* 1.3 58.6 + - + +
386C HIS 3.2 2.8 + - - +
387C TRP* 3.1 15.2 + - - -
503C LEU* 5.3 2.0 - - + -
504C TYR* 5.3 2.5 - - - -
507C LEU* 3.9 25.7 - - + +
522C MET* 3.3 26.8 - - - +
525C LEU* 3.6 39.5 - - + +
526C GLY* 4.0 11.2 - - - +
529C PHE* 4.9 0.9 - - + -
701C S58 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ALA* 4.5 2.2 - - + -
205C PHE* 5.0 2.4 - - - -
206C THR* 3.1 34.0 - - + +
209C PHE* 5.7 0.2 - + - -
210C PHE* 3.6 15.7 - + + -
348C TYR* 2.8 35.3 + - - -
381C PHE* 3.1 46.4 + + - +
382C ASN 3.0 5.6 + - - +
383C THR 2.7 4.4 + - - -
384C LEU* 1.3 75.8 - - + +
386C HIS* 1.3 61.1 + - - +
387C TRP* 2.8 36.1 + + - +
530C SER* 4.3 5.4 + - - -
682C HEM 3.4 16.7 - - + +
701C S58 3.0 37.4 - + + +
----------------------------------------------------------
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