Contacts of the helix formed by residues 376 - 381 (chain C) in PDB entry 2C11
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 376 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C HIS* 5.2 0.2 + - - -
246C GLU* 3.2 29.5 - - - -
265C PHE* 4.1 7.7 - - - -
374C GLY* 3.2 1.0 - - - -
375C ASN* 1.3 95.2 + - - +
377C PRO* 1.3 58.0 - - - +
379C ALA* 3.2 12.0 + - - -
380C MET* 2.5 39.1 + - - +
498C ALA* 3.4 16.0 - - - +
499C PHE* 4.2 6.4 + - - +
501C PHE* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TRP* 3.6 24.2 - - + -
246C GLU* 3.0 13.0 - - - +
265C PHE* 3.4 36.6 - - + -
270C TYR* 3.3 24.0 - - + +
375C ASN 4.0 2.0 - - - +
376C SER* 1.3 81.3 - - - +
378C ALA* 1.3 60.0 + - - +
380C MET* 3.5 5.7 - - + +
381C THR* 2.8 28.6 + - - -
553D TRP* 3.4 27.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C THR* 4.0 17.3 - - + -
226C TRP* 3.9 29.5 - - + +
228C GLY* 5.1 4.0 - - - +
230C TYR* 5.9 1.8 - - - +
246C GLU* 3.3 25.7 + - + +
377C PRO* 1.3 77.9 - - - +
379C ALA* 1.3 64.9 + - - +
381C THR* 3.2 7.4 + - - -
382C THR* 2.7 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLU* 4.3 1.6 + - - +
372C TYR* 3.7 12.8 - - + +
373C GLY 4.2 18.6 + - - +
374C GLY* 4.2 6.1 - - - -
376C SER* 3.2 19.4 + - - +
378C ALA* 1.3 76.0 - - - +
380C MET* 1.3 54.8 + - - +
381C THR 2.4 15.9 + - - -
382C THR* 2.8 22.0 + - - -
498C ALA* 4.9 3.6 - - + -
518C THR* 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C TYR* 4.2 2.5 - - - +
372C TYR 4.7 0.7 - - - +
373C GLY* 4.8 1.6 - - - -
374C GLY 3.2 16.1 + - - +
375C ASN 4.7 3.8 - - - +
376C SER 2.5 23.4 + - - +
377C PRO* 3.5 10.3 - - - +
379C ALA* 1.3 70.9 - - - +
381C THR* 1.3 60.9 + - - +
382C THR 3.9 0.2 - - - -
383C ARG* 3.8 14.7 + - - -
549D MET* 6.3 0.4 - - - -
552D PRO* 3.2 40.8 - - + -
553D TRP* 3.5 18.4 - - + -
559D LEU* 3.5 18.9 - - + +
561D ARG* 3.0 51.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C THR* 6.3 0.2 - - - -
214C ALA 3.6 6.1 - - - +
215C PRO* 3.8 8.0 - - - +
218C LEU* 5.8 4.9 - - + -
226C TRP* 4.9 4.5 - - - -
377C PRO 2.8 13.5 + - - -
378C ALA* 3.2 4.5 + - - -
379C ALA 2.4 14.1 + - - -
380C MET* 1.3 79.6 - - + +
382C THR* 1.3 57.2 + - - +
383C ARG* 3.4 26.1 + - - +
621C MET* 5.3 0.7 - - - +
551D VAL* 5.7 0.7 - - + -
553D TRP* 4.0 25.0 - - + -
559D LEU* 3.8 29.4 - - + -
----------------------------------------------------------
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