Contacts of the helix formed by residues 376 - 381 (chain D) in PDB entry 2C10
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D HIS* 5.7 0.9 + - - -
246D GLU* 3.1 29.3 - - - -
265D PHE* 3.7 15.0 - - - -
374D GLY* 3.5 0.4 - - - -
375D ASN* 1.3 82.2 - - - +
377D PRO* 1.3 71.2 - - - +
378D ALA 3.1 0.9 + - - -
379D ALA* 3.2 6.4 + - - +
380D MET* 3.0 23.5 + - - +
498D ALA* 4.1 19.4 - - - +
499D PHE* 4.5 5.0 + - - +
501D PHE* 3.9 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C TRP* 4.0 13.8 - - + -
226D TRP* 3.5 37.5 - - + -
246D GLU* 3.4 9.0 - - - +
265D PHE* 3.5 28.7 - - + -
270D TYR* 3.4 33.9 - - + +
375D ASN 4.5 0.7 - - - +
376D SER* 1.3 82.2 - - - +
378D ALA* 1.3 62.2 + - - +
380D MET* 3.2 11.3 + - + +
381D THR* 3.2 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D THR* 3.8 20.8 - - + +
226D TRP* 4.0 21.0 - - + +
228D GLY* 5.1 5.6 - - - +
230D TYR* 6.0 2.2 - - - +
246D GLU* 3.1 28.6 + - + +
377D PRO* 1.3 80.2 - - - +
379D ALA* 1.3 58.6 + - - +
381D THR* 4.0 1.6 + - - -
382D THR* 2.4 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D GLU* 4.8 1.6 + - - +
372D TYR* 3.3 35.9 - - + +
373D GLY 3.4 18.3 - - - +
374D GLY* 4.0 5.6 - - - -
375D ASN 5.1 0.7 - - - +
376D SER* 3.2 6.4 + - - +
378D ALA* 1.3 77.1 - - - +
380D MET* 1.3 63.5 + - - +
382D THR* 3.9 5.1 + - - -
498D ALA* 5.2 8.1 - - + -
518D THR* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C PRO* 4.4 10.8 - - + -
553C TRP* 4.0 19.7 - - - -
559C LEU* 4.0 18.2 - - + +
560C GLN 4.9 2.3 - - - +
561C ARG* 3.5 54.6 - - - +
562C LEU 5.7 0.5 + - - -
270D TYR* 4.4 8.3 - - - +
372D TYR 3.8 3.5 - - - +
373D GLY* 4.7 1.6 - - - -
374D GLY 4.0 8.9 - - - +
375D ASN 3.6 26.2 - - - +
376D SER 3.0 16.4 + - - +
377D PRO 3.2 8.2 + - - +
379D ALA* 1.3 78.9 - - - +
381D THR* 1.3 62.9 + - + +
382D THR 3.6 0.2 - - - -
383D ARG* 3.5 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C TRP* 4.0 17.7 - - + -
559C LEU* 3.7 30.3 - - + -
213D THR* 6.0 0.7 - - - -
214D ALA 3.5 9.0 - - - +
215D PRO* 3.6 13.7 - - - +
218D LEU* 5.4 9.2 - - + -
226D TRP* 4.1 15.4 - - - -
377D PRO 3.2 12.7 + - - -
378D ALA 4.0 1.3 + - - -
380D MET* 1.3 81.1 - - - +
382D THR* 1.3 62.2 + - - +
383D ARG* 3.5 12.8 + - - +
621D MET* 5.5 0.3 - - - +
----------------------------------------------------------
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