Contacts of the helix formed by residues 300 - 312 (chain A) in PDB entry 2CDZ
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 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 1.3 80.1 - - - +
301A HIS* 1.3 57.4 + - - +
302A GLU* 2.7 31.8 + - - +
303A GLN* 3.7 20.0 + - - +
304A PHE* 2.8 28.4 + - - +
360A ARG* 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL 3.9 0.2 + - - -
300A SER* 1.3 71.5 + - - +
302A GLU* 1.3 74.0 + - + +
304A PHE* 3.8 1.9 - + - +
305A ARG* 2.8 45.7 + - - +
354A LEU* 4.1 31.4 - - + +
355A ARG* 3.4 66.7 + - + +
360A ARG* 3.7 19.6 - - - +
389A ASP* 4.4 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER* 2.7 27.8 + - - +
301A HIS* 1.3 87.6 + - + +
303A GLN* 1.3 56.9 + - - +
305A ARG* 3.7 6.1 + - - +
306A ALA* 3.0 27.7 + - - +
355A ARG* 3.4 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.9 19.1 - - + +
300A SER* 3.4 24.1 + - - +
301A HIS 3.3 0.4 - - - -
302A GLU* 1.3 75.9 - - - +
304A PHE* 1.3 59.9 + - - +
306A ALA* 3.3 8.3 - - + +
307A ALA* 3.0 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 4.8 6.3 - - + +
300A SER 2.8 21.1 + - - +
301A HIS* 3.8 4.5 - + - +
303A GLN* 1.3 70.2 - - - +
305A ARG* 1.3 70.2 + - - +
307A ALA* 3.2 9.2 + - + +
308A LEU* 3.1 48.4 + - + +
354A LEU* 4.0 14.4 - - + -
360A ARG* 3.2 69.1 - - + +
361A GLU* 4.0 32.1 - - - -
363A LEU* 4.2 7.9 - - + -
364A PHE* 4.6 13.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 2.8 34.9 + - - +
302A GLU* 3.9 5.8 - - - +
304A PHE* 1.3 76.8 - - - +
306A ALA* 1.3 56.9 + - - +
308A LEU* 3.4 2.4 + - - +
309A GLN* 2.9 46.5 + - - +
354A LEU* 3.7 29.0 - - + +
386A LEU* 3.6 36.8 + - + +
388A GLY* 2.7 38.2 + - - +
389A ASP* 5.0 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLU 3.0 19.8 + - - +
303A GLN* 3.3 12.3 - - + +
304A PHE 3.2 0.2 - - - -
305A ARG* 1.3 74.2 - - - +
307A ALA* 1.3 64.2 + - - +
309A GLN* 3.3 20.1 + - - +
310A LEU* 3.4 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN* 3.0 13.3 + - + +
304A PHE* 3.2 11.4 + - + +
306A ALA* 1.3 74.3 - - - +
308A LEU* 1.3 62.5 + - - +
310A LEU* 3.3 27.0 + - - +
311A VAL* 3.6 10.9 - - - +
364A PHE* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.1 38.4 + - + +
305A ARG* 3.6 7.9 - - - +
307A ALA* 1.3 76.9 - - - +
309A GLN* 1.3 58.8 + - - +
311A VAL* 3.1 21.6 + - + +
312A VAL* 3.1 27.4 + - + +
354A LEU* 4.2 22.9 - - + -
363A LEU* 4.4 5.8 - - + +
364A PHE* 3.7 40.1 - - + +
367A VAL* 4.8 4.9 - - + -
386A LEU* 4.3 7.4 - - + -
391A LEU* 4.4 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 2.9 34.5 + - - +
306A ALA* 3.5 12.3 - - - +
307A ALA 3.3 0.6 - - - -
308A LEU* 1.3 76.8 - - - +
310A LEU* 1.3 61.0 + - - +
311A VAL 3.4 0.2 + - - -
312A VAL* 3.7 19.4 - - + +
314A PRO* 5.9 4.4 - - + +
386A LEU* 3.7 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA 3.4 11.3 + - - +
307A ALA* 3.3 15.5 + - - +
308A LEU 3.2 0.6 - - - -
309A GLN* 1.3 78.3 - - - +
311A VAL* 1.3 62.2 + - + +
312A VAL 4.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA 3.6 15.9 - - - +
308A LEU* 3.1 10.2 + - + +
310A LEU* 1.3 80.4 - - + +
312A VAL* 1.3 66.1 + - + +
364A PHE* 3.6 26.0 - - + -
367A VAL* 3.7 28.3 - - + +
368A VAL* 4.3 11.7 - - + -
371A ARG* 3.9 28.9 + - - +
384A SER* 4.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.1 27.1 + - + +
309A GLN* 3.7 19.5 - - + +
310A LEU 3.8 2.1 - - - +
311A VAL* 1.3 83.2 - - + +
313A ASP* 1.3 73.2 + - - +
314A PRO* 3.5 7.2 - - + +
367A VAL* 4.8 3.8 - - + -
384A SER* 3.4 23.8 - - - +
386A LEU* 4.0 26.9 - - + +
391A LEU* 3.6 31.0 - - + -
----------------------------------------------------------
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