Contacts of the helix formed by residues 312 - 322 (chain A) in PDB entry 1CG1
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 THR 312 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.9 7.0 - - - +
311A ASP* 1.3 69.7 - - - +
313A VAL* 1.3 63.9 + - - +
315A VAL* 3.8 9.2 - - - -
316A ARG* 3.0 40.1 + - - +
343A LEU* 3.8 14.2 - - - +
344A CYS 2.9 18.0 + - - -
345A VAL* 4.8 0.2 - - - -
402A ILE* 5.2 5.2 - - - +
405A LEU* 3.4 44.1 - - + +
406A THR* 3.9 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASP* 2.9 10.6 + - - +
312A THR* 1.3 77.2 - - - +
314A ALA* 1.3 67.5 + - - +
316A ARG* 3.1 18.9 + - - +
317A ARG 3.3 7.3 + - - -
344A CYS* 3.8 2.7 - - - +
345A VAL 3.4 35.0 - - - +
346A ALA* 3.4 14.4 - - - +
347A TYR* 3.7 17.7 - - + -
356A THR* 3.5 29.1 - - - +
357A THR* 3.9 5.3 - - - +
358A THR* 3.6 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR 5.1 2.4 - - - +
10A GLN* 6.6 0.4 - - + -
11A TRP* 4.8 6.7 - - + -
227A LEU* 3.8 31.4 - - + +
311A ASP* 3.1 28.6 + - + +
313A VAL* 1.3 77.0 - - - +
315A VAL* 1.3 63.9 + - + +
317A ARG* 2.9 17.3 + - - +
318A ALA* 3.2 9.8 + - - +
347A TYR* 4.0 5.8 - - - +
358A THR* 3.5 12.4 - - + +
365A TRP* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 4.7 5.2 - - - +
10A GLN* 4.2 15.3 - - + +
266A LEU* 3.6 27.4 - - + -
310A LEU* 3.8 12.1 - - + -
311A ASP 3.0 22.7 + - - +
312A THR* 4.1 7.2 - - - -
314A ALA* 1.3 75.2 - - + +
316A ARG* 1.3 57.6 + - - +
318A ALA* 3.2 9.5 + - - +
319A VAL* 2.9 24.1 + - - +
327A PHE* 3.4 36.1 - - + -
402A ILE* 6.0 0.4 - - + -
406A THR* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 3.0 36.2 + - - +
313A VAL* 3.1 11.7 + - - +
315A VAL* 1.3 74.6 - - - +
317A ARG* 1.3 64.4 + - - +
319A VAL* 3.4 9.2 + - + +
320A GLN* 3.4 24.7 + - - +
345A VAL* 3.1 30.1 + - - +
356A THR* 3.7 33.5 + - - +
405A LEU* 3.1 32.8 + - - +
406A THR* 4.0 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.8 13.2 - - + -
232A HIS 5.5 2.5 - - - +
313A VAL 3.3 7.1 + - - +
314A ALA 2.9 11.3 + - - +
316A ARG* 1.3 75.0 - - - +
318A ALA* 1.3 60.1 + - - +
320A GLN* 3.4 27.9 + - - +
321A LEU* 2.9 57.7 + - + +
357A THR* 4.1 12.3 - - - +
358A THR* 2.6 57.3 + - + +
360A LEU* 3.5 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 3.5 37.5 - - + +
226A THR* 3.8 24.8 - - + +
314A ALA 3.2 4.0 + - - +
315A VAL 3.2 11.6 + - - +
317A ARG* 1.3 77.9 - - - +
319A VAL* 1.3 65.7 + - - +
321A LEU 4.5 0.2 - - - +
322A ASN* 3.0 34.8 + - - +
324A LEU* 3.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL 2.9 21.5 + - - +
316A ARG* 3.6 14.8 - - + +
317A ARG 3.3 0.4 - - - -
318A ALA* 1.3 75.5 - - - +
320A GLN* 1.3 59.0 + - + +
323A SER* 2.9 26.7 + - - -
324A LEU* 3.3 32.1 + - + +
327A PHE* 3.9 15.7 - - + -
406A THR* 4.3 15.0 - - - +
408A VAL* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG 3.4 11.8 + - - +
317A ARG* 3.4 40.8 + - - +
319A VAL* 1.3 81.6 - - + +
321A LEU* 1.3 70.3 + - + +
322A ASN 3.2 0.7 + - - -
323A SER* 3.4 8.7 + - - +
357A THR* 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 4.0 17.5 - - + -
227A LEU* 5.9 0.2 - - + -
232A HIS* 3.5 55.9 - - + +
244A THR* 4.0 17.9 - - + -
245A ALA* 4.8 2.9 - - - +
246A GLY 5.4 1.7 + - - -
317A ARG* 2.9 49.7 + - + +
318A ALA* 4.3 2.5 - - - +
320A GLN* 1.3 76.3 - - + +
322A ASN* 1.3 62.0 + - - +
323A SER* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.0 15.5 - - - +
226A THR* 2.7 28.9 + - - +
244A THR* 3.1 14.1 - - - -
245A ALA* 2.7 40.5 + - + +
262A VAL* 3.4 19.2 - - + +
318A ALA* 3.0 30.2 + - - +
321A LEU* 1.3 76.2 - - - +
323A SER* 1.3 75.8 + - - +
324A LEU* 3.3 15.7 + - + +
----------------------------------------------------------
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