Contacts of the helix formed by residues 294 - 301 (chain C) in PDB entry 4QGC
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 ARG 294 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 3.0 43.1 - - - +
292C VAL* 3.6 14.8 - - + -
293C ALA* 1.3 72.7 - - - +
295C GLY* 1.3 52.3 + - - +
297C LEU* 3.2 8.8 + - - +
298C GLY* 2.8 32.7 + - - -
306C VAL* 4.3 8.4 - - + +
310C GLN* 3.2 39.9 + - + +
326C CYS* 3.5 23.0 - - - -
327C ALA 3.1 23.3 + - - -
328C THR* 3.0 6.2 + - - +
329C GLN* 3.0 21.9 + - - +
330C MET* 3.0 27.9 - - - -
347C ASP* 2.8 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 5.4 0.4 - - - -
294C ARG* 1.3 76.5 - - - +
296C ASP* 1.3 57.0 + - - +
298C GLY* 3.0 16.4 + - - -
299C ILE* 3.2 22.3 + - - +
328C THR* 2.9 16.2 + - - -
329C GLN* 3.5 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ASP* 5.1 7.7 - - - +
210C ASN* 4.5 15.5 + - - +
244C PHE* 4.8 7.2 - - + -
272C GLU* 3.1 51.9 - - + +
293C ALA* 3.4 16.9 + - + +
294C ARG 3.4 0.2 - - - -
295C GLY* 1.3 74.9 - - - +
297C LEU* 1.3 62.4 + - - +
299C ILE* 3.5 13.3 + - - +
300C GLU* 3.3 15.8 - - - +
328C THR* 4.0 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE 3.7 11.0 - - - +
272C GLU 3.4 28.5 - - - +
273C ASN* 3.6 16.8 - - - +
277C VAL* 4.2 7.2 - - + -
292C VAL* 3.9 13.9 - - + -
293C ALA 3.0 15.5 + - - +
294C ARG* 3.3 11.2 - - - +
296C ASP* 1.3 78.5 - - - +
298C GLY* 1.3 53.7 + - - +
300C GLU* 3.2 1.9 + - - +
301C ILE* 2.7 50.6 + - + +
306C VAL* 4.2 18.4 - - + +
309C ALA* 4.9 4.3 - - + -
313C MET* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 4.5 13.2 - - - -
294C ARG 2.8 14.4 + - - -
295C GLY 3.0 6.4 + - - -
297C LEU* 1.3 78.2 - - - +
299C ILE* 1.3 59.5 + - - +
301C ILE 2.9 19.1 - - - +
303C ALA* 5.0 2.9 + - - +
306C VAL* 3.9 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 4.0 29.8 + - + -
178C ASP* 4.1 9.6 - - - +
179C GLY* 4.0 34.3 - - - +
210C ASN* 3.7 35.7 - - + +
212C PRO* 4.2 11.0 - - + +
295C GLY* 3.2 26.7 + - - +
296C ASP* 3.9 9.2 - - - +
297C LEU 3.3 0.6 - - - -
298C GLY* 1.3 79.0 - - - +
300C GLU* 1.3 72.5 + - - +
301C ILE 4.8 0.5 - - - +
329C GLN* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ASN* 3.9 22.0 - - - +
211C LEU 4.7 3.0 + - - +
212C PRO* 3.4 36.5 - - - +
272C GLU 3.7 12.4 - - - +
273C ASN* 3.9 16.4 - - - +
274C HIS* 4.3 19.6 + - + +
296C ASP 3.3 16.6 - - - +
297C LEU 3.2 4.0 + - - +
299C ILE* 1.3 87.2 - - - +
301C ILE* 1.3 61.3 + - + +
302C PRO* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.7 25.4 - - + -
274C HIS* 4.1 30.1 - - + +
277C VAL* 3.8 23.3 - - + -
297C LEU* 2.7 30.4 + - + +
298C GLY* 2.9 23.1 - - - +
299C ILE 5.1 0.2 - - - -
300C GLU* 1.3 79.2 - - + +
302C PRO* 1.3 86.8 - - + +
303C ALA 3.5 0.2 + - - -
305C LYS* 3.7 19.5 - - + -
306C VAL* 3.9 10.7 - - + +
309C ALA* 5.0 3.8 - - + -
----------------------------------------------------------
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