Contacts of the helix formed by residues 301 - 312 (chain C) in PDB entry 3QNQ
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 301 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C GLY* 4.0 11.5 - - - +
297C GLY 4.2 0.9 - - - -
299C GLY* 2.8 13.7 + - - -
300C ALA* 1.3 73.9 - - - +
302C LEU* 1.3 57.3 + - - +
303C ALA 3.2 0.9 - - - -
304C LEU* 3.1 14.3 + - + +
305C VAL* 2.9 42.2 + - + +
328C GLY* 5.7 3.4 - - - -
333C ASN* 3.4 41.1 + - + -
336C VAL* 4.4 18.8 - - + +
337C THR* 5.3 0.3 - - - +
342C ILE* 5.3 0.9 - - - +
352C PHE* 4.9 3.8 - - - -
415C TYR* 4.3 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C MET* 4.5 6.1 - - + +
296C GLY* 3.4 20.9 - - - +
300C ALA 2.4 15.0 + - - +
301C THR* 1.3 74.0 - - - +
303C ALA* 1.3 57.0 + - - +
305C VAL* 3.7 5.1 + - + -
306C VAL* 3.1 29.8 + - + +
325C ILE* 4.0 25.4 - - + -
328C GLY* 3.9 25.8 - - - +
329C ILE* 4.2 10.5 - - + +
331C ASN* 6.0 0.2 - - - +
386C ILE* 4.0 38.8 - - + -
408C PHE* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ALA 3.0 3.7 + - - +
302C LEU* 1.3 75.5 - - - +
304C LEU* 1.3 57.6 + - - +
306C VAL* 3.5 1.3 + - - +
307C GLY* 2.7 32.4 + - - -
408C PHE* 3.6 26.5 - - + -
411C ALA* 3.6 16.4 - - + -
412C PHE* 3.3 41.8 - - + +
415C TYR* 4.8 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C THR* 3.4 13.1 - - + +
303C ALA* 1.3 76.4 - - - +
305C VAL* 1.3 63.5 + - - +
307C GLY* 3.4 1.9 + - - -
308C MET* 3.1 28.2 + - + +
336C VAL* 4.5 9.0 - - + -
340C MET* 4.2 19.5 - - + -
342C ILE* 3.5 32.5 - - + -
348C LEU* 5.7 2.7 - - + -
415C TYR* 3.6 56.2 - - + +
419C LEU* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C THR* 2.9 36.6 + - + +
302C LEU* 3.9 9.2 - - + +
304C LEU* 1.3 73.9 - - + +
306C VAL* 1.3 61.8 + - - +
308C MET* 2.9 15.4 + - + +
309C LEU* 2.8 25.9 + - + +
321C GLY* 4.0 11.4 - - - +
324C SER* 4.1 12.3 - - - +
325C ILE* 3.8 42.2 - - + +
328C GLY* 5.6 1.8 - - - -
336C VAL* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 3.1 23.2 + - + +
303C ALA* 3.9 5.2 - - - +
305C VAL* 1.3 75.1 - - - +
307C GLY* 1.3 53.3 + - - +
309C LEU* 2.8 16.9 + - + +
310C LEU* 2.7 60.4 + - + +
325C ILE* 4.5 16.8 - - + -
408C PHE* 4.3 18.6 - - + -
412C PHE* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA 2.7 22.7 + - - -
304C LEU* 3.7 2.9 - - - -
305C VAL 3.2 0.2 - - - -
306C VAL* 1.3 73.5 - - - +
308C MET* 1.3 55.6 + - - +
310C LEU* 4.6 0.4 - - - -
311C PHE* 3.0 31.5 + - - +
412C PHE* 4.0 21.3 - - - -
416C LEU* 4.9 1.1 - - - -
419C LEU* 3.2 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU* 3.1 15.8 + - - +
305C VAL* 2.9 15.5 + - + +
307C GLY* 1.3 75.1 - - - +
309C LEU* 1.3 64.0 + - - +
312C ALA* 2.9 37.1 + - + +
317C LEU* 3.8 29.6 - - + +
318C LYS* 5.0 1.2 - - - +
320C LEU* 3.6 15.0 - - + -
321C GLY* 3.2 34.1 - - - +
324C SER* 4.0 7.0 - - - +
336C VAL* 4.9 2.9 - - + -
340C MET* 3.9 29.4 - - + +
419C LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL* 2.8 12.2 + - + +
306C VAL* 2.8 28.4 + - + +
308C MET* 1.3 72.0 - - - +
310C LEU* 1.3 61.8 + - + +
318C LYS* 5.1 3.4 - - - +
321C GLY* 3.8 7.4 - - - +
322C ARG* 3.8 38.1 - - + +
325C ILE* 3.8 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C VAL* 2.7 39.5 + - + +
307C GLY* 4.4 0.9 - - - +
309C LEU* 1.3 80.7 - - + +
311C PHE* 1.3 87.2 + - + +
312C ALA 3.8 1.1 - - - -
313C ARG* 4.4 5.5 + - - -
412C PHE* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLY 3.0 15.5 + - - +
310C LEU* 1.3 98.8 - - + +
312C ALA* 1.3 62.6 + - - +
313C ARG* 3.4 29.4 + - - +
412C PHE* 3.5 22.0 - + - -
416C LEU* 3.4 46.0 - - + -
419C LEU* 5.3 2.9 - - + -
423C ASP* 3.5 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLY 4.0 0.2 + - - -
308C MET* 2.9 27.0 + - - +
310C LEU 3.8 1.0 - - - -
311C PHE* 1.3 77.3 - - - +
313C ARG* 1.3 65.0 + - - +
314C SER 4.5 0.2 - - - +
317C LEU* 4.0 11.0 - - + -
318C LYS* 3.3 52.0 - - + +
419C LEU* 6.3 1.3 - - + -
423C ASP* 3.5 5.8 - - - -
----------------------------------------------------------
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