Contacts of the helix formed by residues 300 - 313 (chain A) in PDB entry 2QPA
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 ASP 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLY* 5.4 1.2 - - - -
139A GLU* 5.1 5.7 - - - +
298A LEU 3.3 4.5 + - - +
299A PRO* 1.3 70.5 - - - +
301A LEU* 1.3 70.0 + - - +
302A ALA* 2.9 19.8 + - - +
303A ALA* 3.2 26.9 + - - +
304A ARG* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP* 1.3 79.6 + - - +
302A ALA* 1.3 56.6 + - - +
304A ARG* 3.1 16.2 + - - +
305A THR* 2.8 34.1 + - - +
325A ARG* 3.0 42.4 - - + +
328A GLY* 3.2 37.9 - - - +
329A ALA* 3.2 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 5.9 2.9 - - - +
300A ASP* 2.9 14.1 + - - +
301A LEU* 1.3 77.3 - - - +
303A ALA* 1.3 64.1 + - - +
305A THR* 3.7 3.9 - - - -
306A THR* 2.9 28.6 + - - +
325A ARG* 3.2 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 4.8 2.4 - - + -
137A GLY* 4.1 28.5 - - - +
138A LEU 5.4 0.2 - - - +
299A PRO* 3.7 11.4 - - + -
300A ASP* 3.2 32.9 + - - +
301A LEU 3.0 0.4 - - - -
302A ALA* 1.3 81.5 - - - +
304A ARG* 1.3 63.0 + - - +
306A THR* 3.2 6.2 + - - -
307A MET* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PRO* 3.0 42.4 + - + +
300A ASP* 2.7 40.4 + - - +
301A LEU* 3.3 17.1 - - - +
303A ALA* 1.3 68.2 - - - +
305A THR* 1.3 67.7 + - - +
307A MET* 3.0 6.5 + - - +
308A PHE* 3.0 27.7 + - - -
328A GLY 2.5 36.0 + - - +
329A ALA* 3.8 4.4 - - - +
331A THR* 2.9 25.8 + - - +
332A GLU* 3.4 28.7 - - - +
333A GLY 4.8 1.8 - - - +
334A TYR 4.0 5.6 - - - +
339A ILE* 3.4 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 2.8 23.5 + - - +
302A ALA* 3.7 4.7 - - - -
304A ARG* 1.3 73.3 - - - +
306A THR* 1.3 63.0 + - - +
308A PHE* 3.3 6.1 + - - +
309A GLU* 3.2 36.9 + - - +
321A LYS 4.9 0.9 - - - +
324A TYR* 3.6 30.8 + - + -
325A ARG* 3.5 42.2 + - - +
328A GLY* 3.8 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 5.0 12.0 + - - +
302A ALA 2.9 15.9 + - - -
303A ALA* 3.5 8.4 - - - -
305A THR* 1.3 73.5 - - - +
307A MET* 1.3 58.6 + - - +
309A GLU* 2.8 19.3 + - + +
310A ILE* 2.6 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.4 32.8 - - + -
177A THR* 5.7 2.0 - - - +
299A PRO* 3.7 32.5 - - + -
303A ALA 3.0 13.0 + - - +
304A ARG* 3.0 9.6 + - - +
306A THR* 1.3 77.3 - - - +
308A PHE* 1.3 62.2 + - - +
310A ILE* 4.3 8.7 - - + -
311A ASN* 2.6 39.6 + - - +
336A GLY* 3.3 33.2 - - - +
339A ILE* 4.2 14.1 - - + -
800A ADP 3.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG 3.0 24.3 + - - -
305A THR* 3.5 9.2 - - - +
307A MET* 1.3 76.9 - - - +
309A GLU* 1.3 59.3 + - - +
311A ASN* 3.5 1.6 - - - +
312A VAL* 2.9 35.4 + - - +
324A TYR* 3.6 14.4 - + + -
327A LEU* 3.7 44.9 - - + -
328A GLY* 4.5 1.6 - - - -
331A THR* 3.5 39.5 - - + -
339A ILE* 3.6 24.7 - - + -
342A VAL* 4.0 24.0 - - + -
343A VAL* 3.9 15.5 - - + -
406A PHE* 4.2 10.5 - + - -
410A ILE* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 3.2 26.0 + - - +
306A THR* 2.8 22.4 + - + +
308A PHE* 1.3 75.4 - - - +
310A ILE* 1.3 70.5 + - - +
312A VAL* 3.3 0.9 + - - +
313A GLY* 2.9 18.7 + - - -
321A LYS* 4.5 11.6 - - - +
324A TYR* 3.6 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU 5.1 4.7 - - - +
134A ASP* 4.4 22.4 - - - +
135A VAL 5.4 0.2 - - - -
136A ALA* 5.0 4.7 - - - +
306A THR* 2.6 43.7 + - + +
307A MET* 3.8 7.9 - - - +
309A GLU* 1.3 78.0 - - + +
311A ASN* 1.3 70.2 + - - +
312A VAL 3.0 0.3 + - - -
313A GLY* 3.0 12.5 + - - -
800A ADP 4.9 22.7 - - + +
162C ASN* 5.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 2.6 35.2 + - - +
308A PHE 3.5 2.9 - - - +
310A ILE* 1.3 80.1 - - - +
312A VAL* 1.3 64.2 + - - +
336A GLY 5.3 1.0 - - - +
339A ILE* 4.5 2.6 - - - +
340A ALA* 3.8 35.3 + - - +
343A VAL* 3.7 21.5 - - + +
344A LYS 5.8 0.2 - - - +
347A LEU* 4.3 6.4 - - - +
800A ADP 5.3 12.4 + - - -
162C ASN* 3.9 17.7 + - - +
----------------------------------------------------------
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 PHE 2.9 25.7 + - - +
309A GLU* 3.8 2.7 - - - +
310A ILE 3.0 0.4 + - - -
311A ASN* 1.3 75.1 - - - +
313A GLY* 1.3 66.4 + - - +
314A ASP 3.8 0.3 + - - -
315A THR* 3.0 38.5 + - - +
317A SER* 4.9 0.4 - - - -
324A TYR* 3.9 24.7 - - + +
343A VAL* 3.8 20.9 - - + -
347A LEU* 4.4 4.6 - - + +
401A LEU* 3.8 24.2 - - + -
406A PHE* 3.9 19.1 - - + -
162C ASN* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU 2.9 11.1 + - - -
310A ILE 3.0 10.0 + - - -
312A VAL* 1.3 80.7 - - - +
314A ASP* 1.3 58.3 + - - -
315A THR 3.1 14.7 + - - +
162C ASN* 5.6 3.4 - - - -
----------------------------------------------------------
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