Contacts of the helix formed by residues 313 - 323 (chain A) in PDB entry 2QUK
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 GLN 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A CYS* 3.5 19.3 - - - +
310A ALA* 3.2 33.1 + - + +
311A ILE 3.0 0.6 - - - -
312A ASP* 1.3 84.1 + - - +
314A ASP* 1.3 60.6 + - - +
315A PRO* 3.5 2.2 - - - -
316A TYR* 3.4 28.0 - - + +
317A PHE* 2.8 40.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.5 29.4 - - + +
109A SER* 5.2 0.2 - - - -
141A ARG* 2.6 45.7 + - - -
310A ALA 4.0 1.2 + - - -
311A ILE 3.5 6.6 + - - +
313A GLN* 1.3 73.7 - - - +
315A PRO* 1.3 65.2 - - + +
316A TYR 2.8 11.2 + - - -
317A PHE* 3.0 15.1 + - - -
318A ARG* 3.2 13.5 + - - +
334A LEU* 3.3 13.5 - - - +
336A HIS* 3.3 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.4 30.1 - - + -
266A ILE* 3.7 19.6 - - + +
312A ASP 3.9 8.7 - - - +
313A GLN 3.6 1.3 - - - -
314A ASP* 1.3 93.7 - - + +
316A TYR* 1.3 75.7 + - + +
318A ARG* 4.1 23.1 - - + +
319A MET 4.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 4.0 28.4 + - + -
267A PHE* 4.0 26.4 - + + -
312A ASP 4.5 9.9 - - - -
313A GLN* 3.4 26.7 - - + +
314A ASP 2.8 0.6 + - - -
315A PRO* 1.3 99.6 - - + +
317A PHE* 1.3 68.8 + + + +
318A ARG 3.1 5.4 + - - -
319A MET* 3.8 17.3 + - - +
320A THR* 4.1 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 6.2 0.4 - - - -
159A TYR* 4.9 9.6 - + - -
284A GLN* 5.9 8.5 - - + -
288A SER* 5.5 1.1 - - - -
307A ILE* 3.9 42.8 - - + -
309A CYS* 4.0 16.4 - - + -
313A GLN* 2.8 51.6 - - + -
314A ASP* 3.0 6.2 + - - +
316A TYR* 1.3 81.9 - + + +
318A ARG* 1.3 60.0 + - - +
319A MET 3.4 0.2 - - - -
320A THR* 3.9 17.7 - - + -
321A ARG* 2.9 34.7 + - + +
332A PRO* 5.8 0.4 - - + -
334A LEU* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG 5.7 1.0 + - - -
107A PHE* 4.0 21.8 + - - +
108A GLY* 5.6 1.0 - - - -
141A ARG* 5.1 11.3 - - - +
266A ILE* 6.0 1.8 - - + -
314A ASP* 3.2 18.7 + - - +
315A PRO* 4.1 19.0 - - + +
316A TYR 3.1 0.4 - - - -
317A PHE* 1.3 75.7 - - - +
319A MET* 1.3 57.0 + - - +
321A ARG* 2.9 7.6 + - - +
322A ASP* 2.7 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 4.4 5.8 - - + -
258A VAL* 4.0 39.0 - - + -
262A GLN* 5.0 9.2 - - + +
263A VAL* 4.6 5.4 - - + -
266A ILE* 4.5 20.7 - - + +
267A PHE* 4.7 8.7 - - + -
281A PRO* 3.6 42.4 - - - +
282A ALA* 5.0 0.2 - - - -
285A ALA* 3.9 8.3 - - + -
315A PRO 4.9 0.6 + - - -
316A TYR 3.8 11.6 + - - +
318A ARG* 1.3 81.6 - - - +
320A THR* 1.3 84.5 + - - +
322A ASP* 3.1 8.3 + - - +
323A VAL* 3.1 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PRO 5.0 0.2 + - - -
285A ALA* 3.2 31.5 - - + +
288A SER* 3.7 30.5 - - - +
289A PHE* 4.0 7.7 - - + -
316A TYR 4.2 6.8 + - - -
317A PHE* 3.6 20.2 + - + -
318A ARG 3.3 0.2 - - - -
319A MET* 1.3 89.8 - - - +
321A ARG* 1.3 62.5 + - - +
323A VAL* 3.5 9.1 - - - +
324A ALA* 3.5 18.4 + - - +
332A PRO* 4.3 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 3.1 43.6 - - - +
142A ASP* 2.4 34.3 + - - -
317A PHE* 2.9 28.6 + - + +
318A ARG* 2.9 7.7 + - - +
320A THR* 1.3 73.7 - - - +
322A ASP* 1.3 64.3 + - - +
324A ALA* 3.3 6.3 - - - +
325A PRO* 3.6 0.7 - - - +
331A LYS* 2.7 73.3 - - - +
332A PRO* 3.1 41.6 + - + -
334A LEU* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLN* 5.7 3.9 - - - +
318A ARG* 2.7 43.1 + - - +
319A MET* 3.5 7.7 + - - +
321A ARG* 1.3 73.0 - - - +
323A VAL* 1.3 61.2 + - + +
324A ALA 3.0 9.5 + - - -
325A PRO* 3.4 11.8 - - - +
326A ARG* 4.0 17.5 + - - +
331A LYS* 4.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 3.9 28.3 - - + -
257A HIS* 3.6 36.6 - - + +
258A VAL* 3.6 16.2 - - + -
262A GLN* 5.2 3.6 - - - +
289A PHE* 4.9 3.8 - - + -
319A MET* 3.1 15.6 + - + +
320A THR* 3.5 17.7 - - - +
322A ASP* 1.3 75.5 - - + +
324A ALA* 1.3 57.9 + - - +
326A ARG* 4.0 18.8 - - - +
327A ILE* 3.1 27.0 - - + +
----------------------------------------------------------
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