Contacts of the helix formed by residues 295 - 313 (chain A) in PDB entry 2QFZ
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 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA* 3.5 20.3 + - - +
292A LEU* 3.0 14.9 + - - +
293A ILE 3.3 10.9 - - - +
294A LEU* 1.3 74.2 - - - +
296A PRO* 1.4 67.8 - - + +
297A LYS* 3.2 3.1 - - + +
298A VAL* 2.9 27.4 + - + +
299A THR 3.4 1.0 + - - -
346A VAL 2.8 27.2 + - - -
347A ASP* 3.1 16.2 + - - +
348A VAL* 2.9 36.2 + - + +
349A SER 4.2 0.5 + - - -
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Residues in contact with PRO 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU 3.2 8.7 - - - +
295A GLN* 1.4 83.9 - - + +
297A LYS* 1.3 66.9 - - + +
299A THR* 3.7 8.8 + - - +
300A GLU* 3.5 19.9 + - - +
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN* 3.2 1.5 - - + -
296A PRO* 1.3 84.1 - - + +
298A VAL* 1.3 65.3 + - + +
300A GLU* 3.7 5.9 + - - +
301A ILE* 3.2 29.9 + - + +
348A VAL* 4.8 17.3 - - + -
349A SER* 6.5 0.9 - - - -
356A LEU* 4.8 12.1 - - + -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.3 39.7 - - + +
293A ILE* 4.3 6.3 - - + +
295A GLN* 2.9 16.4 + - + +
297A LYS* 1.3 76.9 - - - +
299A THR* 1.3 59.0 + - - +
301A ILE* 3.3 6.9 + - - +
302A PHE* 2.9 65.6 + - + -
330A PHE* 4.2 6.5 - - + -
348A VAL* 3.4 35.4 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A HIS* 6.1 0.4 - - + -
284A ILE* 3.7 19.0 - - + +
285A PRO* 4.4 13.9 - - + +
293A ILE* 2.5 34.7 + - - +
294A LEU* 4.7 0.5 - - - -
295A GLN 3.4 2.9 + - - -
296A PRO* 4.1 10.6 - - - +
297A LYS 3.4 0.6 - - - -
298A VAL* 1.3 78.9 - - - +
300A GLU* 1.3 61.7 + - - +
302A PHE* 3.8 1.8 - - - +
303A GLU* 3.1 44.5 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO 3.5 14.8 + - - +
297A LYS* 4.0 7.0 - - - +
298A VAL 3.3 0.6 - - - -
299A THR* 1.3 76.1 - - - +
301A ILE* 1.3 64.5 + - + +
303A GLU* 3.6 9.6 + - - +
304A ARG* 3.1 31.7 + - - +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 3.2 21.7 + - + +
298A VAL* 3.7 3.6 - - - +
300A GLU* 1.3 76.9 - - + +
302A PHE* 1.3 66.6 + - + +
304A ARG* 3.2 10.3 + - - +
305A ILE* 2.9 34.4 + - + +
330A PHE* 3.8 34.8 - - + -
348A VAL* 5.5 0.7 - - + -
356A LEU* 4.1 32.8 - - + +
360A GLU* 3.6 42.1 - - + +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ILE* 4.0 13.2 - - + -
287A MET* 4.0 14.8 - - + -
292A LEU* 4.8 2.0 - - + -
293A ILE* 3.7 23.6 - - + -
298A VAL* 2.9 46.3 + - + +
299A THR 3.8 4.0 - - - +
301A ILE* 1.3 83.2 - - + +
303A GLU* 1.3 57.2 + - - +
305A ILE* 3.5 4.6 + - - +
306A LEU* 3.1 37.9 + - + +
323A ASN 4.5 0.9 - - - -
326A VAL* 3.9 28.9 - - + +
327A THR* 3.5 37.0 - - + -
330A PHE* 3.8 28.0 - + - -
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 2.8 38.6 + - + -
280A ILE* 3.7 28.2 - - + +
281A HIS* 3.8 26.8 + - - -
284A ILE* 4.0 8.1 - - + -
285A PRO* 4.3 3.3 - - - +
299A THR* 3.1 40.2 + - - +
300A GLU* 3.9 7.6 - - - +
302A PHE* 1.3 72.1 - - - +
304A ARG* 1.3 60.8 + - - +
306A LEU* 3.9 0.5 - - - +
307A PHE* 2.8 33.4 + - - +
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 4.1 0.4 - - - -
261A ILE* 4.1 33.9 - - - +
300A GLU* 3.1 19.7 + - - +
301A ILE* 3.2 14.8 + - - +
303A GLU* 1.3 78.2 - - - +
305A ILE* 1.3 65.5 + - - +
307A PHE* 3.9 5.2 - - + +
308A ILE* 3.0 39.2 + - + +
357A CYS* 5.7 5.5 - - - -
360A GLU* 2.8 36.0 + - - +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 3.6 19.9 + - - +
301A ILE* 2.9 37.7 + - + +
302A PHE* 3.8 3.8 - - - +
304A ARG* 1.3 76.1 - - - +
306A LEU* 1.3 59.7 + - - +
309A TRP* 2.9 28.2 + - - +
326A VAL* 4.1 15.5 - - + -
330A PHE* 5.6 0.4 - - + -
360A GLU* 3.7 19.1 - - + +
363A THR* 3.7 28.0 - - + -
364A TYR* 3.8 20.2 - - + +
367A MET* 3.9 28.9 - - + -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.9 16.1 - - + +
284A ILE* 3.5 18.8 - - + -
302A PHE* 3.1 25.3 + - + +
303A GLU 4.0 2.2 - - - +
305A ILE* 1.3 72.2 - - - +
307A PHE* 1.3 67.1 + - - +
309A TRP* 3.5 6.4 + - + +
310A ALA* 3.0 24.6 + - - +
318A TYR* 4.6 11.1 - - + -
322A ILE* 3.9 22.4 - - + -
323A ASN* 3.5 39.9 - - + +
326A VAL* 3.7 26.2 - - + -
367A MET* 4.5 5.4 - - + -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 4.8 12.6 - - + -
273A HIS* 3.6 42.4 - + + -
276A THR* 4.3 7.9 - - + -
277A TYR* 4.0 34.5 - + + -
280A ILE* 3.6 10.2 - - + +
303A GLU 2.8 23.7 + - - +
304A ARG* 3.9 6.3 - - + +
306A LEU* 1.3 73.2 - - - +
308A ILE* 1.3 68.2 + - + +
310A ALA* 3.4 3.3 + - - +
311A ILE* 3.1 52.4 + - + +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A TYR* 3.8 25.4 - - + +
260A PHE* 3.9 20.0 - - + -
261A ILE* 3.8 36.6 - - + +
264A TYR* 4.3 17.9 - - + -
304A ARG* 3.0 25.4 + - + +
305A ILE 3.9 2.5 - - - +
307A PHE* 1.3 78.2 - - + +
309A TRP* 1.3 67.7 + - - +
311A ILE* 3.4 6.2 + - - +
312A ARG* 3.1 28.7 + - + +
364A TYR* 3.6 24.5 - - + +
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Residues in contact with TRP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ILE 2.9 18.7 + - - +
306A LEU* 3.8 7.6 - - + +
308A ILE* 1.3 75.9 - - - +
310A ALA* 1.3 62.3 + - + +
312A ARG 3.3 0.7 + - - -
313A HIS* 2.7 80.3 + + + +
316A SER* 3.8 19.5 - - - -
317A GLY 3.3 22.2 - - - -
318A TYR* 5.7 0.4 - - - -
322A ILE* 3.6 26.9 - - + -
364A TYR* 3.6 10.3 - + + -
367A MET* 3.7 21.1 - - + -
368A SER* 3.5 26.7 + - - +
371A LEU* 3.4 36.9 - - + +
372A ASP* 5.8 1.0 + - - -
378A TYR* 5.1 2.5 - + + -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A THR* 3.9 19.7 - - + -
306A LEU 3.0 17.8 + - - +
307A PHE 3.6 4.9 - - - +
308A ILE 3.2 0.2 - - - -
309A TRP* 1.3 83.9 - - + +
311A ILE* 1.3 64.0 + - - +
313A HIS 3.2 19.8 + - - +
314A PRO* 3.9 2.8 - - - +
317A GLY* 3.7 30.8 - - - +
318A TYR* 3.7 8.5 - - + +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A TYR* 3.2 58.7 + - + -
273A HIS* 3.3 41.6 - - + +
276A THR* 5.3 3.4 - - + +
307A PHE* 3.1 42.4 + - + +
308A ILE* 3.5 11.2 - - - +
310A ALA* 1.3 78.0 - - + +
312A ARG* 1.3 62.8 + - - +
313A HIS 3.5 0.9 + - - -
314A PRO* 4.1 11.6 - - - +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.5 48.4 - - - -
264A TYR* 2.6 48.6 + - + +
308A ILE* 3.1 17.0 + - - +
310A ALA 3.3 0.2 - - - -
311A ILE* 1.3 76.3 - - - +
313A HIS* 1.3 80.7 + - + +
314A PRO* 3.5 8.4 - - - +
364A TYR* 3.6 17.3 + - - +
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Residues in contact with HIS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TRP* 2.7 78.0 + + + +
310A ALA 3.2 4.7 + - - +
312A ARG* 1.3 95.6 + - + +
314A PRO* 1.3 61.3 - - - +
315A ALA* 3.3 3.1 - - - -
316A SER* 3.1 6.8 + - - +
317A GLY* 2.9 24.3 + - - -
364A TYR* 4.2 7.2 - - - -
368A SER* 4.8 5.8 - - - -
372A ASP* 4.4 15.6 + - - -
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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) + - + + + + + -
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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