Contacts of the helix formed by residues 352 - 373 (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 PRO 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A TYR* 6.3 0.9 - - + -
350A GLY 3.4 8.2 - - - +
351A VAL* 1.4 92.2 - - + +
353A ALA* 1.3 65.0 + - - +
354A GLU* 3.3 6.3 - - + +
355A VAL* 3.2 23.2 + - + +
356A LEU* 3.0 18.9 + - - +
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Residues in contact with ALA 353 (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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351A VAL 3.5 2.5 + - - -
352A PRO* 1.3 72.2 - - - +
354A GLU* 1.3 62.7 + - - +
356A LEU* 3.4 9.9 + - - +
357A CYS* 3.0 32.9 + - - -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PRO* 3.3 4.8 - - + +
353A ALA* 1.3 78.5 - - - +
355A VAL* 1.3 65.1 + - + +
357A CYS* 3.6 7.2 + - - +
358A ASN* 3.3 31.6 + - - +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TYR* 3.9 45.0 - - + -
351A VAL* 3.5 18.6 - - + -
352A PRO* 3.2 28.8 + - + +
354A GLU* 1.3 79.5 - - + +
356A LEU* 1.3 59.5 + - - +
358A ASN* 3.2 13.6 + - + +
359A ILE* 3.0 26.8 + - + +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 4.8 12.1 - - + -
301A ILE* 4.1 24.5 - - + +
330A PHE* 5.0 1.3 - - + -
334A ILE* 3.5 32.5 - - + -
348A VAL* 3.6 22.0 - - + +
351A VAL* 3.5 26.9 - - + +
352A PRO 3.0 13.4 + - - +
353A ALA* 3.7 9.9 - - - +
355A VAL* 1.3 75.6 - - - +
357A CYS* 1.3 59.5 + - - +
359A ILE* 3.4 9.3 + - + +
360A GLU* 3.0 27.1 + - - +
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Residues in contact with CYS 357 (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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258A PHE* 3.4 30.8 - - + -
261A ILE* 6.3 2.9 - - + -
304A ARG* 5.7 4.9 - - - -
353A ALA* 3.0 24.7 + - - -
354A GLU* 3.8 9.9 - - - +
356A LEU* 1.3 74.5 - - - +
358A ASN* 1.3 57.5 + - - +
360A GLU* 3.3 13.6 + - - +
361A ALA 3.1 22.3 + - - -
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Residues in contact with ASN 358 (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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254A GLN* 3.6 30.6 + - - +
258A PHE* 3.5 20.2 - - - -
337A TYR* 6.1 0.7 - - - +
354A GLU* 3.3 16.5 + - - +
355A VAL* 3.2 16.2 + - - +
357A CYS* 1.3 75.7 - - - +
359A ILE* 1.3 65.1 - - + +
361A ALA* 3.3 2.6 + - - +
362A ASP* 3.0 32.1 + - - +
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Residues in contact with ILE 359 (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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330A PHE* 4.0 24.7 - - + +
333A PHE* 4.0 20.4 - - + +
334A ILE* 3.7 37.9 - - + +
337A TYR* 3.8 29.2 - - + -
351A VAL* 4.5 1.3 - - + -
355A VAL* 3.0 24.2 + - + +
356A LEU* 3.6 13.5 - - + +
358A ASN* 1.3 77.2 - - + +
360A GLU* 1.3 54.0 + - - +
362A ASP* 3.4 9.0 + - - +
363A THR* 2.8 45.1 + - - +
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Residues in contact with GLU 360 (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* 2.6 36.6 + - + +
261A ILE* 3.9 3.4 - - - +
301A ILE* 3.6 34.3 - - + +
304A ARG* 2.8 48.8 + - - +
305A ILE* 3.7 7.5 - - + +
330A PHE* 5.5 0.4 - - - -
356A LEU 3.0 13.6 + - - +
357A CYS* 3.6 14.6 - - - +
358A ASN 3.3 0.2 - - - -
359A ILE* 1.3 76.1 - - - +
361A ALA* 1.3 58.1 + - - +
363A THR* 3.4 7.0 + - - -
364A TYR* 2.9 28.2 + - - +
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Residues in contact with ALA 361 (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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254A GLN* 3.6 34.5 - - + -
257A TYR* 3.7 28.0 - - + -
258A PHE* 4.1 2.5 - - + -
357A CYS 3.1 13.9 + - - +
358A ASN 3.6 7.4 - - - +
360A GLU* 1.3 73.2 - - - +
362A ASP* 1.3 65.5 + - - +
364A TYR* 3.2 2.6 + - - +
365A TRP* 3.0 31.0 + - + -
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Residues in contact with ASP 362 (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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233A LYS* 2.7 27.5 + - - +
238A TYR* 2.8 39.3 + - + -
250A LEU* 3.6 2.2 - - - +
254A GLN* 3.0 24.0 + - - +
333A PHE* 3.8 19.3 - - + +
358A ASN* 3.0 15.9 + - - +
359A ILE* 3.6 8.6 - - - +
361A ALA* 1.3 73.5 - - - +
363A THR* 1.3 63.6 + - - +
365A TRP* 3.3 1.2 + - - +
366A CYS* 3.0 30.1 + - - +
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Residues in contact with THR 363 (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* 3.7 21.1 - - + -
326A VAL* 3.8 31.6 - - + +
329A PHE* 3.9 8.9 - - + +
330A PHE* 3.6 22.8 - - + +
333A PHE* 3.6 14.2 - - - -
359A ILE* 2.8 24.5 + - - +
360A GLU* 3.6 5.8 - - - -
362A ASP* 1.3 76.7 - - - +
364A TYR* 1.3 62.9 + - - +
366A CYS* 4.2 0.3 - - - +
367A MET* 3.0 28.6 + - + +
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Residues in contact with TYR 364 (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* 3.5 30.3 - + + -
260A PHE* 4.0 10.0 - + - -
305A ILE* 3.8 30.4 - - + +
308A ILE* 3.6 21.6 - - + +
309A TRP* 3.6 26.8 - - + -
312A ARG* 3.6 27.2 + - - +
313A HIS* 4.2 6.4 - - - -
360A GLU 2.9 15.0 + - - +
361A ALA 3.2 6.9 + - - +
363A THR* 1.3 76.5 - - - +
365A TRP* 1.3 86.2 + + - +
367A MET* 3.9 2.9 - - + +
368A SER* 2.9 48.2 + - - -
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Residues in contact with TRP 365 (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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238A TYR* 3.3 44.9 - + + -
253A LYS* 2.9 34.3 + - + -
256A GLU* 3.8 24.5 - - + -
257A TYR* 3.8 10.5 - - + +
260A PHE* 3.8 31.0 - + - -
361A ALA* 3.0 28.7 + - + +
362A ASP 3.3 0.4 + - - +
364A TYR* 1.3 94.4 - + - +
366A CYS* 1.3 58.3 + - - +
368A SER* 3.4 10.3 + - - -
369A LYS* 3.1 31.7 + - + +
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Residues in contact with CYS 366 (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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232A TRP 4.9 1.3 - - - -
233A LYS* 4.3 5.2 - - - -
236A SER* 3.8 13.9 - - - +
238A TYR* 3.8 34.5 - - - -
329A PHE* 3.6 34.4 - - + -
333A PHE* 3.9 17.9 - - + -
362A ASP 3.0 20.2 + - - +
363A THR 4.2 0.7 - - - +
365A TRP* 1.3 74.7 - - - +
367A MET* 1.3 64.9 + - - +
369A LYS* 3.2 8.8 + - - +
370A LEU 3.1 18.2 + - - -
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Residues in contact with MET 367 (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* 3.9 20.4 - - + -
306A LEU* 4.5 2.5 - - + -
309A TRP* 3.7 37.5 - - + -
322A ILE* 4.4 11.4 - - + -
325A LEU* 4.0 22.0 - - + +
326A VAL* 3.4 35.7 - - - -
329A PHE* 3.7 17.4 - - + -
363A THR* 3.0 20.1 + - + +
364A TYR* 3.9 3.6 - - + +
366A CYS* 1.3 75.3 - - - +
368A SER* 1.3 62.1 + - - +
369A LYS 3.3 0.2 + - - -
370A LEU* 3.3 4.1 + - + +
371A LEU* 2.9 38.7 + - + +
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Residues in contact with SER 368 (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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309A TRP* 3.5 30.2 + - - +
313A HIS* 4.8 4.9 - - - -
364A TYR* 2.9 42.9 + - - -
365A TRP* 3.5 16.2 - - - -
366A CYS 3.3 0.2 - - - -
367A MET* 1.3 71.8 - - - +
369A LYS* 1.3 57.2 + - - +
371A LEU* 3.3 2.1 + - - +
372A ASP* 2.9 39.6 + - - +
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Residues in contact with LYS 369 (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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236A SER* 3.1 35.0 - - - +
237A GLY* 4.3 17.1 + - - -
238A TYR* 5.1 5.6 - - + +
253A LYS* 5.1 7.3 - - - +
365A TRP* 3.1 15.7 + - + +
366A CYS* 3.4 11.9 - - - +
367A MET 3.2 0.2 - - - -
368A SER* 1.3 73.9 - - - +
370A LEU* 1.3 67.8 + - - +
372A ASP* 3.3 20.3 + - + +
373A GLY* 3.5 7.3 + - - -
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Residues in contact with LEU 370 (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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325A LEU* 4.1 15.7 - - + -
329A PHE* 3.6 15.3 - - + -
366A CYS 3.1 12.2 + - - +
367A MET* 3.4 9.0 - - - +
369A LYS* 1.3 78.1 - - - +
371A LEU* 1.3 65.8 + - + +
373A GLY* 3.2 9.9 + - - -
374A ILE* 3.5 31.7 + - + +
425A LEU* 4.1 9.6 - - + -
439A TRP* 3.5 40.4 - - + -
449A PHE* 3.8 39.0 - - + +
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Residues in contact with LEU 371 (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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309A TRP* 3.4 42.0 - - + +
322A ILE* 3.9 17.7 - - + -
325A LEU* 4.0 15.3 - - + -
367A MET* 2.9 43.1 + - + +
368A SER 3.8 3.6 - - - +
369A LYS 3.3 0.4 - - - -
370A LEU* 1.3 79.7 - - + +
372A ASP* 1.3 59.8 + - - +
374A ILE* 3.0 23.5 + - + +
375A GLN* 3.4 14.1 + - - +
378A TYR* 3.7 35.2 - - + -
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Residues in contact with ASP 372 (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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309A TRP* 5.8 0.9 + - - -
313A HIS* 4.4 17.2 + - - -
368A SER* 2.9 27.0 + - - +
369A LYS* 3.3 16.1 + - + +
371A LEU* 1.3 77.2 - - - +
373A GLY* 1.3 55.1 + - - +
374A ILE 3.4 0.2 - - - -
375A GLN* 3.2 37.0 + - - +
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Residues in contact with GLY 373 (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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369A LYS 3.5 5.2 + - - -
370A LEU 3.2 8.5 + - - -
371A LEU 3.2 1.2 - - - -
372A ASP* 1.3 76.8 - - - +
374A ILE* 1.3 67.9 + - - +
375A GLN 3.7 1.5 + - - -
450A SER* 3.7 17.0 + - - -
1007A UNX 4.2 11.7 - - - -
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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
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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