Contacts of the helix formed by residues 315 - 335 (chain A) in PDB entry 2DQM
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 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.2 18.4 - - - +
310A CYS* 3.5 8.5 - - + -
311A ARG* 3.8 10.5 - - - +
312A ASP* 3.2 48.7 + - - +
313A TRP 3.0 1.2 - - - -
314A PHE* 1.3 79.9 - - - +
316A LEU* 1.3 63.8 + - - +
317A SER 3.2 3.1 - - - -
318A LEU* 2.8 22.0 + - + +
365A ARG* 3.9 7.8 + - - +
416A ALA 4.1 12.1 - - - +
417A THR* 3.4 20.4 - - + +
418A CYS* 2.9 38.6 + - - +
419A ASP 4.7 0.3 + - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.8 8.1 - - - +
310A CYS* 4.2 6.1 - - - -
312A ASP 4.2 0.2 + - - -
313A TRP* 3.1 24.1 + - + +
314A PHE 3.2 2.6 + - - -
315A GLN* 1.3 76.7 - - - +
317A SER* 1.3 62.6 + - - +
319A LYS* 3.1 20.0 + - - +
320A GLU* 3.0 37.6 + - + -
366A PRO* 5.9 1.6 - - + -
372A MET* 3.6 17.3 - - + -
375A PHE 3.5 24.2 - - - +
376A TYR* 3.6 39.9 - - + +
380A VAL* 3.8 13.2 - - + -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE 4.9 0.2 + - - -
315A GLN 3.1 1.4 + - - -
316A LEU* 1.3 74.9 - - - +
318A LEU* 1.3 66.2 + - - +
319A LYS 3.0 0.2 - - - -
321A GLY* 2.8 27.7 + - - +
322A LEU* 3.6 2.1 + - - +
364A ILE* 3.4 35.6 + - - +
380A VAL* 2.8 29.0 + - - +
384A GLY* 3.5 16.1 - - - -
388A ILE* 5.5 2.6 - - - +
418A CYS* 4.7 8.3 - - - -
440A TYR* 5.4 2.2 - - - -
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR* 5.3 0.3 - - - -
308A VAL 5.8 0.2 - - - +
309A THR 3.7 15.9 - - - +
310A CYS* 4.5 5.8 - - - -
315A GLN* 2.8 17.0 + - + +
317A SER* 1.3 78.2 - - - +
319A LYS* 1.3 57.2 + - + +
322A LEU* 3.4 23.7 - - - +
388A ILE* 5.9 0.2 - - - +
407A TYR* 3.4 27.1 + - + +
416A ALA* 3.3 37.2 - - + +
417A THR 3.6 11.4 - - - +
418A CYS* 3.9 16.9 - - - +
421A PHE* 3.5 33.1 - - + -
440A TYR* 6.1 0.4 - - - -
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 2.6 30.6 + - - -
185A TYR* 3.4 30.1 - - - +
264A GLU* 2.9 20.0 + - - +
301A HIS* 3.8 4.7 - - + -
304A THR 3.6 19.7 - - - +
305A GLY* 3.7 16.2 - - - -
308A VAL 5.4 0.2 - - - +
309A THR 6.0 0.2 - - - -
310A CYS* 3.8 15.7 - - - -
313A TRP* 4.1 6.3 - - - -
316A LEU* 3.1 19.6 + - - +
317A SER 3.0 0.2 - - - -
318A LEU* 1.3 83.1 - - + +
320A GLU* 1.3 86.0 + - - +
321A GLY 3.6 0.2 - - - -
322A LEU* 4.2 0.6 - - - +
323A THR* 2.6 35.1 + - - -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 4.1 0.9 - - - +
297A HIS* 3.4 1.4 + - - -
301A HIS* 3.3 3.0 + - - -
316A LEU* 3.0 33.1 + - + +
319A LYS* 1.3 102.0 + - - +
321A GLY* 1.3 60.8 + - - +
324A VAL* 2.9 36.9 + - - +
380A VAL* 4.2 7.4 - - + -
381A TYR* 3.2 44.5 + - + +
900A ZN 2.1 38.3 - - - -
901A BES 3.1 6.9 + - - -
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 2.8 23.1 + - - -
320A GLU* 1.3 73.5 - - - +
322A LEU* 1.3 57.6 + - - +
324A VAL 3.4 0.2 + - - -
325A PHE* 3.0 24.3 + - - +
380A VAL 3.8 1.0 + - - -
381A TYR 3.8 6.3 - - - -
384A GLY 3.7 22.9 - - - -
385A ALA* 3.4 13.6 - - - +
388A ILE* 3.9 7.6 - - - -
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Residues in contact with LEU 322 (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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241A PHE* 5.6 0.4 - - + -
304A THR* 3.4 32.5 - - + -
317A SER 3.6 4.2 + - - -
318A LEU 3.4 22.9 - - - +
319A LYS 4.2 0.9 - - - +
320A GLU 3.3 0.2 - - - -
321A GLY* 1.3 78.2 - - - +
323A THR* 1.3 56.8 + - - +
325A PHE* 3.4 4.4 + - + +
326A ARG* 3.0 31.3 + - - -
388A ILE* 3.9 33.0 - - + +
400A PHE* 4.6 3.1 - - + -
404A MET* 4.1 17.0 - - + -
407A TYR* 4.3 7.9 - - + +
421A PHE* 3.7 32.8 - - + -
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Residues in contact with THR 323 (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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297A HIS* 3.1 50.8 + - + +
300A PHE* 4.0 11.4 - - + -
301A HIS* 3.1 13.1 + - + +
304A THR* 2.8 29.2 + - - -
319A LYS 2.6 23.2 + - - -
320A GLU 4.1 0.2 - - - -
322A LEU* 1.3 73.6 - - - +
324A VAL* 1.3 61.1 + - - +
326A ARG* 3.3 6.1 + - - +
327A ASP* 2.8 23.2 + - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 4.0 16.8 - - - +
297A HIS* 3.7 11.0 - - + -
320A GLU 2.9 25.2 + - - +
321A GLY 3.7 3.6 - - - +
323A THR* 1.3 73.6 - - - +
325A PHE* 1.3 65.5 + - - +
327A ASP* 3.1 10.1 + - - +
328A GLN* 2.9 40.9 + - - +
381A TYR* 3.6 40.2 - - + +
382A GLU* 4.9 4.5 - - + -
385A ALA* 3.5 20.0 - - + -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 5.1 2.0 - - - -
241A PHE* 4.6 6.1 - + - -
321A GLY 3.0 14.5 + - - +
322A LEU* 3.4 13.2 - - + +
324A VAL* 1.3 77.1 - - - +
326A ARG* 1.3 61.3 + - + +
328A GLN* 3.3 6.4 + - - +
329A GLU* 3.0 48.7 + - + +
385A ALA* 3.8 10.5 - - + +
388A ILE* 3.6 20.9 - - + -
389A ARG* 3.6 64.6 - - + -
392A HIS* 4.0 27.4 - + + -
400A PHE* 3.7 26.0 - + - -
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Residues in contact with ARG 326 (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 TRP* 3.3 16.0 - - + -
237A ASP* 2.8 42.0 + - - -
241A PHE* 3.4 44.0 - - + +
243A LEU* 3.9 10.5 - - - +
300A PHE* 2.9 44.0 + - + +
303A TRP* 4.5 2.6 - - - +
304A THR* 3.0 34.7 + - - +
322A LEU* 3.0 26.8 + - - +
323A THR* 3.5 8.1 - - - +
324A VAL 3.1 0.4 - - - -
325A PHE* 1.3 82.9 - - + +
327A ASP* 1.3 56.3 + - - +
329A GLU* 3.3 1.8 + - - -
330A PHE* 3.0 24.8 + - - +
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 2.8 61.8 + - + +
297A HIS* 2.8 35.3 + - + +
300A PHE* 3.8 9.6 - - + -
323A THR 2.8 14.3 + - - +
324A VAL* 3.1 12.7 + - - +
326A ARG* 1.3 73.8 - - - +
328A GLN* 1.3 66.6 + - - +
330A PHE* 3.5 2.1 - - + +
331A SER* 3.0 33.1 + - - -
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 5.4 3.2 - - - +
324A VAL* 2.9 40.3 + - + +
325A PHE* 3.6 5.1 - - - +
327A ASP* 1.3 82.1 + - - +
329A GLU* 1.3 60.2 + - - +
331A SER* 3.5 4.4 + - - +
332A SER* 2.7 39.6 + - - +
340A ASN* 4.9 0.8 - - - +
341A ARG* 4.5 1.2 + - - -
344A ASN* 3.3 44.2 + - - +
382A GLU* 5.1 10.1 + - - +
385A ALA* 4.3 12.7 - - - +
386A GLU* 4.4 8.5 + - - +
389A ARG* 3.1 27.8 + - - +
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Residues in contact with GLU 329 (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 TRP* 3.7 12.8 - - + -
240A ARG* 3.0 35.1 + - - +
241A PHE* 5.3 1.3 - - + -
325A PHE* 3.0 43.8 + - + +
326A ARG* 3.3 2.7 + - - +
328A GLN* 1.3 73.8 - - - +
330A PHE* 1.3 59.6 + - - +
332A SER* 4.3 1.1 + - - -
333A ASP* 2.8 36.7 + - - +
337A ARG* 2.9 32.7 + - - -
389A ARG* 2.9 35.2 + - - -
392A HIS* 5.4 2.3 + - - -
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Residues in contact with PHE 330 (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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229A SER 4.3 0.7 - - - -
232A ASN* 3.7 22.0 - - + -
233A SER* 3.4 28.9 - - - -
236A TRP* 3.5 33.4 - + + -
292A GLU* 3.4 41.7 - - + -
293A ARG* 5.0 1.8 - - - -
296A GLY* 4.1 2.0 - - - -
300A PHE* 3.5 23.8 - + + -
326A ARG 3.0 16.9 + - - +
327A ASP* 3.5 6.3 - - - +
329A GLU* 1.3 74.7 - - - +
331A SER* 1.3 70.6 + - - +
333A ASP* 3.8 0.2 - - - +
334A LEU* 3.0 56.3 + - + +
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU 5.0 1.0 + - - -
292A GLU* 4.4 18.5 + - - +
293A ARG* 4.0 24.4 - - - +
327A ASP 3.0 17.0 + - - -
328A GLN* 3.9 3.8 - - - -
330A PHE* 1.3 77.8 - - - +
332A SER* 1.3 58.6 + - - +
334A LEU* 3.8 1.1 - - - +
335A GLY* 2.8 26.7 + - - -
340A ASN* 3.3 29.4 + - - -
672A HIS* 5.3 0.3 - - - -
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLN* 2.7 26.1 + - - +
329A GLU* 3.8 0.8 + - - -
331A SER* 1.3 78.5 - - - +
333A ASP* 1.3 62.3 + - - +
335A GLY 3.3 17.7 - - - +
337A ARG* 3.5 53.8 + - - +
340A ASN* 3.3 26.2 - - - +
341A ARG* 4.9 1.0 + - - +
344A ASN* 5.4 0.5 + - - -
389A ARG* 5.5 0.7 + - - -
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 2.9 32.1 + - + +
240A ARG* 2.9 25.4 + - - -
329A GLU 2.8 20.6 + - - +
330A PHE 3.8 0.7 - - - +
332A SER* 1.3 74.3 - - - +
334A LEU* 1.3 63.6 + - + +
335A GLY 4.4 2.3 - - - +
337A ARG* 3.0 21.4 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ASN* 4.2 18.2 - - + +
236A TRP* 3.9 17.9 - - + -
292A GLU* 3.7 25.6 - - - +
330A PHE* 3.0 54.5 + - + +
331A SER 4.1 2.0 - - - +
333A ASP* 1.3 81.9 - - + +
335A GLY* 1.3 57.6 + - - +
672A HIS* 3.1 20.8 - - - +
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Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A SER 2.8 14.5 + - - -
332A SER 3.3 9.7 - - - +
333A ASP 3.5 2.5 - - - +
334A LEU* 1.3 81.1 - - - +
336A SER* 1.3 60.9 + - - -
337A ARG 3.7 0.7 + - - -
340A ASN* 4.9 0.7 - - - -
672A HIS* 3.4 30.2 + - - -
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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