Contacts of the helix formed by residues 311 - 330 (chain A) in PDB entry 2P02
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 LYS 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 4.2 3.0 - - - +
76A VAL 3.4 27.3 + - - +
77A ALA* 4.2 12.7 - - + +
135A GLN* 3.7 24.0 - - - +
155A GLY* 4.8 12.1 - - - +
156A ASP* 6.1 2.7 - - + -
307A LYS* 3.8 31.0 - - + +
308A ASP* 2.7 39.1 + - - +
309A TYR 3.9 2.4 - - - +
310A THR* 1.3 82.6 + - - +
312A VAL* 1.3 65.3 + - - +
313A ASP* 3.1 4.5 - - + +
314A ARG* 3.0 14.9 + - - +
315A SER* 3.3 9.4 + - - -
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 4.0 22.7 - - + -
156A ASP* 3.6 30.3 - - + +
157A GLN 5.0 0.9 - - - +
160A MET* 3.7 19.8 - - + +
310A THR 3.2 2.6 + - - +
311A LYS* 1.3 66.6 - - - +
313A ASP* 1.3 67.3 + - - +
314A ARG 3.0 2.2 - - - -
315A SER* 3.5 15.0 - - - +
316A ALA* 2.9 27.6 + - + +
317A ALA 3.7 1.0 + - - -
342A TYR* 4.0 27.8 - - + -
379A PRO* 4.0 21.3 - - + -
382A ILE* 5.9 0.7 - - + -
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Residues in contact with ASP 313 (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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156A ASP* 5.0 10.5 - - - +
157A GLN 4.9 6.3 - - - +
158A GLY* 5.2 1.9 - - - -
159A LEU 4.9 2.1 - - - +
160A MET* 3.7 22.9 - - - +
302A GLY* 3.5 26.3 + - - +
303A ALA 3.6 15.7 - - - +
304A PHE* 3.3 21.0 - - - -
307A LYS* 2.8 25.8 + - + +
311A LYS* 3.1 2.7 + - + +
312A VAL* 1.3 79.2 - - - +
314A ARG* 1.3 57.9 + - - +
317A ALA* 3.4 9.9 - - - +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 2.8 42.6 + - - -
64A LEU* 3.4 19.4 - - - +
304A PHE* 3.1 39.1 + - + +
305A SER* 4.2 0.4 - - - +
306A GLY 3.9 0.4 - - - +
307A LYS* 3.4 17.5 + - + +
308A ASP 5.2 2.2 - - - +
309A TYR* 6.1 0.9 - - - +
311A LYS* 3.0 8.0 + - - +
312A VAL 3.0 0.4 - - - -
313A ASP* 1.3 78.3 - - - +
315A SER* 1.3 68.1 + - - +
316A ALA 3.3 1.8 - - - -
317A ALA* 3.1 2.8 + - - +
318A TYR* 2.9 58.6 + - + -
393A TYR* 3.2 25.5 - - - -
396A THR* 3.0 21.2 + - - -
401A HIS* 3.6 6.3 - - - -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 2.8 32.0 + - - +
311A LYS 3.3 1.8 + - - -
312A VAL* 3.5 16.8 - - - +
314A ARG* 1.3 80.1 - - - +
316A ALA* 1.3 59.3 + - - +
318A TYR* 3.4 4.4 + - - +
319A ALA* 2.9 27.5 + - - +
379A PRO* 4.5 4.5 - - - +
382A ILE* 3.6 14.8 - - - +
388A LEU* 3.6 28.9 - - - -
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Residues in contact with ALA 316 (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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160A MET* 4.0 9.4 - - - -
312A VAL* 2.9 21.2 + - + +
315A SER* 1.3 76.5 + - - +
317A ALA* 1.3 60.8 + - - +
319A ALA* 3.7 1.3 - - - +
320A ALA* 2.8 29.8 + - - +
340A VAL* 4.1 6.7 - - + +
342A TYR* 3.3 41.7 - - + +
382A ILE* 4.2 9.0 - - + -
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Residues in contact with ALA 317 (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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160A MET* 4.0 16.9 - - + +
161A PHE 4.4 10.8 - - - +
304A PHE* 3.4 25.4 - - + -
312A VAL 3.7 3.0 + - - -
313A ASP 3.4 20.4 - - - +
314A ARG 3.1 2.0 + - - +
316A ALA* 1.3 75.2 - - - +
318A TYR* 1.3 67.5 - - - +
320A ALA* 3.3 4.7 + - - +
321A ARG* 3.0 23.2 + - - +
402A PHE* 4.0 5.0 - - + -
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Residues in contact with TYR 318 (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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304A PHE* 4.1 9.4 - + - -
314A ARG* 2.9 58.7 + - + +
315A SER* 3.6 4.9 - - - +
317A ALA* 1.3 76.9 - - - +
319A ALA* 1.3 63.5 + - - +
321A ARG* 3.3 4.9 + - - +
322A TRP 3.0 18.0 + - - -
386A LEU* 4.0 12.8 - - + -
388A LEU* 4.2 11.2 - - + -
393A TYR* 4.2 9.2 - + - -
396A THR* 3.6 6.2 + - - +
401A HIS* 2.7 34.8 + - + -
402A PHE* 3.6 27.1 - + - -
409A TRP* 3.5 53.6 - + + +
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Residues in contact with ALA 319 (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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315A SER 2.9 17.3 + - - +
316A ALA* 3.8 4.0 - - - +
317A ALA 3.3 0.2 - - - -
318A TYR* 1.3 76.4 - - - +
320A ALA* 1.3 56.7 + - - +
322A TRP* 3.1 11.3 + - + +
323A VAL* 2.9 32.5 + - - +
377A LEU* 3.9 14.8 - - + -
382A ILE* 3.7 33.0 - - + -
386A LEU* 3.8 9.5 - - + +
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Residues in contact with ALA 320 (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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161A PHE* 3.8 5.2 - - - +
162A GLY* 3.4 26.4 - - - +
316A ALA 2.8 18.3 + - - +
317A ALA* 3.8 4.3 - - - +
318A TYR 3.3 0.2 - - - -
319A ALA* 1.3 73.0 - - - +
321A ARG* 1.3 60.0 + - - +
323A VAL* 3.4 9.3 + - - +
324A ALA* 2.9 28.9 + - - +
338A VAL* 4.2 17.5 - - + +
340A VAL* 4.6 12.1 - - + -
377A LEU* 5.5 1.7 - - - +
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Residues in contact with ARG 321 (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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162A GLY* 3.7 3.4 - - - -
163A TYR 2.9 20.0 + - - -
164A ALA* 3.7 8.3 - - - +
170A GLU 2.8 24.0 + - - -
171A CYS* 3.0 19.8 + - - +
172A MET* 3.8 14.4 - - - -
293A TYR* 3.4 25.6 - - - +
317A ALA 3.0 12.4 + - - +
318A TYR 3.5 8.3 - - - +
320A ALA* 1.3 75.9 - - - +
322A TRP* 1.3 57.1 + - - +
324A ALA* 3.2 2.2 + - - +
325A LYS* 2.8 41.1 + - - +
402A PHE* 3.6 21.3 - - + +
403A GLY 3.8 6.1 - - - +
409A TRP* 4.1 7.9 - - + +
410A GLU* 2.8 43.8 + - - +
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Residues in contact with TRP 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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318A TYR 3.0 12.9 + - - +
319A ALA* 3.1 16.4 + - + +
321A ARG* 1.3 76.3 - - - +
323A VAL* 1.3 57.2 + - - +
325A LYS* 3.9 1.2 - - - +
326A SER* 2.7 37.3 + - - -
375A PHE* 3.7 28.5 - + - -
377A LEU* 5.8 1.6 - - + -
382A ILE* 6.1 2.7 - - + -
385A ASP* 3.8 39.3 - - + -
386A LEU* 3.8 20.9 - - + -
408A PRO 3.8 7.5 + - - -
409A TRP* 3.3 25.6 - - + +
411A VAL 2.8 29.6 + - - -
412A PRO* 4.5 0.7 - - + -
413A LYS* 3.5 41.6 - - + +
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Residues in contact with VAL 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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319A ALA 2.9 20.2 + - - +
320A ALA* 3.6 9.9 - - - +
321A ARG 3.3 0.2 - - - -
322A TRP* 1.3 74.6 - - - +
324A ALA* 1.3 64.0 + - - +
326A SER* 3.2 2.6 + - - -
327A LEU* 3.0 24.4 + - + +
338A VAL* 4.0 19.1 - - + -
371A VAL* 3.7 37.7 - - + -
375A PHE* 3.7 41.5 - - + -
377A LEU* 4.3 13.9 - - + -
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Residues in contact with ALA 324 (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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162A GLY 4.0 2.9 - - - -
163A TYR* 3.6 35.7 - - - +
164A ALA* 3.6 10.2 - - - +
320A ALA 2.9 16.9 + - - +
321A ARG 3.7 3.1 - - - +
323A VAL* 1.3 75.3 - - - +
325A LYS* 1.3 62.7 + - - +
327A LEU* 3.2 5.5 + - - +
328A VAL* 3.1 21.0 + - - +
336A VAL* 3.6 16.7 - - + +
338A VAL* 4.0 8.7 - - + +
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Residues in contact with LYS 325 (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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164A ALA* 3.7 8.6 - - - +
170A GLU* 3.8 23.0 + - - +
171A CYS* 4.2 19.5 - - + -
321A ARG* 2.8 32.0 + - - +
322A TRP* 4.0 4.5 - - - +
324A ALA* 1.3 73.1 - - - +
326A SER* 1.3 57.5 + - - +
328A VAL* 4.0 0.8 - - - +
329A LYS* 2.8 48.9 + - + +
403A GLY* 5.3 0.6 - - - -
409A TRP 4.7 1.1 - - - +
410A GLU* 2.7 64.5 + - - +
412A PRO* 4.7 6.7 - - + -
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Residues in contact with SER 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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322A TRP* 2.7 27.1 + - - -
323A VAL 3.2 4.5 + - - -
325A LYS* 1.3 77.4 - - - +
327A LEU* 1.3 57.7 + - - +
330A GLY* 2.9 27.0 + - - -
375A PHE* 3.9 14.3 - - - -
412A PRO* 3.5 12.7 - - - +
413A LYS* 2.9 41.8 + - - +
415A LEU* 3.8 11.9 - - - +
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Residues in contact with LEU 327 (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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323A VAL* 3.0 22.1 + - + +
324A ALA* 3.2 6.9 + - - +
326A SER* 1.3 76.9 - - - +
328A VAL* 1.3 59.9 + - - +
330A GLY 3.8 0.2 - - - -
331A GLY 3.4 2.6 + - - -
332A LEU* 3.0 55.4 + - + +
333A CYS* 3.6 15.4 + - - -
336A VAL* 4.1 25.6 - - + -
338A VAL* 4.6 0.4 - - + -
354A ILE* 4.5 11.4 - - + -
367A LEU* 4.7 12.3 - - + +
370A ILE* 4.8 4.0 - - + -
371A VAL* 4.0 30.1 - - + -
375A PHE* 6.0 0.9 - - + -
415A LEU* 4.0 12.3 - - + -
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Residues in contact with VAL 328 (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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164A ALA* 3.8 20.4 - - + +
165A THR 4.6 0.2 - - - -
166A ASP* 4.0 25.4 - - + +
171A CYS* 3.9 20.6 - - - -
324A ALA 3.1 16.1 + - - +
325A LYS 4.0 2.7 - - - +
327A LEU* 1.3 75.0 - - - +
329A LYS* 1.3 62.2 + - + +
331A GLY* 3.0 19.6 + - - -
333A CYS* 3.4 23.2 - - - +
334A ARG 4.0 13.7 - - - +
336A VAL* 4.0 13.5 - - + -
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Residues in contact with LYS 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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169A GLU* 2.9 51.0 + - - +
171A CYS* 3.8 18.3 - - - -
325A LYS* 2.8 38.5 + - + +
328A VAL* 1.3 74.0 - - + +
330A GLY* 1.3 59.8 + - - +
331A GLY* 3.2 1.7 + - - -
412A PRO* 4.0 28.7 - - + -
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Residues in contact with GLY 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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326A SER 2.9 20.2 + - - -
327A LEU 3.9 1.1 - - - -
328A VAL 3.2 0.4 - - - -
329A LYS* 1.3 76.0 - - - +
331A GLY* 1.3 61.1 + - - +
332A LEU* 3.3 6.3 + - - +
412A PRO* 5.7 0.2 - - - +
413A LYS 6.1 0.7 - - - -
415A LEU* 5.3 6.7 - - - -
417A TYR* 3.9 16.9 + - - -
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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