Contacts of the helix formed by residues 369 - 388 (chain A) in PDB entry 3REP
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 ASN 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A GLU* 4.9 2.5 - - - +
368A THR* 1.3 72.1 + - - +
370A ARG* 1.3 61.7 + - - +
371A ARG* 3.1 14.0 + - - +
372A SER* 3.0 36.9 + - - +
373A ALA* 3.1 20.8 + - - +
433A PRO* 5.3 6.8 - - + +
434A ALA* 6.2 1.2 - - - +
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Residues in contact with ARG 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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314A LEU* 3.7 28.0 - - + -
315A ILE 5.9 2.2 - - - +
318A HIS 4.8 10.8 + - - +
319A ALA* 5.8 4.2 - - - +
356A VAL* 5.8 1.6 - - - +
360A ALA* 3.9 25.2 + - - +
363A LYS 5.3 0.8 + - - -
365A PRO* 3.8 33.0 - - + +
368A THR* 3.2 27.8 + - - +
369A ASN* 1.3 70.0 + - - +
371A ARG* 1.3 66.1 + - - +
373A ALA* 3.2 12.0 + - - +
374A ASP* 2.9 43.0 + - - +
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Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A HIS* 3.0 74.0 + - + +
310A THR 5.0 0.8 - - - -
311A LEU 3.8 9.3 + - - -
312A GLU* 5.0 7.1 + - - +
314A LEU* 3.6 28.9 - - + +
369A ASN* 3.1 8.8 + - - +
370A ARG* 1.3 77.7 - - - +
372A SER* 1.3 63.1 + - - +
374A ASP 3.3 1.6 + - - -
375A MET* 3.2 19.1 + - - +
437A PRO 5.5 0.2 - - - +
438A LYS* 4.6 25.3 - - + +
439A PHE* 4.4 0.5 - - - -
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASN* 3.0 29.4 + - - +
371A ARG* 1.3 73.1 - - - +
373A ALA* 1.3 67.4 + - - +
375A MET* 3.2 14.9 + - - +
376A TRP 3.2 5.9 + - - -
433A PRO* 3.1 43.2 + - - -
434A ALA* 4.8 1.4 - - - -
436A ARG* 3.1 22.8 + - - -
437A PRO 5.7 1.6 - - - -
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Residues in contact with ALA 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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357A ALA* 3.9 13.0 + - + +
359A GLU* 3.8 18.5 + - + +
360A ALA* 4.2 16.8 - - + -
368A THR* 4.9 2.5 - - - +
369A ASN 3.1 14.2 + - - +
370A ARG* 3.5 24.0 - - - +
372A SER* 1.3 76.3 - - - +
374A ASP* 1.3 61.2 - - - +
376A TRP* 3.2 18.9 + - - +
377A SER* 3.3 9.5 + - - -
436A ARG* 3.8 0.6 - - - +
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Residues in contact with ASP 374 (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 MET* 3.7 19.6 - - + +
309A HIS* 2.8 30.9 + - + +
314A LEU* 5.3 0.5 - - - +
318A HIS* 3.9 17.3 + - - +
319A ALA* 5.1 0.9 - - - -
320A LEU* 3.9 9.4 + - + +
370A ARG* 2.9 39.8 + - - +
371A ARG 3.6 7.6 - - - +
372A SER 3.2 0.2 - - - -
373A ALA* 1.3 76.1 - - - +
375A MET* 1.3 57.2 + - - +
377A SER* 3.1 12.5 + - - -
378A PHE 3.0 21.3 + - - -
439A PHE* 3.5 8.6 - - + -
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Residues in contact with MET 375 (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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371A ARG 3.2 10.1 + - - +
372A SER* 3.2 11.9 + - - +
374A ASP* 1.3 72.7 - - - +
376A TRP* 1.3 61.1 + - - +
378A PHE* 3.2 10.9 + - - -
379A ALA 2.9 24.8 + - - -
428A CYS* 3.5 41.1 - - + +
436A ARG* 4.0 11.2 - - + -
437A PRO* 3.3 31.4 - - + +
438A LYS 3.7 3.6 - - - +
439A PHE* 3.5 47.7 - - + +
442A ILE* 3.8 9.4 - - + -
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Residues in contact with TRP 376 (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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354A ALA 4.8 1.8 + - - -
355A TRP 3.7 7.3 - - - -
356A VAL 3.6 12.5 + - - -
357A ALA* 3.5 28.5 - - + -
358A PRO* 3.6 24.9 - - + -
372A SER 3.2 3.6 + - - -
373A ALA 3.2 11.3 + - - +
375A MET* 1.3 77.9 - - - +
377A SER* 1.3 61.7 + - - +
379A ALA* 3.0 14.4 + - - +
380A VAL* 3.1 24.5 + - + +
404A VAL* 5.2 3.7 - - + +
410A ARG* 3.7 34.3 - - - -
411A PRO* 5.0 4.0 - - + +
428A CYS 3.7 10.7 + - - -
429A MET* 3.3 48.5 - - + -
430A ASN 3.7 7.9 - - - -
431A GLU* 3.7 9.0 - - - -
436A ARG* 3.5 28.7 - - - +
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Residues in contact with SER 377 (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* 6.1 0.2 - - - +
320A LEU* 3.3 37.1 + - - +
355A TRP* 2.7 28.1 + - - -
356A VAL* 4.4 4.0 - - - +
357A ALA 4.8 0.2 + - - -
373A ALA 3.3 10.6 + - - -
374A ASP* 3.1 14.0 + - - -
376A TRP* 1.3 77.7 - - - +
378A PHE* 1.3 62.7 + - - +
380A VAL* 3.2 5.7 + - - +
381A LEU* 3.0 24.7 + - - +
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Residues in contact with PHE 378 (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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298A ALA* 3.3 33.0 - - + -
301A MET* 4.1 12.6 - - + -
302A ALA* 4.0 10.1 - - + -
320A LEU* 3.9 13.1 - - + +
374A ASP 3.0 5.9 + - - -
375A MET* 3.4 12.8 - - - +
377A SER* 1.3 77.4 - - - +
379A ALA* 1.3 58.3 + - - +
381A LEU* 3.1 13.0 + - + +
382A LEU* 2.8 61.1 + - + +
424A LEU* 5.3 0.2 - - + -
428A CYS* 4.6 0.7 - - - -
439A PHE* 3.6 31.4 - + + -
442A ILE* 3.2 28.7 - - + -
446A LEU* 3.7 15.9 - - + -
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Residues in contact with ALA 379 (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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375A MET 2.9 7.2 + - - +
376A TRP 3.0 9.8 + - - +
378A PHE* 1.3 76.3 - - - +
380A VAL* 1.3 56.1 + - - +
382A LEU* 3.2 11.9 + - - +
383A TRP* 3.0 23.2 + - - +
425A MET* 4.0 5.8 - - - +
428A CYS* 3.5 30.1 - - + -
429A MET* 3.6 40.1 - - + +
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Residues in contact with VAL 380 (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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354A ALA 3.7 20.6 - - - +
355A TRP* 3.4 28.3 - - + +
376A TRP* 3.1 35.3 + - + +
377A SER 3.2 7.2 + - - +
379A ALA* 1.3 72.1 - - - +
381A LEU* 1.3 60.2 - - - +
383A TRP* 3.2 6.3 + - + +
384A GLU* 2.8 27.3 + - - +
391A PRO* 3.8 20.6 - - + -
411A PRO* 4.7 9.2 - - + -
429A MET* 4.2 15.5 - - + -
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Residues in contact with LEU 381 (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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277A LEU* 3.9 12.6 - - + -
281A LEU* 6.1 0.2 - - + -
301A MET* 3.7 31.0 - - + -
320A LEU* 3.5 40.6 - - + -
321A ASN* 4.0 2.0 - - - -
322A SER* 3.6 29.6 - - - +
355A TRP* 3.9 5.8 - - + +
377A SER 3.0 13.4 + - - +
378A PHE* 3.3 13.5 - - + +
380A VAL* 1.3 76.9 - - - +
382A LEU* 1.3 56.9 + - - +
384A GLU* 3.2 23.5 + - - +
385A LEU* 2.8 36.0 + - + +
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Residues in contact with LEU 382 (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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298A ALA* 4.0 17.5 - - + -
378A PHE* 2.8 57.4 + - + +
379A ALA* 3.2 10.3 + - - +
381A LEU* 1.3 72.1 - - - +
383A TRP* 1.3 62.5 + - - +
385A LEU* 3.2 8.7 + - + +
386A VAL* 2.9 28.0 + - + +
421A VAL* 6.1 3.4 - - + -
424A LEU* 3.9 33.2 - - + -
425A MET* 4.1 28.7 - - + +
428A CYS* 4.5 3.8 - - - -
446A LEU* 4.8 1.8 - - + -
449A MET* 6.3 1.1 - - + -
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Residues in contact with TRP 383 (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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379A ALA 3.0 13.5 + - - +
380A VAL* 3.2 12.8 + - + +
382A LEU* 1.3 73.7 - - - +
384A GLU* 1.3 62.8 + - + +
386A VAL* 3.2 2.2 + - - +
387A THR* 2.8 66.3 + - + +
389A GLU* 3.3 35.4 - - + -
390A VAL 4.2 2.0 - - - -
391A PRO* 3.5 34.8 - - + -
392A PHE 4.9 1.8 - - - -
411A PRO* 3.6 25.5 - - + +
412A THR 2.8 32.4 + - - +
414A PRO* 3.8 15.0 - - + +
425A MET* 3.9 18.5 - - - +
429A MET* 4.6 4.7 - - + -
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Residues in contact with GLU 384 (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 LEU* 4.0 11.0 - - + +
282A HIS* 2.5 36.1 + - + +
322A SER* 2.7 32.1 + - - -
355A TRP* 2.9 36.4 + - - -
380A VAL 2.8 14.3 + - - +
381A LEU* 3.4 11.1 - - - +
383A TRP* 1.3 87.4 - - + +
385A LEU* 1.3 56.6 + - - +
387A THR* 3.8 1.6 - - - -
388A ARG* 2.8 32.6 + - - -
389A GLU 3.5 9.0 - - - +
391A PRO* 4.1 4.3 - - + -
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Residues in contact with LEU 385 (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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277A LEU* 4.4 5.4 - - + -
281A LEU* 3.7 34.5 - - + -
291A GLN* 3.2 14.6 + - - +
294A ALA* 3.9 36.8 - - + +
297A PHE* 4.3 13.2 - - + -
298A ALA* 4.0 18.8 - - + +
301A MET* 4.1 18.6 - - + -
381A LEU* 2.8 26.2 + - + +
382A LEU* 3.6 9.4 - - + +
384A GLU* 1.3 71.4 - - - +
386A VAL* 1.3 62.0 + - + +
388A ARG* 2.8 25.8 + - - +
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Residues in contact with VAL 386 (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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291A GLN* 4.1 14.4 + - - +
382A LEU* 2.9 20.2 + - + +
383A TRP 3.6 3.4 - - - +
385A LEU* 1.3 80.4 - - + +
387A THR* 1.3 62.7 + - - +
388A ARG* 4.5 2.6 - - - +
414A PRO* 3.7 26.0 - - + -
417A ILE* 3.7 23.8 - - + -
421A VAL* 3.8 29.2 - - + -
425A MET* 3.8 9.9 - - + -
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Residues in contact with THR 387 (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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383A TRP* 2.8 60.3 + - + +
384A GLU 3.7 0.3 + - - -
386A VAL* 1.3 73.9 - - - +
388A ARG* 1.3 73.4 + - - +
389A GLU* 3.1 35.4 + - - +
414A PRO* 3.7 23.8 - - + -
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.1 29.6 + - - +
282A HIS* 4.1 13.9 + - - -
288A VAL* 3.7 17.0 - - + +
289A VAL* 2.8 45.1 + - - +
290A ASP 3.4 13.1 + - - -
291A GLN* 2.8 24.3 + - - -
294A ALA* 3.6 8.1 - - - +
384A GLU 2.8 15.8 + - - -
385A LEU* 2.8 24.5 + - - +
386A VAL 4.5 2.9 - - - +
387A THR* 1.3 81.7 - - - +
389A GLU* 1.3 61.5 + - - +
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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
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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