Contacts of the helix formed by residues 370 - 387 (chain A) in PDB entry 1OMW
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 SER 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A HIS* 3.4 47.9 + - - +
314A VAL* 4.1 10.0 - - - +
342A PHE* 4.0 15.1 - - - -
369A ASP* 1.3 80.3 + - - +
371A SER* 1.3 61.5 + - - +
372A ALA 3.2 1.7 + - - -
373A ASP 3.6 7.6 + - - -
374A TRP* 3.3 21.2 + - - -
438A GLY 5.4 2.5 + - - -
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Residues in contact with SER 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLU* 3.4 17.3 + - - +
368A TYR* 4.3 2.6 - - - +
369A ASP* 3.4 24.4 + - - -
370A SER* 1.3 75.7 + - - +
372A ALA* 1.3 64.2 + - - +
373A ASP 3.2 1.6 + - - -
374A TRP* 3.7 4.8 + - - +
375A PHE 3.7 7.1 + - - -
433A VAL* 4.2 16.0 - - - +
436A ARG* 2.7 24.3 + - - -
438A GLY 5.7 0.2 + - - -
439A CYS* 3.3 31.6 - - - -
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 4.0 10.5 - - + -
316A ARG* 5.3 4.9 - - + -
357A MET* 5.4 0.2 - - - -
358A ALA* 4.1 7.8 + - - +
360A GLU* 4.1 7.0 - - - +
361A VAL* 3.5 27.6 - - + -
368A TYR* 3.8 12.1 - - + -
369A ASP 3.2 14.8 + - - +
371A SER* 1.3 78.9 + - - +
373A ASP* 1.3 55.2 + - - +
375A PHE* 3.9 2.6 + - - +
376A SER* 2.4 33.4 + - - -
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Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.8 22.6 - - + +
309A HIS* 2.8 33.2 + - + -
314A VAL* 3.5 7.1 - - - +
315A TYR* 2.9 26.7 + - - +
316A ARG* 2.8 31.3 + - - -
318A LEU* 4.4 3.9 - - + +
370A SER 3.6 1.6 + - - +
371A SER 3.2 0.8 - - - -
372A ALA* 1.3 79.0 - - - +
374A TRP* 1.3 54.5 + - - +
376A SER* 3.2 6.8 + - - -
377A LEU* 2.7 36.8 + - - +
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Residues in contact with TRP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.3 16.2 - - + -
305A LEU* 3.4 39.0 - - + -
309A HIS* 3.9 20.0 + + - -
370A SER* 3.3 20.9 + - - -
371A SER* 3.7 5.6 + - - +
372A ALA 3.5 0.4 - - - -
373A ASP* 1.3 73.9 - - - +
375A PHE* 1.3 59.5 + - - +
377A LEU* 4.0 19.5 - - + +
378A GLY 3.2 17.8 + - - -
428A LEU* 3.5 23.1 - - + +
436A ARG* 4.5 3.4 - - - -
437A LEU 3.6 17.0 - - - +
438A GLY* 3.4 36.5 + - - -
439A CYS* 4.1 7.0 - - - -
443A GLY* 4.5 2.6 - - - -
444A ALA* 3.5 38.8 - - + -
447A VAL* 4.3 15.0 - - + -
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Residues in contact with PHE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR 4.7 0.2 - - - -
357A MET 3.5 18.4 - - - -
358A ALA* 3.4 24.9 - - + -
359A PRO* 3.7 11.9 - - + -
371A SER 3.7 3.4 + - - -
373A ASP 3.4 0.2 - - - -
374A TRP* 1.3 76.2 - - - +
376A SER* 1.4 61.5 + - - +
377A LEU 3.2 0.2 - - - -
379A CYS* 3.1 50.4 + - - -
391A PHE* 3.4 28.3 - + - -
406A THR* 3.7 13.9 - - + -
428A LEU 3.5 7.4 + - - -
429A LEU* 3.2 38.6 - - + +
430A GLN 4.2 2.2 - - - -
431A ARG* 4.6 2.5 - - + -
436A ARG* 3.3 36.3 - - - +
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 4.8 6.4 + - - -
318A LEU* 4.1 21.6 - - - +
356A TYR* 2.6 35.3 + - - +
357A MET* 4.4 1.9 - - - -
372A ALA 2.4 23.7 + - - -
373A ASP* 3.2 12.6 + - - -
375A PHE* 1.4 75.2 - - - +
377A LEU* 1.3 60.1 - - - +
379A CYS* 3.2 2.8 + - - +
380A MET* 3.0 29.6 + - - +
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Residues in contact with LEU 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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298A ALA* 5.1 0.2 - - - -
301A ILE* 3.6 31.4 - - + -
302A ILE* 3.6 33.7 - - + -
305A LEU* 4.3 2.5 - - + -
318A LEU* 3.9 13.7 - - + +
373A ASP 2.7 20.0 + - - +
374A TRP* 4.0 20.2 - - + +
376A SER* 1.3 70.9 - - - +
378A GLY* 1.3 60.7 + - - +
379A CYS 3.0 5.7 + - - -
380A MET* 4.5 6.1 - - - +
381A LEU* 2.9 50.1 + - + +
428A LEU* 4.6 11.7 - - + -
447A VAL* 5.0 0.9 - - + -
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Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TRP 3.2 11.9 + - - -
375A PHE 3.3 0.8 + - - -
376A SER 3.3 0.2 - - - -
377A LEU* 1.3 76.7 - - - +
379A CYS* 1.3 56.9 + - - +
381A LEU* 4.6 1.1 - - - -
382A PHE* 3.3 28.1 + - - +
425A LEU* 3.9 12.4 - - - +
428A LEU* 4.0 20.8 - - - +
429A LEU* 3.8 24.5 - - - +
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Residues in contact with CYS 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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355A GLY 3.9 13.7 - - - +
356A TYR* 3.7 23.7 - - + -
375A PHE* 3.1 45.8 + - - +
376A SER 3.4 8.7 - - - +
377A LEU 3.0 0.8 - - - -
378A GLY* 1.3 79.2 - - - +
380A MET* 1.3 62.9 + - - +
382A PHE 3.7 0.2 + - - -
383A LYS* 3.3 18.2 + - - +
390A PRO* 3.4 23.9 - - + +
391A PHE* 4.0 12.8 - - - -
429A LEU* 4.0 7.6 - - - -
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.6 1.1 - - + -
297A TYR* 5.2 1.6 - - + -
301A ILE* 4.9 4.9 - - + -
318A LEU* 4.1 14.8 - - + +
319A LYS* 3.7 10.3 - - - -
320A PRO* 3.6 24.0 - - + -
323A ILE* 3.5 35.0 - - + -
356A TYR* 3.8 15.9 - - + -
376A SER 3.0 16.3 + - - +
377A LEU* 3.5 7.8 + - - +
379A CYS* 1.3 76.2 - - - +
381A LEU* 1.3 80.7 + - + +
383A LYS* 3.1 6.8 + - - +
384A LEU* 3.1 58.5 + - + +
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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
----------------------------------------------------------
294A MET* 3.3 45.7 - - + +
298A ALA* 3.8 24.0 - - + +
377A LEU* 2.9 44.0 - - + +
378A GLY* 4.2 3.6 - - - +
380A MET* 1.3 93.6 - - + +
382A PHE* 1.3 66.0 + - - +
383A LYS 3.1 1.9 + - - -
384A LEU* 3.2 13.0 + - + +
385A LEU* 3.3 19.6 + - - +
424A LEU* 4.6 14.6 - - + -
425A LEU* 4.9 7.0 - - + -
428A LEU* 4.8 3.4 - - + -
453A PHE* 5.4 0.4 - - + -
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Residues in contact with PHE 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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378A GLY 3.3 19.1 + - - +
379A CYS 4.0 0.2 - - - +
380A MET 3.4 0.2 - - - -
381A LEU* 1.3 79.1 - - - +
383A LYS* 1.3 60.5 + - - +
385A LEU* 3.2 12.0 + - - +
386A ARG* 3.0 35.5 + - + +
388A HIS* 3.1 37.0 - + - -
389A SER 3.7 2.7 - - - -
390A PRO* 3.4 46.0 - - + -
411A VAL* 4.6 4.0 - - + -
412A GLU 4.8 1.6 - - - -
413A LEU* 4.5 15.9 - - + -
414A PRO* 4.6 7.2 - - + -
417A PHE* 4.0 31.0 - + - -
425A LEU* 4.6 10.7 - - + +
429A LEU* 5.5 2.7 - - + -
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Residues in contact with LYS 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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280A HIS* 4.7 16.9 + - - -
283A LEU* 3.9 25.6 - - + +
320A PRO* 4.2 12.3 - - + +
356A TYR* 3.4 26.3 + - + +
379A CYS 3.3 12.0 + - - +
380A MET* 3.1 14.1 + - - +
381A LEU 3.1 0.6 - - - -
382A PHE* 1.3 74.9 - - - +
384A LEU* 1.3 62.4 + - - +
387A GLY* 2.6 39.3 + - - -
388A HIS* 3.0 36.7 - - - +
389A SER* 3.9 2.9 + - - +
392A ARG* 6.0 3.4 - - - +
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Residues in contact with LEU 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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279A LEU* 4.1 22.0 - - + +
283A LEU* 3.7 22.8 - - + +
288A VAL* 3.4 8.0 - - - +
289A PHE* 2.9 36.4 + - + -
294A MET* 4.4 19.3 - - + -
297A TYR* 4.2 21.3 - - + -
320A PRO* 3.8 33.4 - - + -
380A MET* 3.1 37.9 + - + +
381A LEU* 3.2 6.7 + - - +
383A LYS* 1.3 76.8 - - - +
385A LEU* 1.3 59.5 + - - +
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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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288A VAL* 3.5 17.7 - - - +
289A PHE 3.5 21.0 - - - +
290A SER 4.1 0.7 - - - -
291A GLU* 3.7 27.8 - - + +
294A MET* 4.2 15.7 - - + -
381A LEU* 3.3 14.2 + - + +
382A PHE* 3.2 8.5 + - - +
383A LYS 3.1 0.2 - - - -
384A LEU* 1.3 81.0 - - - +
386A ARG* 1.3 69.7 + - + +
417A PHE* 3.8 16.8 - - + -
421A LEU* 3.4 45.1 - - + -
425A LEU* 4.6 3.4 - - + -
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Residues in contact with ARG 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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288A VAL* 3.7 7.1 - - - +
382A PHE* 3.0 32.9 + - + +
385A LEU* 1.3 83.1 - - - +
387A GLY* 1.3 60.3 + - - +
388A HIS* 3.4 25.8 + - + -
414A PRO* 3.4 28.4 - - - +
416A SER* 4.8 4.0 - - - -
417A PHE* 3.8 30.3 - - + -
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Residues in contact with GLY 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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283A LEU* 5.1 6.8 - - - +
288A VAL* 3.5 14.8 - - - +
383A LYS* 2.6 36.7 + - - -
386A ARG* 1.3 73.9 - - - +
388A HIS* 1.3 59.2 + - - +
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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