Contacts of the helix formed by residues 366 - 385 (chain B) in PDB entry 4OMC
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 GLY 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ASN* 3.9 3.1 - - - -
329B TYR* 3.5 20.9 - - - -
342B SER* 2.6 24.4 + - - -
343B SER* 3.1 9.3 + - - -
365B THR* 1.3 73.7 - - - +
367B THR* 1.3 67.1 + - - -
368B SER 3.0 2.9 - - - -
369B ALA* 3.1 9.2 + - - -
370B SER 3.9 0.3 + - - -
603B FMT 3.7 17.0 - - - -
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.3 18.7 - - - +
293B SER* 3.4 7.4 + - - -
294B GLY 3.1 36.4 + - - -
295B ASN* 2.9 41.6 + - - +
317B ILE 4.3 2.8 + - - -
318B SER* 5.5 0.2 - - - -
319B SER* 3.7 14.1 + - - -
329B TYR* 3.5 4.1 - - - -
366B GLY* 1.3 71.6 - - - -
368B SER* 1.3 65.0 + - - +
370B SER* 3.1 15.6 + - - -
371B ALA 3.8 1.2 + - - -
5I 00S 3.6 21.8 - - + -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B HIS* 2.7 35.9 + - - -
198B CYS* 3.6 3.1 - - - -
253B SER* 2.9 28.0 + - - -
292B ALA* 4.7 0.2 - - - -
295B ASN* 4.7 2.1 + - - +
364B HIS* 4.1 10.3 - - - -
365B THR 3.9 11.2 - - - -
366B GLY 3.0 0.6 - - - -
367B THR* 1.3 81.6 - - - +
369B ALA* 1.3 56.6 + - - +
372B PRO* 2.9 14.7 - - - +
5I 00S 3.2 20.3 + - - -
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 2.5 35.2 - - - +
341B TYR 4.7 0.4 - - - -
342B SER* 3.6 18.8 - - - +
351B ILE* 3.6 19.5 - - + -
364B HIS* 3.6 15.3 - - + -
365B THR 3.8 6.7 + - - +
366B GLY 3.1 3.5 + - - +
368B SER* 1.3 79.3 - - - +
370B SER* 1.3 61.6 + - - +
372B PRO* 3.4 2.8 - - - +
373B LEU* 3.5 10.9 - - - +
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Residues in contact with SER 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 4.1 8.1 - - - -
318B SER 3.6 11.9 - - - -
319B SER* 2.7 29.9 + - - -
340B THR* 2.9 42.7 + - - +
341B TYR 3.6 1.7 + - - -
342B SER* 3.6 6.6 - - - -
366B GLY 3.9 0.4 + - - -
367B THR 3.1 7.8 + - - -
369B ALA* 1.3 77.8 - - - +
371B ALA* 1.3 67.3 + - - +
373B LEU* 3.2 2.8 + - - +
374B ALA* 3.2 13.7 + - - +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER* 4.0 8.7 - - - +
252B ALA 4.5 2.9 - - - +
253B SER* 4.0 9.2 - - - +
290B VAL* 3.5 16.3 - - + +
291B TRP* 3.9 7.2 - - - -
292B ALA* 3.7 31.4 - - + +
317B ILE* 4.3 7.5 - - - +
367B THR 3.8 3.2 + - - -
370B SER* 1.3 75.5 - - - +
372B PRO* 1.3 65.5 - - + +
374B ALA* 3.0 5.2 + - - +
375B ALA* 2.8 24.9 + - - +
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Residues in contact with PRO 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 5.3 0.2 - - + -
198B CYS* 3.5 33.0 - - + +
201B GLU* 3.3 24.2 - - + +
202B VAL* 3.4 19.1 - - + +
251B SER* 3.8 13.5 - - - +
253B SER* 3.8 4.9 - - - +
368B SER 2.9 26.2 - - - +
369B ALA 3.4 3.8 - - - +
370B SER 3.4 3.8 - - - -
371B ALA* 1.3 93.7 - - + +
373B LEU* 1.3 55.2 + - - +
375B ALA* 3.1 1.6 + - + -
376B GLY* 2.9 24.1 + - - -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 3.9 34.1 - - + -
124B LEU* 4.5 0.9 - - + -
132B LEU* 4.1 21.1 - - + -
201B GLU* 3.5 29.2 - - + +
215B VAL* 3.7 25.9 - - + +
340B THR* 4.2 10.1 - - - +
341B TYR 3.4 25.8 - - - +
351B ILE* 4.6 4.3 - - + -
369B ALA 3.5 8.7 - - - +
370B SER 3.2 6.3 + - - +
372B PRO* 1.3 76.8 - - - +
374B ALA* 1.3 63.5 + - - +
376B GLY* 3.2 2.3 + - - -
377B ILE* 3.0 28.2 + - - +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 4.0 4.5 - - + -
317B ILE* 3.7 28.5 - - + -
340B THR* 4.0 3.1 - - + +
370B SER 3.2 6.6 + - - +
371B ALA 3.0 9.3 + - - +
373B LEU* 1.3 76.9 - - - +
375B ALA* 1.3 66.0 + - - +
377B ILE* 3.2 2.3 + - - +
378B ILE* 2.9 33.3 + - + +
429B LEU* 3.6 29.2 - - + -
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.4 8.8 - - + +
202B VAL* 4.4 4.5 - - + -
249B ILE* 3.7 21.0 - - + +
251B SER* 4.1 23.1 - - - +
290B VAL* 4.2 13.6 - - + +
371B ALA 2.8 12.2 + - - +
372B PRO* 3.1 10.7 + - + +
374B ALA* 1.3 75.7 - - - +
376B GLY* 1.3 57.9 + - - +
378B ILE* 3.4 4.0 + - - +
379B ALA* 2.9 27.1 + - - +
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Residues in contact with GLY 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.1 16.5 - - - +
215B VAL* 3.5 19.2 - - - +
216B ALA* 3.9 3.3 - - - +
372B PRO 2.9 13.8 + - - -
373B LEU 3.2 3.3 + - - -
374B ALA 3.1 0.2 - - - -
375B ALA* 1.3 75.2 - - - +
377B ILE* 1.3 65.5 + - - +
379B ALA* 3.0 15.7 + - - +
380B LEU* 3.0 16.3 + - - +
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.2 28.9 - - + -
134B VAL* 4.4 2.2 - - + -
215B VAL* 3.9 15.9 - - + -
340B THR* 5.0 0.2 - - + -
373B LEU 3.0 17.8 + - - +
374B ALA* 3.2 6.7 + - - +
376B GLY* 1.3 74.8 - - - +
378B ILE* 1.3 62.3 + - + +
380B LEU* 3.1 9.1 + - - +
381B THR* 2.9 26.5 + - - +
429B LEU* 3.8 35.0 - - + -
431B ALA* 4.0 35.0 - - + +
434B MET* 4.2 20.0 - - + -
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Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 3.8 16.2 - - + -
288B ILE* 4.0 13.0 - - + -
290B VAL* 3.7 26.2 - - + -
315B LEU* 3.9 25.6 - - + -
317B ILE* 6.1 0.9 - - + -
374B ALA* 2.9 27.2 + - + +
375B ALA* 3.6 4.7 - - - +
377B ILE* 1.3 75.4 - - + +
379B ALA* 1.3 59.5 + - - +
381B THR* 3.1 8.4 + - - -
382B LEU* 2.9 27.5 + - + +
393B MET* 3.6 31.9 - - + -
397B VAL* 5.3 3.1 - - + -
429B LEU* 5.7 3.4 - - + -
434B MET* 4.7 8.5 - - + -
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY* 4.2 1.6 - - - -
147B ILE* 3.4 28.5 - - + +
149B VAL* 4.2 10.5 - - + -
216B ALA* 3.9 17.0 - - + -
219B ALA* 4.9 0.9 - - + -
249B ILE* 3.5 15.5 - - + +
375B ALA 2.9 14.3 + - - +
376B GLY* 3.0 10.1 + - - +
378B ILE* 1.3 78.7 - - - +
380B LEU* 1.3 63.2 + - - +
382B LEU 3.4 1.3 + - - +
383B GLU* 3.2 18.0 + - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 4.4 4.0 - - + -
137B ALA* 3.8 24.9 - - + -
138B TRP* 4.3 5.6 - - - +
142B TYR* 3.5 10.4 - - + +
143B THR* 3.3 41.7 - - - +
144B GLY 3.3 1.6 - - - +
215B VAL* 3.8 32.5 - - + +
216B ALA* 3.9 5.2 - - + -
376B GLY 3.0 15.2 + - - +
377B ILE* 3.1 10.3 + - + +
379B ALA* 1.3 76.9 - - - +
381B THR* 1.3 62.8 + - - +
383B GLU* 3.3 7.2 + - - +
384B ALA 3.1 16.8 + - - -
431B ALA* 4.6 4.5 - - + -
435B VAL* 3.5 20.2 - - + +
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Residues in contact with THR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ILE 2.9 14.1 + - - -
378B ILE* 3.4 11.2 - - - -
380B LEU* 1.3 79.1 - - - +
382B LEU* 1.3 61.9 + - - +
384B ALA* 3.1 5.1 + - - +
385B ASN 3.0 17.2 + - - -
388B LEU* 3.6 12.2 - - + +
393B MET* 3.9 10.1 - - - -
396B LEU* 3.6 31.9 - - + -
434B MET* 3.5 31.1 - - + +
435B VAL* 4.1 8.7 + - - +
438B ALA* 3.7 9.1 - - + +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.7 17.0 - - + -
248B HIS* 3.8 30.7 - - + -
249B ILE* 4.1 17.5 - - + -
282B ARG* 3.3 37.0 - - - +
288B ILE* 4.5 4.7 - - + -
378B ILE* 2.9 16.9 + - + +
379B ALA 3.8 2.7 - - - +
381B THR* 1.3 73.4 - - - +
383B GLU* 1.3 66.6 + - - +
385B ASN 3.8 14.1 - - - +
386B LYS* 2.9 33.3 + - - +
388B LEU* 4.2 3.8 - - + -
393B MET* 3.8 20.2 - - + -
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 4.3 5.7 - - - +
142B TYR* 3.5 20.2 - - + -
143B THR* 2.9 13.5 + - - -
144B GLY* 2.7 30.1 + - - -
145B HIS* 3.4 40.9 - - - +
147B ILE* 3.9 9.8 - - + +
379B ALA 3.2 13.5 + - - +
380B LEU 3.6 7.6 - - - +
381B THR 3.2 0.4 - - - -
382B LEU* 1.3 78.2 - - - +
384B ALA* 1.3 61.6 + - - +
385B ASN* 3.3 0.7 + - - -
386B LYS* 4.5 13.0 + - - +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 3.4 31.9 + - + +
380B LEU 3.1 10.7 + - - +
381B THR 3.1 10.6 + - - +
383B GLU* 1.3 79.5 - - - +
385B ASN* 1.3 60.3 + - - +
435B VAL* 3.8 28.0 - - + +
438B ALA* 4.1 5.4 - - + -
439B GLN* 4.1 14.2 - - + +
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Residues in contact with ASN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B THR 3.0 4.9 + - - -
382B LEU* 3.0 9.5 + - - +
384B ALA* 1.3 81.2 - - - +
386B LYS* 1.3 61.2 + - - +
387B ASN* 3.0 27.2 + - - +
388B LEU* 3.2 45.1 + - + +
438B ALA* 2.8 28.8 + - + +
439B GLN* 4.6 4.2 + - - -
441B TRP 3.9 14.1 + - - +
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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