Contacts of the helix formed by residues 366 - 385 (chain F) in PDB entry 4OMD
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ASN* 3.9 8.5 - - - -
329F TYR* 3.5 25.5 - - - -
342F SER* 2.8 24.1 + - - -
343F SER* 3.0 9.9 + - - -
365F THR* 1.3 74.6 - - - +
367F THR* 1.3 67.5 + - - -
368F SER 3.0 5.0 + - - -
369F ALA 3.1 7.8 + - - -
370F SER 4.0 0.2 + - - -
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Residues in contact with THR 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F ALA* 3.3 18.8 - - - +
293F SER* 3.5 7.3 + - - -
294F GLY 3.2 31.3 + - - -
295F ASN* 2.9 41.4 + - - +
317F ILE 4.2 3.5 + - - -
319F SER* 3.7 14.8 + - - -
329F TYR* 3.5 5.2 - - - -
366F GLY* 1.3 71.4 - - - -
368F SER* 1.3 65.2 + - - +
370F SER* 3.1 16.2 + - - -
371F ALA 3.8 0.9 + - - -
5N 00S 3.5 24.5 - - + -
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Residues in contact with SER 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F HIS* 2.6 37.9 + - - -
198F CYS* 3.7 3.3 - - - -
253F SER* 2.8 26.7 + - - -
295F ASN* 4.7 1.4 + - - -
364F HIS* 4.0 9.2 - - - -
365F THR 3.9 11.7 - - - -
366F GLY* 3.0 0.8 - - - -
367F THR* 1.3 80.8 - - - +
369F ALA* 1.3 56.1 + - - +
372F PRO* 2.9 15.9 - - - +
5N 00S 3.1 20.4 - - - -
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Residues in contact with ALA 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F GLU* 2.5 33.6 - - - +
341F TYR 4.7 0.4 - - - -
342F SER* 3.6 13.0 - - - +
351F ILE* 3.5 31.0 - - + -
364F HIS* 3.7 17.2 + - + +
365F THR 4.0 3.6 + - - +
366F GLY 3.1 3.7 + - - +
368F SER* 1.3 77.4 - - - +
370F SER* 1.3 64.1 + - - +
372F PRO* 3.5 1.5 - - - +
373F LEU* 3.4 11.7 - - - +
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Residues in contact with SER 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F ILE* 4.1 8.7 - - - -
318F SER 3.6 11.2 - - - -
319F SER* 2.6 29.1 + - - -
340F THR* 2.9 44.1 + - - +
341F TYR 3.6 6.4 + - - -
342F SER* 3.6 1.6 - - - -
366F GLY 4.0 0.2 + - - -
367F THR 3.1 8.4 + - - -
369F ALA* 1.3 77.3 - - - +
371F ALA* 1.3 67.4 + - - +
373F LEU* 3.2 10.4 + - - +
374F ALA* 3.2 6.9 + - - +
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Residues in contact with ALA 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F SER* 4.0 8.3 - - - +
252F ALA 4.4 3.1 - - - +
253F SER* 3.9 11.2 - - - +
290F VAL* 3.5 16.4 - - + +
291F TRP* 3.9 7.2 - - - -
292F ALA* 3.8 28.2 - - + +
317F ILE* 4.4 5.5 - - - +
367F THR 3.8 2.8 + - - -
370F SER* 1.3 75.5 - - - +
372F PRO* 1.3 67.2 - - + +
374F ALA* 3.0 7.0 + - - +
375F ALA* 2.8 25.8 + - - +
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Residues in contact with PRO 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ILE* 5.3 0.4 - - + -
198F CYS* 3.5 34.5 - - + +
201F GLU* 3.2 23.1 - - + +
202F VAL* 3.2 20.9 - - + +
251F SER* 4.0 10.5 - - - +
253F SER* 3.7 3.6 - - - +
368F SER 2.9 28.7 - - - +
369F ALA 3.5 3.1 - - - +
370F SER 3.4 4.0 - - - -
371F ALA* 1.3 89.8 - - + +
373F LEU* 1.3 56.3 + - - +
375F ALA* 3.2 1.5 + - + -
376F GLY* 2.9 23.4 + - - -
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Residues in contact with LEU 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F TYR* 4.0 35.4 - - + -
124F LEU* 4.9 0.2 - - + -
132F LEU* 4.1 20.9 - - + -
201F GLU* 3.3 32.5 - - + +
215F VAL* 3.7 25.0 - - + +
340F THR* 4.1 6.7 - - - +
341F TYR 3.6 21.5 - - - +
351F ILE* 4.4 3.8 - - + -
369F ALA 3.4 11.9 - - - +
370F SER 3.2 6.4 + - - +
372F PRO* 1.3 73.8 - - - +
374F ALA* 1.3 66.6 + - - +
376F GLY* 3.2 1.9 + - - -
377F ILE* 3.0 29.1 + - - +
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Residues in contact with ALA 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290F VAL* 3.9 5.2 - - + -
317F ILE* 3.6 30.7 - - + -
340F THR* 4.0 3.0 - - + +
370F SER 3.2 6.9 + - - +
371F ALA 3.0 9.1 + - - +
373F LEU* 1.3 78.2 - - - +
375F ALA* 1.3 57.6 + - - +
377F ILE* 3.2 1.8 + - - +
378F ILE* 2.8 39.9 + - + +
429F LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F VAL* 4.5 4.3 - - + +
202F VAL* 4.2 9.0 - - + -
249F ILE* 3.8 20.1 - - + +
251F SER* 4.1 24.0 - - - -
290F VAL* 4.0 14.1 - - + +
371F ALA 2.8 12.3 + - - +
372F PRO* 3.4 9.4 - - + +
374F ALA* 1.3 77.2 - - - +
376F GLY* 1.3 57.3 + - - +
378F ILE* 3.4 4.1 + - - +
379F ALA* 2.9 27.4 + - - +
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Residues in contact with GLY 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL* 4.0 17.0 - - - +
215F VAL* 3.5 20.5 - - - +
216F ALA* 3.8 3.4 - - - +
372F PRO 2.9 14.1 + - - -
373F LEU 3.2 3.8 + - - -
375F ALA* 1.3 77.9 - - - +
377F ILE* 1.3 61.2 + - - +
379F ALA* 3.0 14.3 + - - +
380F LEU* 3.1 16.5 + - - +
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Residues in contact with ILE 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F LEU* 4.2 30.1 - - + -
134F VAL* 4.5 2.0 - - + -
215F VAL* 3.9 16.8 - - + -
340F THR* 5.1 0.2 - - + -
373F LEU 3.0 20.9 + - - +
374F ALA* 3.7 4.7 - - - +
376F GLY* 1.3 75.6 - - - +
378F ILE* 1.3 63.1 + - + +
380F LEU* 3.1 8.0 + - + +
381F THR* 3.0 25.7 + - - +
429F LEU* 3.9 32.1 - - + -
431F ALA* 3.8 35.2 - - + +
434F MET* 4.1 20.9 - - + -
435F VAL* 5.3 0.4 - - + +
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Residues in contact with ILE 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ILE* 3.8 14.6 - - + -
288F ILE* 3.9 15.5 - - + -
290F VAL* 3.8 20.9 - - + -
315F LEU* 3.6 32.1 - - + -
317F ILE* 6.1 0.4 - - + -
374F ALA* 2.8 27.1 + - + +
375F ALA* 3.7 5.2 - - - +
377F ILE* 1.3 77.9 - - + +
379F ALA* 1.3 56.5 + - - +
381F THR* 3.2 7.7 + - - -
382F LEU* 2.9 27.8 + - + +
393F MET* 3.4 29.6 - - + -
397F VAL* 5.2 2.7 - - + -
429F LEU* 5.6 3.4 - - + -
434F MET* 4.7 8.3 - - + -
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Residues in contact with ALA 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F GLY* 4.4 2.1 - - - -
147F ILE* 3.5 26.3 - - + +
149F VAL* 4.2 10.1 - - + -
216F ALA* 3.9 17.5 - - + -
219F ALA* 4.8 1.1 - - + -
249F ILE* 3.5 17.5 - - + +
375F ALA 2.9 12.8 + - - +
376F GLY* 3.0 10.5 + - - +
378F ILE* 1.3 76.2 - - - +
380F LEU* 1.3 65.7 + - - +
382F LEU* 3.3 1.4 + - - -
383F GLU* 3.2 18.0 + - - +
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Residues in contact with LEU 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F VAL* 4.4 8.3 - - + -
137F ALA* 3.9 24.7 - - + -
138F TRP* 4.5 0.9 - - + -
142F TYR* 3.7 11.3 - - + +
143F THR* 3.4 39.9 - - - +
144F GLY 3.4 1.1 - - - +
215F VAL* 3.7 33.4 - - + +
216F ALA* 3.8 7.0 - - + -
376F GLY 3.1 12.2 + - - +
377F ILE* 3.1 9.6 + - + +
379F ALA* 1.3 75.2 - - - +
381F THR* 1.3 63.0 + - - +
383F GLU* 3.2 8.7 + - - +
384F ALA* 3.1 20.8 + - - +
431F ALA* 4.5 4.7 - - + -
435F VAL* 3.8 16.2 - - + +
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Residues in contact with THR 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F ILE 3.0 14.7 + - - -
378F ILE* 3.4 9.2 - - - -
379F ALA 3.2 0.2 - - - -
380F LEU* 1.3 77.2 - - - +
382F LEU* 1.3 62.6 + - - +
384F ALA* 3.1 5.9 + - - +
385F ASN 3.1 18.2 + - - +
388F LEU* 3.7 7.3 - - + +
393F MET* 4.1 7.6 - - - -
396F LEU* 3.6 20.6 - - + -
434F MET* 3.3 34.5 - - + +
435F VAL* 4.1 7.8 + - - +
438F ALA* 3.5 23.9 - - + +
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Residues in contact with LEU 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ILE* 3.8 13.5 - - + -
248F HIS* 3.8 32.1 - - + -
249F ILE* 4.2 16.2 - - + -
282F ARG* 3.4 35.9 - - - +
288F ILE* 4.5 4.5 - - + -
378F ILE 2.9 12.8 + - - +
379F ALA 3.3 6.0 + - - +
381F THR* 1.3 73.6 - - - +
383F GLU* 1.3 61.0 + - - +
385F ASN 2.9 37.9 - - - +
386F LYS* 2.9 13.6 + - - +
388F LEU* 4.1 4.7 - - + -
393F MET* 3.7 23.6 - - + -
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Residues in contact with GLU 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F GLY 4.5 3.7 - - - +
142F TYR* 3.3 20.9 - - + +
143F THR* 2.8 15.2 + - - -
144F GLY* 2.7 25.0 + - - -
145F HIS* 3.0 47.4 - - - +
147F ILE* 4.0 9.1 - - + +
379F ALA 3.2 12.5 + - - +
380F LEU 3.5 7.0 - - - +
381F THR 3.2 0.4 - - - -
382F LEU* 1.3 78.0 - - - +
384F ALA* 1.3 62.1 + - - +
385F ASN* 3.2 1.4 + - - -
386F LYS* 4.3 12.8 - - - +
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Residues in contact with ALA 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F TYR* 3.5 32.2 + - + +
380F LEU 3.1 12.0 + - - +
381F THR 3.1 10.8 + - - +
383F GLU* 1.3 77.6 - - - +
385F ASN* 1.3 59.2 + - - +
435F VAL* 3.8 27.6 - - + +
438F ALA* 4.1 3.1 - - + -
439F GLN* 3.9 16.4 - - + +
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Residues in contact with ASN 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F THR 3.1 3.4 + - - +
382F LEU* 2.9 10.7 + - - +
383F GLU 3.1 0.4 - - - -
384F ALA* 1.3 82.3 - - - +
386F LYS* 1.3 60.8 + - - +
387F ASN* 2.9 26.4 + - - +
388F LEU* 3.3 45.0 + - + +
438F ALA 2.9 28.8 + - - +
439F GLN* 4.7 4.7 + - - -
441F TRP 3.9 14.3 + - - -
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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