Contacts of the helix formed by residues 366 - 385 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ASN* 3.9 2.7 - - - -
329C TYR* 3.5 21.8 - - - -
342C SER* 2.7 23.8 + - - -
343C SER* 3.1 9.3 + - - -
365C THR* 1.3 73.8 - - - +
367C THR* 1.3 68.5 + - - -
368C SER 3.0 2.7 - - - -
369C ALA 3.1 9.4 + - - -
370C SER 3.9 0.2 + - - -
601C FMT 3.7 16.3 - - - -
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Residues in contact with THR 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ALA* 3.3 17.8 - - - +
293C SER* 3.4 7.4 + - - -
294C GLY 3.1 32.9 + - - -
295C ASN* 2.8 42.0 + - - +
317C ILE 4.3 2.9 + - - -
318C SER* 5.6 0.3 - - - -
319C SER* 3.7 13.8 + - - -
329C TYR* 3.5 3.9 - - - -
366C GLY* 1.3 71.4 - - - -
368C SER* 1.3 65.4 + - - +
370C SER* 3.1 15.6 + - - -
371C ALA 3.8 1.4 + - - -
5J 00S 3.5 25.4 - - + -
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C HIS* 2.7 36.0 + - - -
198C CYS* 3.5 3.3 - - - -
253C SER* 2.8 27.1 + - - -
292C ALA* 4.6 0.2 - - - -
295C ASN* 4.7 1.9 + - - +
364C HIS* 4.1 10.3 - - - -
365C THR 3.9 10.8 - - - -
366C GLY* 3.0 0.8 - - - -
367C THR* 1.3 82.7 - - - +
369C ALA* 1.3 56.4 + - - +
372C PRO* 3.0 14.9 - - - +
5J 00S 3.1 21.0 + - - -
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Residues in contact with ALA 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 2.5 29.4 - - - +
341C TYR 4.7 0.4 - - - -
342C SER* 3.7 12.3 - - - +
351C ILE* 3.5 30.7 - - + -
364C HIS* 3.6 18.4 - - + -
365C THR 3.8 5.8 + - - +
366C GLY 3.1 3.5 + - - +
368C SER* 1.3 78.0 - - - +
370C SER* 1.3 63.0 + - - +
372C PRO* 3.5 2.2 - - - +
373C LEU* 3.4 11.1 - - - +
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Residues in contact with SER 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 4.0 7.9 - - - -
318C SER 3.6 11.4 - - - -
319C SER* 2.6 29.0 + - - -
340C THR* 2.8 42.0 + - - -
341C TYR 3.6 6.8 + - - -
342C SER* 3.6 1.6 - - - -
366C GLY 3.9 0.2 + - - -
367C THR 3.1 9.0 + - - -
369C ALA* 1.3 76.7 - - - +
371C ALA* 1.3 66.2 + - - +
373C LEU* 3.2 3.3 + - - +
374C ALA* 3.1 15.8 + - - +
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Residues in contact with ALA 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C SER* 4.0 8.7 - - - +
252C ALA 4.5 2.5 - - - +
253C SER* 4.0 9.9 - - - +
290C VAL* 3.4 17.3 - - + +
291C TRP* 3.9 7.4 - - - -
292C ALA* 3.8 30.0 - - - +
317C ILE* 4.4 5.3 - - - +
367C THR 3.8 3.2 + - - -
370C SER* 1.3 76.2 - - - +
372C PRO* 1.3 66.7 - - + +
374C ALA* 3.0 7.4 + - - +
375C ALA* 2.8 25.6 + - - +
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Residues in contact with PRO 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE* 5.3 0.7 - - + -
198C CYS* 3.5 34.8 - - + +
201C GLU* 3.3 24.5 - - + +
202C VAL* 3.4 18.4 - - + +
251C SER* 3.8 13.9 - - - +
253C SER* 3.7 2.9 - - - +
368C SER 3.0 24.9 - - - +
369C ALA 3.5 3.8 - - - +
370C SER 3.4 3.8 - - - -
371C ALA* 1.3 93.8 - - + +
373C LEU* 1.3 56.0 + - - +
375C ALA* 3.1 1.4 + - + -
376C GLY* 2.9 25.1 + - - -
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Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C TYR* 4.0 36.1 - - + -
124C LEU* 4.6 0.7 - - + -
132C LEU* 4.2 14.8 - - + -
201C GLU* 3.3 30.7 - - + +
215C VAL* 3.7 26.4 - - + +
340C THR* 4.2 10.5 - - - +
341C TYR 3.5 25.1 - - - +
351C ILE* 4.3 5.2 - - + -
369C ALA 3.4 9.0 - - - +
370C SER 3.2 6.6 + - - +
372C PRO* 1.3 76.7 - - - +
374C ALA* 1.3 64.1 + - - +
376C GLY* 3.3 2.1 + - - -
377C ILE* 3.0 28.5 + - - +
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C VAL* 4.1 4.3 - - + -
317C ILE* 3.7 29.2 - - + -
340C THR* 4.0 2.6 - - + +
370C SER 3.1 9.3 + - - +
371C ALA 3.0 9.1 + - - +
373C LEU* 1.3 74.7 - - - +
375C ALA* 1.3 65.2 + - - +
377C ILE* 3.2 2.3 + - - +
378C ILE* 2.9 33.2 + - + +
429C LEU* 3.5 28.9 - - + -
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Residues in contact with ALA 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C VAL* 4.5 5.2 - - + +
202C VAL* 4.5 8.1 - - + -
249C ILE* 4.0 20.2 - - + +
251C SER* 4.0 24.0 - - - +
290C VAL* 4.1 13.6 - - + +
371C ALA 2.8 16.0 + - - +
372C PRO* 3.4 9.2 - - + +
374C ALA* 1.3 74.4 - - - +
376C GLY* 1.3 58.1 + - - +
378C ILE* 3.4 4.8 + - - +
379C ALA* 2.9 26.7 + - - +
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Residues in contact with GLY 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C VAL* 4.1 17.9 - - - +
215C VAL* 3.6 19.8 - - - +
216C ALA* 3.8 3.6 - - - +
372C PRO 2.9 14.0 + - - -
373C LEU 3.7 3.1 - - - -
374C ALA 3.2 0.2 - - - -
375C ALA* 1.3 75.4 - - - +
377C ILE* 1.3 64.4 + - - +
379C ALA* 3.0 15.2 + - - +
380C LEU* 3.0 16.3 + - - +
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Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 4.1 31.6 - - + -
134C VAL* 4.5 1.6 - - + -
215C VAL* 3.8 16.6 - - + -
373C LEU 3.0 17.9 + - - +
374C ALA 3.7 4.3 - - - +
376C GLY* 1.3 75.9 - - - +
378C ILE* 1.3 61.9 + - + +
380C LEU* 3.1 9.4 + - + +
381C THR* 2.8 25.6 + - - +
429C LEU* 4.0 33.2 - - + -
431C ALA* 3.9 36.6 - - + +
434C MET* 4.2 20.2 - - + -
435C VAL* 5.3 0.4 - - + +
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Residues in contact with ILE 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ILE* 3.8 15.7 - - + -
288C ILE* 4.0 12.6 - - + -
290C VAL* 3.7 25.6 - - + -
315C LEU* 4.0 25.4 - - + -
317C ILE* 6.0 1.1 - - + -
374C ALA* 2.9 26.5 + - + +
375C ALA* 3.6 5.6 - - - +
377C ILE* 1.3 77.8 - - + +
379C ALA* 1.3 57.4 + - - +
381C THR* 3.1 8.3 + - - -
382C LEU* 2.9 27.6 + - + +
393C MET* 3.7 33.0 - - + -
397C VAL* 5.3 2.9 - - + -
429C LEU* 5.7 3.4 - - + -
434C MET* 4.6 9.2 - - + -
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLY* 4.2 2.4 - - - -
147C ILE* 3.4 32.2 - - + +
149C VAL* 4.1 10.1 - - + -
216C ALA* 3.9 17.0 - - + -
219C ALA* 4.8 0.9 - - + -
249C ILE* 3.5 12.5 - - + +
375C ALA 2.9 14.1 + - - +
376C GLY* 3.0 11.0 + - - +
378C ILE* 1.3 75.2 - - - +
380C LEU* 1.3 65.1 + - - +
382C LEU* 3.4 1.5 + - - +
383C GLU* 3.2 17.5 + - - +
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 4.2 9.2 - - + -
137C ALA* 3.7 26.9 - - + -
138C TRP* 4.4 1.1 - - - +
142C TYR* 3.4 19.1 - - + +
143C THR* 3.3 33.2 - - - -
144C GLY 3.5 4.0 - - - +
215C VAL* 3.7 32.3 - - + +
216C ALA* 3.9 3.8 - - - -
376C GLY 3.0 15.6 + - - +
377C ILE* 3.4 6.7 - - + +
379C ALA* 1.3 76.1 - - - +
381C THR* 1.3 62.7 + - - +
383C GLU* 3.3 4.6 + - - +
384C ALA* 3.1 17.5 + - - +
431C ALA* 4.4 8.1 - - + -
435C VAL* 3.7 19.1 - - + +
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Residues in contact with THR 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C ILE 2.8 15.4 + - - -
378C ILE* 3.1 8.9 + - - -
380C LEU* 1.3 75.8 - - - +
382C LEU* 1.3 64.3 + - - +
384C ALA* 3.1 5.6 + - - +
385C ASN 3.1 18.5 + - - +
388C LEU* 3.9 6.9 - - + +
393C MET* 4.0 10.8 - - + -
396C LEU* 3.6 30.3 - - + -
434C MET* 3.5 33.5 - - + +
435C VAL* 4.1 7.5 - - - +
438C ALA* 3.6 12.9 - - + +
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Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE* 3.6 15.7 - - + -
248C HIS* 3.8 32.3 - - + -
249C ILE* 3.9 18.6 - - + -
282C ARG* 3.4 35.0 - - - +
288C ILE* 4.6 5.4 - - + -
378C ILE 2.9 14.7 + - - +
379C ALA 3.8 2.5 - - - +
380C LEU 3.3 0.2 - - - -
381C THR* 1.3 73.3 - - - +
383C GLU* 1.3 62.9 + - - +
385C ASN 3.7 14.4 - - - +
386C LYS* 2.9 37.5 + - - +
388C LEU* 4.2 3.8 - - + +
393C MET* 3.8 20.0 - - + -
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Residues in contact with GLU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLY 4.3 5.9 - - - +
142C TYR* 3.4 21.8 - - + +
143C THR* 2.8 15.8 + - - -
144C GLY* 2.7 27.9 + - - -
145C HIS* 3.3 35.6 - - - +
147C ILE* 3.8 15.2 - - + +
379C ALA 3.2 12.7 + - - +
380C LEU 3.6 7.6 - - - +
381C THR 3.2 0.2 - - - -
382C LEU* 1.3 77.9 - - - +
384C ALA* 1.3 61.2 + - - +
385C ASN* 3.3 0.9 + - - -
386C LYS* 4.5 14.0 - - - +
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TYR* 3.4 34.0 + - + -
380C LEU 3.1 11.9 + - - +
381C THR 3.1 9.8 + - - +
383C GLU* 1.3 77.5 - - - +
385C ASN* 1.3 60.9 + - - +
435C VAL* 3.8 25.6 - - + +
438C ALA* 4.1 5.4 - - + -
439C GLN* 4.2 14.2 - - + +
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Residues in contact with ASN 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C THR 3.1 4.9 + - - -
382C LEU* 2.9 9.5 + - - +
383C GLU 3.2 0.4 - - - -
384C ALA* 1.3 82.1 - - - +
386C LYS* 1.3 61.2 + - - +
387C ASN* 3.0 26.8 + - - +
388C LEU* 3.3 44.4 + - + +
438C ALA* 2.8 30.4 + - + +
439C GLN* 4.7 4.4 + - - -
441C TRP 4.0 13.9 + - - +
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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
------------------------------------------------------------
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