Contacts of the helix formed by residues 366 - 385 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D ASN* 3.9 0.9 - - - -
329D TYR* 3.4 21.3 - - - -
342D SER* 2.7 23.9 + - - -
343D SER* 3.0 9.5 + - - -
365D THR* 1.3 74.8 - - - +
367D THR* 1.3 67.2 + - - -
368D SER 3.0 3.1 - - - -
369D ALA 3.1 9.2 + - - -
370D SER 3.9 0.2 + - - -
603D FMT 3.6 18.5 + - - -
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Residues in contact with THR 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ALA* 3.3 18.5 - - - +
293D SER* 3.4 7.3 + - - -
294D GLY 3.1 35.5 + - - -
295D ASN* 2.8 41.4 + - - +
317D ILE 4.3 2.6 + - - -
318D SER* 5.5 0.3 - - - -
319D SER* 3.7 14.3 + - - -
329D TYR* 3.4 4.3 - - - -
366D GLY* 1.3 71.6 - - - -
368D SER* 1.3 65.7 + - - +
370D SER* 3.1 15.9 + - - -
371D ALA 3.8 1.2 + - - -
5K 00S 3.6 21.8 - - + -
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Residues in contact with SER 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D HIS* 2.6 37.4 + - - -
198D CYS* 3.6 2.9 - - - -
253D SER* 2.9 27.7 + - - -
295D ASN* 4.7 2.2 + - - +
364D HIS* 4.1 10.8 - - - -
365D THR 3.9 11.0 - - - -
366D GLY* 3.0 0.4 - - - -
367D THR* 1.3 82.1 - - - +
369D ALA* 1.3 55.8 + - - +
372D PRO* 2.9 15.6 - - - +
4K ARG 4.4 0.2 - - - -
5K 00S 3.2 20.1 - - - -
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Residues in contact with ALA 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 2.5 36.1 - - - +
341D TYR 4.7 0.4 - - - -
342D SER* 3.6 12.8 - - - +
351D ILE* 3.5 25.6 - - + -
364D HIS* 3.6 14.8 - - + -
365D THR 3.8 6.5 + - - +
366D GLY 3.1 4.1 + - - +
368D SER* 1.3 78.5 - - - +
370D SER* 1.3 62.9 + - - +
372D PRO* 3.6 1.5 - - - +
373D LEU* 3.4 11.6 - - - +
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Residues in contact with SER 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ILE* 4.0 8.7 - - - -
318D SER 3.6 11.4 - - - -
319D SER* 2.6 30.0 + - - -
340D THR* 2.8 41.1 + - - +
341D TYR 3.6 1.9 + - - -
342D SER* 3.5 7.1 - - - -
367D THR* 3.1 7.9 + - - -
369D ALA* 1.3 78.1 - - - +
371D ALA* 1.3 67.0 + - - +
373D LEU 3.2 3.1 + - - -
374D ALA* 3.2 14.6 + - - +
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D SER* 4.0 8.1 - - - +
252D ALA 4.4 3.1 - - - +
253D SER* 4.0 9.9 - - - +
290D VAL* 3.5 17.0 - - + +
291D TRP* 3.9 6.7 - - - -
292D ALA* 3.7 30.5 - - + +
317D ILE* 4.4 7.7 - - - +
367D THR 3.8 2.6 + - - -
370D SER* 1.3 77.7 - - - +
372D PRO* 1.3 64.3 - - + +
374D ALA* 3.0 5.1 + - - +
375D ALA* 2.8 25.5 + - - +
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Residues in contact with PRO 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 5.3 0.2 - - + -
198D CYS* 3.6 34.1 - - + +
201D GLU* 3.4 24.0 - - + +
202D VAL* 3.3 19.9 - - + +
251D SER* 3.8 13.7 - - - +
253D SER* 3.6 4.9 - - - +
368D SER 2.9 28.9 - - - +
369D ALA 3.6 3.1 - - - +
370D SER 3.5 3.1 - - - -
371D ALA* 1.3 91.3 - - + +
373D LEU* 1.3 56.2 + - - +
375D ALA* 3.1 1.4 + - + -
376D GLY* 2.9 23.9 + - - -
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Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D TYR* 4.0 35.2 - - + -
124D LEU* 4.7 0.7 - - + -
132D LEU* 4.2 16.8 - - + -
201D GLU* 3.5 24.5 - - + +
215D VAL* 3.8 24.9 - - + +
340D THR* 4.2 11.0 - - - +
341D TYR 3.4 25.4 - - - +
351D ILE* 4.5 5.6 - - + -
369D ALA 3.4 14.8 - - - +
370D SER 3.2 6.3 + - - +
372D PRO* 1.3 77.3 - - - +
374D ALA* 1.3 64.3 + - - +
376D GLY* 3.2 1.7 + - - -
377D ILE* 3.0 28.0 + - - +
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Residues in contact with ALA 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D VAL* 3.9 4.5 - - + -
317D ILE* 3.6 30.5 - - + -
340D THR* 3.9 2.6 - - + +
370D SER 3.2 6.9 + - - +
371D ALA 3.0 8.8 + - - +
373D LEU* 1.3 79.8 - - - +
375D ALA* 1.3 63.2 + - - +
377D ILE* 3.2 2.4 + - - +
378D ILE* 2.9 32.8 + - + +
429D LEU* 3.6 27.1 - - + +
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Residues in contact with ALA 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 4.5 4.8 - - + +
202D VAL* 4.4 8.7 - - + -
249D ILE* 4.0 19.5 - - + +
251D SER* 4.0 23.1 - - - -
290D VAL* 4.1 14.3 - - + +
371D ALA 2.8 12.9 + - - +
372D PRO* 3.1 10.7 + - + +
374D ALA* 1.3 77.4 - - - +
376D GLY* 1.3 56.7 - - - +
378D ILE* 3.4 4.7 + - - +
379D ALA* 2.9 26.5 + - - +
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Residues in contact with GLY 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D VAL* 4.1 16.7 - - - +
215D VAL* 3.5 19.6 - - - +
216D ALA* 3.9 3.3 - - - +
372D PRO 2.9 14.1 + - - -
373D LEU 3.7 3.4 - - - -
374D ALA 3.2 0.2 - - - -
375D ALA* 1.3 75.4 - - - +
377D ILE* 1.3 65.1 + - - +
379D ALA* 3.0 15.4 + - - +
380D LEU* 3.1 16.8 + - - +
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Residues in contact with ILE 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 4.1 31.0 - - + -
134D VAL* 4.4 2.5 - - + -
215D VAL* 3.9 16.2 - - + -
373D LEU 3.0 17.2 + - - +
374D ALA 3.2 4.7 + - - +
376D GLY* 1.3 74.9 - - - +
378D ILE* 1.3 64.0 + - + +
380D LEU* 3.1 8.5 + - - +
381D THR* 2.9 26.1 + - - +
429D LEU* 4.0 32.8 - - + -
431D ALA* 3.9 35.0 - - + +
434D MET* 4.2 19.5 - - + -
435D VAL* 5.3 0.2 - - - +
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Residues in contact with ILE 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ILE* 3.9 15.5 - - + -
288D ILE* 3.9 13.5 - - + -
290D VAL* 3.8 22.0 - - + -
315D LEU* 3.8 29.4 - - + -
317D ILE* 6.1 0.7 - - + -
374D ALA* 2.9 26.7 + - + +
375D ALA* 3.6 5.4 - - - +
377D ILE* 1.3 78.3 - - + +
379D ALA* 1.3 56.8 + - - +
381D THR* 3.2 9.3 + - - -
382D LEU* 2.9 27.8 + - + +
393D MET* 3.7 30.7 - - + -
397D VAL* 5.2 3.6 - - + -
429D LEU* 5.6 2.9 - - + -
434D MET* 4.8 7.4 - - + -
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Residues in contact with ALA 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLY* 4.3 1.9 - - - -
147D ILE* 3.4 31.7 - - + +
149D VAL* 4.1 9.2 - - + -
216D ALA* 3.9 17.5 - - + -
219D ALA* 4.8 1.1 - - + -
249D ILE* 3.6 13.2 - - + +
375D ALA 2.9 13.8 + - - +
376D GLY* 3.0 12.1 + - - +
378D ILE* 1.3 77.4 - - - +
380D LEU* 1.3 61.2 + - - +
382D LEU 3.3 1.0 + - - -
383D GLU* 3.1 18.4 + - - +
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Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 4.4 8.5 - - + -
137D ALA* 3.8 24.2 - - + -
138D TRP* 4.5 0.4 - - - +
142D TYR* 3.5 12.1 - - + +
143D THR* 3.3 41.3 - - - +
144D GLY 3.4 4.3 - - - +
215D VAL* 3.7 33.4 - - + +
216D ALA* 3.8 4.9 - - - -
376D GLY 3.1 15.2 + - - +
377D ILE* 3.4 9.6 - - + +
379D ALA* 1.3 76.9 - - - +
381D THR* 1.3 62.5 + - - +
383D GLU* 3.2 5.9 + - - +
384D ALA* 3.1 20.4 + - - +
431D ALA* 4.5 5.2 - - + -
435D VAL* 3.8 15.2 - - + +
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Residues in contact with THR 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D ILE 2.9 14.4 + - - -
378D ILE* 3.2 10.7 + - - -
380D LEU* 1.3 78.2 - - - +
382D LEU* 1.3 57.0 + - - +
384D ALA* 3.1 5.5 + - - +
385D ASN 3.0 21.1 + - - -
388D LEU* 3.8 9.1 - - + +
393D MET* 4.0 10.1 - - - -
396D LEU* 3.7 20.2 - - + -
434D MET* 3.5 33.1 - - + +
435D VAL* 4.1 8.3 + - - +
438D ALA* 3.6 22.6 - - + +
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Residues in contact with LEU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ILE* 3.7 16.4 - - + -
248D HIS* 3.9 31.0 - - + -
249D ILE* 3.9 20.0 - - + -
282D ARG* 3.2 35.7 - - - +
288D ILE* 4.5 4.7 - - + -
378D ILE* 2.9 15.8 + - + +
379D ALA 3.8 2.0 - - - +
381D THR* 1.3 72.8 - - - +
383D GLU* 1.3 67.1 + - - +
385D ASN 3.7 14.6 - - - +
386D LYS* 2.9 34.3 + - + +
388D LEU* 4.2 3.6 - - + -
393D MET* 3.9 20.6 - - + -
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Residues in contact with GLU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLY 4.3 6.1 - - - +
142D TYR* 3.4 20.8 - - + +
143D THR* 2.8 14.1 + - - -
144D GLY* 2.7 26.4 + - - -
145D HIS* 3.3 40.4 - - - +
147D ILE* 3.8 14.5 - - + +
379D ALA 3.1 12.6 + - - +
380D LEU 3.2 7.8 + - - +
382D LEU* 1.3 77.1 - - - +
384D ALA* 1.3 63.4 + - - +
385D ASN* 3.3 1.2 + - - -
386D LYS* 4.4 15.3 - - - +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D TYR* 3.5 31.2 + - + +
380D LEU 3.1 11.5 + - - +
381D THR 3.1 10.3 + - - +
383D GLU* 1.3 79.8 - - - +
385D ASN* 1.3 61.0 + - - +
435D VAL* 3.8 26.7 - - + +
438D ALA* 4.1 6.3 - - + -
439D GLN* 4.2 13.5 - - + +
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Residues in contact with ASN 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D THR 3.0 4.9 + - - -
382D LEU* 2.9 9.5 + - - +
383D GLU 3.1 0.2 - - - -
384D ALA* 1.3 80.2 - - - +
386D LYS* 1.3 61.5 + - - +
387D ASN* 3.0 25.3 + - - +
388D LEU* 3.2 45.1 + - + +
438D ALA* 2.7 29.8 + - + +
439D GLN* 4.7 3.8 + - - -
441D TRP 3.9 14.5 + - - +
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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
------------------------------------------------------------
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