Contacts of the helix formed by residues 352 - 372 (chain B) in PDB entry 2C6N
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 THR 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ASN* 5.7 4.7 - - - +
280B THR* 3.4 13.9 - - + +
283B MET* 4.1 3.8 - - - +
293B MET* 3.7 6.9 - - - +
350B ARG* 3.4 5.5 + - - +
351B VAL* 1.3 81.1 + - - +
353B MET* 1.3 76.1 + - + +
354B ASP* 3.3 17.5 - - + +
355B GLN* 3.2 15.5 - - - +
356B LEU* 3.0 18.9 + - - +
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Residues in contact with MET 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASP* 2.4 46.7 - - - +
279B VAL* 4.8 2.0 - - + +
280B THR* 2.9 11.2 + - - +
283B MET* 4.3 9.0 - - - -
352B THR* 1.3 74.5 - - + +
354B ASP* 1.3 67.4 + - - +
356B LEU* 3.0 7.5 + - - +
357B SER* 3.0 21.7 + - - -
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Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 5.6 9.0 - - - +
278B ASP* 4.8 1.2 + - - -
352B THR* 3.3 12.8 - - + +
353B MET* 1.3 77.6 - - - +
355B GLN* 1.3 62.4 + - - +
357B SER* 2.5 25.5 + - - -
358B THR* 3.0 12.3 + - - -
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B MET* 3.9 3.6 - - + -
347B GLN* 4.3 4.4 + - - +
349B THR* 4.8 2.5 - - + -
350B ARG 3.6 30.1 - - - +
352B THR* 3.2 22.6 + - - +
354B ASP* 1.3 76.6 - - - +
356B LEU* 1.3 53.7 + - - +
358B THR* 2.6 31.5 + - - -
359B VAL* 2.7 19.0 + - - +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 3.9 16.6 - - + -
288B TRP* 5.6 1.8 - - + -
293B MET* 3.4 23.0 - - + +
352B THR 3.0 9.9 + - - +
353B MET* 3.0 9.6 + - - +
355B GLN* 1.3 75.3 - - - +
357B SER* 1.3 56.0 + - - +
359B VAL* 3.1 9.1 + - - +
360B HIS* 2.9 39.2 + - + +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B MET 3.0 9.3 + - - -
354B ASP* 2.5 27.3 + - - -
356B LEU* 1.3 75.1 - - - +
358B THR* 1.3 60.2 + - - +
360B HIS* 3.2 10.7 + - - +
361B HIS* 2.9 26.9 + - - +
393B ASP* 4.6 5.5 - - - +
396B ALA* 4.6 14.4 - - - +
431B GLU* 4.9 11.9 + - - -
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Residues in contact with THR 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ALA* 3.8 29.6 - - + -
347B GLN* 3.8 13.2 - - + +
354B ASP* 3.0 13.8 + - - +
355B GLN* 2.6 22.8 + - - -
357B SER* 1.3 71.8 + - - +
359B VAL* 1.3 53.3 + - - -
361B HIS* 3.5 6.6 - - + +
362B GLU* 2.8 36.4 + - + +
705B LPR 4.0 29.2 + - + +
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B MET* 4.2 14.4 - - + +
294B PHE* 3.5 63.8 - - + -
297B ALA* 3.8 13.0 - - + -
347B GLN* 4.0 15.3 - - - +
349B THR* 4.3 1.1 - - + +
355B GLN 2.7 17.5 + - - +
356B LEU* 3.1 16.4 + - - +
358B THR* 1.3 78.2 - - - +
360B HIS* 1.3 55.5 + - - +
362B GLU* 4.1 2.3 - - - +
363B MET* 3.1 27.3 + - + +
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Residues in contact with HIS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B MET 5.6 1.1 - - - -
296B VAL* 4.7 8.4 + - + +
297B ALA* 3.7 34.3 - - + +
300B PHE* 4.5 8.5 - - + +
301B PHE* 4.3 9.6 - + + -
356B LEU* 2.9 32.6 + - + -
357B SER* 3.5 9.0 - - - +
358B THR 3.1 0.4 - - - -
359B VAL* 1.3 76.1 - - + +
361B HIS* 1.3 60.5 + - - +
363B MET* 3.3 5.0 + - - +
364B GLY* 2.9 25.5 + - - -
392B GLY* 3.4 19.9 - - - +
395B LEU* 4.6 9.9 - - + -
396B ALA* 4.0 17.5 - - + -
399B VAL* 3.6 38.5 - - + +
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Residues in contact with HIS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B SER 2.9 14.3 + - - +
358B THR* 3.5 9.4 - - - +
360B HIS* 1.3 76.9 - - - +
362B GLU* 1.3 68.6 + - + +
364B GLY* 3.3 9.9 + - - -
365B HIS* 3.5 14.9 + - - -
388B HIS 5.3 0.7 - - - +
389B GLU* 3.1 38.5 + - + -
392B GLY* 3.8 12.3 + - - -
393B ASP* 4.0 18.5 + - - +
701B ZN 2.0 36.3 - - - -
705B LPR 2.6 47.0 + + + -
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 5.5 2.7 - - + -
332B ALA* 3.0 43.4 - - + +
333B SER* 3.8 4.5 - - - +
334B ALA* 3.6 21.3 + - + +
345B ILE* 5.0 13.9 - - + -
347B GLN* 3.8 20.0 - - + +
358B THR* 2.8 23.7 + - + +
359B VAL* 4.1 3.4 - - - +
361B HIS* 1.3 72.7 - - - +
363B MET* 1.3 61.4 + - - +
365B HIS* 2.8 33.8 + - - +
366B ILE* 3.5 5.3 + - - +
705B LPR 3.2 30.7 + - - +
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Residues in contact with MET 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.3 45.3 - - + +
297B ALA* 3.6 24.0 - - + -
298B GLU* 3.8 14.8 - - - -
301B PHE* 3.8 23.1 - - + -
309B MET* 3.9 36.8 - - + -
313B PHE* 4.3 8.5 - - + -
359B VAL 3.1 17.7 + - - +
360B HIS* 3.9 0.7 - - - +
362B GLU* 1.3 74.3 - - - +
364B GLY* 1.3 66.4 + - - +
366B ILE* 3.0 19.9 + - + +
367B GLN* 3.0 14.4 + - + +
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Residues in contact with GLY 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.6 18.8 - - - -
360B HIS 2.9 15.4 + - - -
361B HIS 3.7 0.7 - - - -
362B GLU 3.1 0.8 - - - -
363B MET* 1.3 77.0 - - - +
365B HIS* 1.3 63.5 + - - +
367B GLN* 3.7 1.2 + - - +
368B TYR* 3.3 19.9 + - - +
388B HIS 5.1 0.9 - - - -
391B ILE* 3.8 17.5 - - - +
392B GLY* 3.7 17.9 - - - -
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Residues in contact with HIS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ALA* 3.4 19.1 - - + -
361B HIS* 3.3 19.2 + - - -
362B GLU* 2.8 20.3 + - - +
364B GLY* 1.3 77.9 - - - +
366B ILE* 1.3 64.0 + - - +
368B TYR* 3.0 8.3 + - - +
369B TYR* 3.0 29.0 + - + -
388B HIS* 2.6 44.2 + + + -
389B GLU* 2.6 26.9 + - - -
701B ZN 2.2 31.7 - - - -
705B LPR 3.1 8.6 + - - -
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B MET* 3.0 37.7 - - + -
310B PRO* 5.4 0.7 - - + -
313B PHE* 3.2 37.0 - - + -
334B ALA* 4.8 4.3 - - + -
343B PHE* 4.4 14.6 - - + -
344B ARG 4.7 9.0 - - - +
345B ILE* 4.6 11.2 - - + -
362B GLU 4.1 5.4 - - - +
363B MET* 3.0 20.8 + - + +
365B HIS* 1.3 71.1 - - - +
367B GLN* 1.3 54.0 + - - +
368B TYR 2.6 5.0 + - - -
369B TYR* 2.3 44.4 + - + +
370B LEU* 2.8 24.0 + - + -
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.6 39.2 - - + +
307B SER* 3.1 33.1 + - - -
308B PRO* 4.2 1.8 - - - +
309B MET* 4.4 6.4 - - + +
363B MET* 3.0 6.6 + - + +
364B GLY 4.0 3.1 - - - +
366B ILE* 1.3 79.8 - - - +
368B TYR* 1.3 58.1 + - - +
370B LEU* 3.9 10.8 - - - +
371B GLN* 2.9 62.7 + - - +
391B ILE* 5.5 0.2 - - + -
541B ARG* 3.4 25.4 + - - +
544B LEU* 3.7 14.8 - - + -
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Residues in contact with TYR 368 (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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364B GLY 3.3 8.6 + - - +
365B HIS 3.0 13.9 + - - +
366B ILE 2.6 5.1 + - - -
367B GLN* 1.3 75.8 - - - +
369B TYR* 1.3 50.5 + - - -
371B GLN* 3.3 6.8 + - - +
372B TYR* 2.7 47.4 + + - -
382B GLY* 4.1 5.4 - - - -
383B ALA* 3.3 27.4 + - - +
387B PHE* 4.0 10.3 - - + +
388B HIS* 3.8 41.1 - + + -
391B ILE* 3.6 28.9 - - + -
543B VAL* 3.8 10.4 + - + -
544B LEU* 3.4 46.2 - - + +
547B GLY* 4.1 3.5 + - - -
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Residues in contact with TYR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ALA* 3.3 40.0 + - + +
335B TRP* 3.9 12.1 - - - -
336B ASP* 3.7 36.8 + - + +
343B PHE* 3.6 23.9 - + + -
365B HIS* 3.0 20.9 + - + +
366B ILE* 2.3 33.2 + - + +
368B TYR* 1.3 67.3 - - - +
370B LEU* 1.3 59.6 + - - +
372B TYR* 3.1 37.6 - + - -
373B LYS* 3.3 15.2 + - - +
380B ARG* 4.8 1.5 - - - +
388B HIS* 3.5 24.6 - + - -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER* 3.5 19.5 - - - +
308B PRO 3.4 13.0 - - - +
309B MET* 3.0 36.3 - - + -
310B PRO* 3.7 16.2 - - + -
343B PHE* 3.4 37.7 - - + -
366B ILE* 2.8 20.0 + - + +
367B GLN* 3.9 13.0 - - - +
369B TYR* 1.3 73.3 - - - +
371B GLN* 1.3 62.7 + - - +
372B TYR 3.6 0.3 + - - -
373B LYS* 3.6 29.6 + - - +
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Residues in contact with GLN 371 (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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306B LEU* 3.1 26.8 + - - +
307B SER* 3.7 4.2 - - - -
367B GLN* 2.9 42.4 + - - +
368B TYR 3.3 2.7 + - - +
369B TYR 3.2 0.6 - - - -
370B LEU* 1.3 80.4 - - - +
372B TYR* 1.3 57.7 + - - +
373B LYS 3.6 0.2 - - - -
374B ASP* 4.8 7.5 + - - +
541B ARG* 3.9 14.2 - - - +
544B LEU* 3.4 40.8 - - + -
545B GLN* 3.4 44.9 + - - +
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TYR* 2.7 35.0 - + - -
369B TYR* 3.1 30.1 - + - -
371B GLN* 1.3 74.3 - - - +
373B LYS* 1.3 61.0 + - - +
374B ASP* 2.9 9.1 + - - +
375B LEU* 3.2 20.7 + - + +
379B LEU 4.0 0.2 - - - -
380B ARG* 3.0 57.2 + - + +
381B ARG* 3.1 13.2 - - - -
382B GLY 3.9 1.8 + - - -
388B HIS* 3.1 24.3 + - - -
544B LEU 3.6 12.8 - - - +
545B GLN* 4.4 6.5 - - - +
546B ALA 5.1 0.2 - - - -
547B GLY* 3.1 29.2 - - - +
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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