Contacts of the helix formed by residues 347 - 361 (chain B) in PDB entry 2CXN
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 ARG 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A ARG* 3.9 19.8 - - - +
382A GLU* 3.0 37.2 + - - -
162B LEU* 5.6 5.4 - - - +
165B LEU* 4.6 26.4 - - + +
166B MET* 3.4 30.4 + - + +
169B GLU* 4.6 4.7 - - + -
344B TYR 4.8 0.6 + - - -
345B MET 3.1 1.2 - - - -
346B HIS* 1.3 120.3 + - + +
348B PHE* 1.3 58.0 + - - +
349B ALA 3.4 2.7 - - - -
350B ALA* 3.4 25.8 + - + +
351B TYR* 3.0 23.9 + - - +
382B GLU* 5.1 4.0 + - - -
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Residues in contact with PHE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.7 26.0 - - + +
338B LEU* 4.6 12.1 - - + -
340B PRO* 4.5 7.0 - - + -
345B MET* 3.0 48.6 + - + +
346B HIS 3.5 0.2 - - - -
347B ARG* 1.3 74.5 - - - +
349B ALA* 1.3 68.5 + - - +
351B TYR* 3.3 4.7 + - - +
352B PHE* 3.2 54.6 + + - -
407B LEU* 4.3 20.6 - - + -
487B LEU* 4.4 7.6 - - + -
490B LEU* 4.8 9.2 - - + -
491B ILE* 4.3 15.9 - - + -
494B TYR* 4.0 26.5 - + - -
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 4.1 33.0 - - + +
340B PRO* 5.4 3.6 - - + +
345B MET 4.6 0.6 + - - -
346B HIS 5.1 3.4 + - - +
347B ARG 3.4 0.2 - - - -
348B PHE* 1.3 79.0 - - - +
350B ALA* 1.3 64.2 + - - +
352B PHE* 3.2 2.9 + - - +
353B GLN* 3.0 27.2 + - - +
379B VAL* 4.2 2.6 - - - +
380B TRP* 4.3 4.0 - - - -
381B GLY 3.8 31.2 - - - +
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Residues in contact with ALA 350 (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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382A GLU* 4.0 10.1 - - + +
390A ALA* 5.1 1.0 - - - +
162B LEU* 3.9 19.3 - - + +
346B HIS 5.4 0.6 + - - -
347B ARG* 3.4 46.9 + - + +
348B PHE 3.3 0.6 - - - -
349B ALA* 1.3 77.8 - - - +
351B TYR* 1.3 63.1 + - - +
353B GLN* 3.3 28.3 + - - +
354B GLN 3.7 2.9 + - - -
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Residues in contact with TYR 351 (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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159B GLY* 6.6 0.2 - - - -
162B LEU* 3.8 15.0 - - + +
163B GLY* 3.4 40.6 - - - -
166B MET* 3.7 24.5 - - + -
273B ARG* 3.4 26.6 + - - -
274B TYR* 4.8 1.7 - - - -
275B SER 5.2 0.7 + - - -
276B LEU* 3.4 21.0 + - + +
347B ARG 3.0 14.9 + - - +
348B PHE 3.5 8.1 - - - +
349B ALA 3.2 0.2 - - - -
350B ALA* 1.3 76.6 - - - +
352B PHE* 1.3 92.6 + + - +
354B GLN* 3.2 9.8 + - - +
355B GLY* 3.1 21.6 + - - -
491B ILE* 3.9 9.9 - - + +
495B GLU* 4.2 11.8 + - + +
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Residues in contact with PHE 352 (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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338B LEU* 3.8 23.6 - - + -
348B PHE* 3.2 50.5 + + - +
349B ALA 3.2 1.5 + - - +
351B TYR* 1.3 105.8 - + - +
353B GLN* 1.3 60.7 + - - +
355B GLY* 3.7 7.2 - - - +
356B ASP* 2.8 36.7 + - + +
379B VAL* 4.2 5.8 - - + +
491B ILE* 3.6 20.0 - - + -
494B TYR* 3.3 32.3 - + + -
495B GLU* 4.2 9.2 - - + -
498B ILE* 3.9 25.1 - - + -
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Residues in contact with GLN 353 (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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380A TRP* 3.7 23.6 - - - +
381A GLY 5.1 2.6 + - - +
382A GLU* 3.7 26.1 - - - +
390A ALA* 4.1 3.9 - - + +
391A PHE* 3.8 21.6 - - + +
349B ALA* 3.0 20.0 + - - +
350B ALA* 3.3 16.9 - - - +
351B TYR 3.2 0.2 - - - -
352B PHE* 1.3 74.5 - - - +
354B GLN* 1.3 57.4 + - - +
357B MET* 2.9 43.2 + - - +
358B GLU 3.8 0.2 + - - -
379B VAL* 2.8 34.3 + - - +
380B TRP* 4.1 9.0 - - - +
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Residues in contact with GLN 354 (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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389A HIS 3.2 19.7 + - - -
390A ALA* 3.3 23.9 + - - +
158B GLY* 3.2 6.6 - - - +
159B GLY* 3.2 31.3 + - - +
162B LEU* 3.3 25.2 - - + +
272B GLY* 5.7 0.4 - - - -
273B ARG* 3.6 21.5 - - + +
350B ALA 3.7 1.6 + - - -
351B TYR* 3.2 6.1 + - - +
353B GLN* 1.3 77.0 - - - +
355B GLY* 1.3 66.6 + - - +
358B GLU* 2.9 51.9 + - - +
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Residues in contact with GLY 355 (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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273B ARG* 4.3 19.5 - - - +
274B TYR* 3.9 4.3 + - - -
351B TYR* 3.1 17.2 + - - -
352B PHE* 4.0 12.1 - - - -
353B GLN 3.5 0.4 - - - -
354B GLN* 1.3 75.1 - - - +
356B ASP* 1.3 56.6 + - - +
359B SER* 2.6 29.5 + - - -
498B ILE* 3.7 12.5 - - - +
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Residues in contact with ASP 356 (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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336B HIS* 5.5 1.6 - - - -
352B PHE* 2.8 24.2 + - + +
355B GLY* 1.3 71.8 - - - +
357B MET* 1.3 60.9 + - - +
359B SER* 3.2 3.3 + - - -
360B ASN* 2.8 37.4 + - - +
376B GLY* 4.7 0.2 - - - -
377B PRO* 3.8 25.2 - - - +
379B VAL* 3.6 24.6 - - + +
497B LYS* 4.7 10.9 + - - +
498B ILE* 3.7 28.1 - - + +
501B GLN* 4.6 6.7 - - - +
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Residues in contact with MET 357 (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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380A TRP* 3.7 28.9 - - + -
390A ALA 4.9 0.2 - - - -
391A PHE* 3.8 26.0 - - + +
393A GLN* 4.1 0.2 - - - +
394A LEU* 3.6 40.8 + - + +
395A ILE* 5.5 0.2 - - + -
353B GLN* 2.9 31.1 + - - +
356B ASP* 1.3 72.6 - - - +
358B GLU* 1.3 57.5 + - - +
360B ASN 5.2 0.2 - - - -
361B GLY* 2.9 27.9 + - - +
376B GLY* 6.1 0.2 - - - -
377B PRO 3.4 17.5 - - - +
378B ILE* 3.9 14.8 - - + -
379B VAL* 3.5 30.7 - - + +
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Residues in contact with GLU 358 (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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388A GLN 5.4 0.2 - - - +
389A HIS* 3.7 17.0 - - - +
390A ALA 3.4 16.1 + - - +
393A GLN* 3.5 23.9 + - + +
273B ARG* 2.9 31.5 + - - +
353B GLN 3.8 0.4 + - - -
354B GLN* 2.9 42.3 + - + +
357B MET* 1.3 78.3 - - - +
359B SER* 1.3 61.0 + - - +
362B LYS* 3.4 19.8 + - - -
511B ASP 3.8 0.7 - - - +
512B GLN* 4.1 13.0 - - + +
515B VAL* 4.1 17.0 - - - +
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Residues in contact with SER 359 (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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273B ARG* 2.8 16.1 + - - +
274B TYR* 2.8 16.4 + - - -
354B GLN 3.8 1.2 + - - -
355B GLY 2.6 25.6 + - - -
356B ASP 3.2 3.4 + - - -
358B GLU* 1.3 78.8 - - - +
360B ASN* 1.3 65.7 + - - +
361B GLY 3.6 0.2 - - - -
362B LYS* 2.8 25.6 + - - +
498B ILE* 3.6 17.0 - - - -
509B SER* 3.2 22.9 + - - -
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Residues in contact with ASN 360 (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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356B ASP* 2.8 18.5 + - - +
359B SER* 1.3 75.2 - - - +
361B GLY* 1.3 60.4 + - - +
362B LYS* 2.9 10.4 + - - +
375B THR* 3.3 6.2 + - - -
376B GLY* 3.0 26.8 + - - -
498B ILE* 3.0 38.6 + - - +
501B GLN* 3.9 5.3 + - - +
502B GLY* 3.7 6.8 - - - +
505B TRP* 3.8 23.3 - - + -
507B ILE* 3.2 14.8 - - + +
509B SER* 2.7 26.2 + - - -
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Residues in contact with GLY 361 (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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393A GLN* 3.0 32.7 - - - +
394A LEU* 3.7 26.6 - - - +
397A GLN 3.5 5.2 - - - +
398A GLY* 3.8 9.6 - - - -
357B MET 2.9 20.9 + - - -
358B GLU 4.5 0.2 - - - -
359B SER 3.6 1.2 - - - -
360B ASN* 1.3 72.9 - - - +
362B LYS* 1.3 58.4 - - - -
375B THR* 4.7 0.7 - - - -
376B GLY 4.9 0.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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