Contacts of the helix formed by residues 277 - 293 (chain A) in PDB entry 2JIH
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 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A HIS* 3.3 12.5 + - - -
275A GLY 3.2 1.4 - - - -
276A SER* 1.3 78.2 + - - +
278A LEU* 1.3 64.4 + - - +
279A LYS 3.3 1.7 + - - -
280A HIS* 3.5 5.6 + - - +
281A TYR* 3.0 21.9 + - - +
482A TYR* 4.2 2.8 + - - -
274B HIS 5.4 0.2 + - - -
486B ARG* 3.4 28.9 - - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 4.0 11.7 - - + -
270A MET* 3.5 37.2 - - + +
271A ALA* 3.9 14.8 - - - -
274A HIS* 3.6 30.6 - - + +
275A GLY 3.3 10.8 + - - +
276A SER 3.2 3.4 - - - -
277A GLY* 1.3 76.6 - - - +
279A LYS* 1.3 59.0 + - + +
281A TYR* 3.0 5.7 + - + +
282A LEU* 2.9 36.1 + - + +
311A VAL* 3.4 43.7 - - + -
494B GLU* 5.8 2.0 - - - +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER 4.4 3.2 + - - +
277A GLY 3.3 0.6 - - - -
278A LEU* 1.3 78.0 - - + +
280A HIS* 1.3 62.3 + - - +
282A LEU* 3.4 8.4 + - - +
283A LEU* 3.1 35.1 + - + +
309A ILE* 4.3 35.8 - - + +
311A VAL* 4.5 16.4 - - + -
489B GLN* 4.1 13.0 - - - +
494B GLU* 3.5 26.5 + - - -
495B ASP* 3.2 32.1 + - - +
1556B NI 4.2 3.8 - - - +
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER 5.4 0.4 + - - -
277A GLY 3.5 6.8 + - - +
278A LEU 3.4 0.2 - - - -
279A LYS* 1.3 79.0 - - - +
281A TYR* 1.3 55.6 + - - +
283A LEU* 3.5 6.4 + - - +
284A THR* 2.8 45.5 + - - -
474A PRO* 4.3 19.4 - - + +
481A SER* 2.8 27.9 + - - -
482A TYR* 3.2 24.9 - + - +
1557A CD 2.3 32.9 - - - -
481B SER 4.9 7.7 + - - -
483B ASP* 3.5 14.1 + - + -
486B ARG* 3.7 31.8 - - + +
489B GLN* 5.8 1.0 + - - -
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A MET* 4.3 8.3 - - + -
274A HIS* 3.4 32.3 - + - +
277A GLY 3.0 14.2 + - - +
278A LEU* 3.0 10.5 + - + +
280A HIS* 1.3 76.5 - - - +
282A LEU* 1.3 64.6 + - + +
284A THR* 3.2 3.9 + - - -
285A LEU* 3.0 47.7 + - + +
390A ASP* 2.4 44.8 + - - -
392A GLY* 3.2 22.7 + - - -
393A LEU* 4.0 9.9 - - + -
482A TYR* 3.2 19.7 + + - +
490A PHE* 3.7 35.3 - + - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 3.9 22.2 - - + +
265A VAL 5.1 0.2 - - - -
266A ALA* 4.0 21.1 - - + +
270A MET* 4.0 19.1 - - + -
278A LEU* 2.9 25.3 + - + +
279A LYS* 3.7 9.2 - - - +
281A TYR* 1.3 76.7 - - + +
283A LEU* 1.3 57.5 + - + +
285A LEU* 3.2 11.9 + - + +
286A PHE* 3.0 28.1 + - - +
309A ILE* 4.0 27.8 - - + -
311A VAL* 5.2 0.7 - - + -
356A PHE* 3.6 39.7 - - + -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.3 2.5 - - + -
279A LYS* 3.1 24.5 + - + +
280A HIS* 3.8 7.6 - - - +
282A LEU* 1.3 76.0 - - - +
284A THR* 1.3 60.1 + - - +
286A PHE* 3.8 4.0 - - - -
287A SER* 3.0 21.3 + - - -
306A VAL* 4.1 17.5 - - + -
309A ILE* 4.1 17.5 - - + -
471A ILE* 4.1 25.6 - - + -
472A GLN 4.1 13.5 - - - +
473A LEU* 3.7 19.6 - - + +
474A PRO* 3.4 26.7 - - + +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A HIS* 2.8 46.2 + - - -
281A TYR 3.2 4.9 + - - -
283A LEU* 1.3 76.0 - - - +
285A LEU* 1.3 66.1 + - - +
287A SER* 2.8 23.7 + - - +
288A VAL* 3.3 10.6 + - + +
393A LEU* 4.2 8.7 - - + -
474A PRO* 4.2 6.8 - - + +
478A PRO* 3.7 32.5 - - + -
481A SER* 4.5 1.8 + - - -
482A TYR* 3.7 20.5 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TYR* 3.0 42.1 + - + +
282A LEU* 3.3 11.2 - - + +
284A THR* 1.3 77.5 - - - +
286A PHE* 1.3 61.3 + - - +
288A VAL* 3.5 0.4 + - - -
289A ALA* 3.3 11.4 + - - +
356A PHE* 3.9 33.7 - - + -
390A ASP* 4.7 0.7 - - - +
393A LEU* 3.8 42.6 - - + +
395A ALA* 4.0 13.2 - - + -
396A ALA* 3.2 41.7 - - + +
399A THR* 5.2 2.7 - - - +
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Residues in contact with PHE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 3.5 23.8 - - + -
264A LEU* 3.6 24.2 - - + -
282A LEU 3.0 15.8 + - - +
283A LEU* 4.0 4.9 - - - +
284A THR 3.2 0.2 - - - -
285A LEU* 1.3 74.7 - - + +
287A SER* 1.4 55.5 + - - +
289A ALA* 3.3 3.6 + - + +
290A ALA* 2.8 36.0 + - - +
304A LEU* 3.4 53.4 - - + -
305A VAL 3.9 1.8 - - - -
306A VAL* 3.5 24.0 - - + -
354A ILE* 3.9 24.5 - - + -
356A PHE* 5.6 1.3 - + + -
399A THR* 4.5 10.3 - - + -
403A LEU* 4.4 4.5 - - + -
473A LEU* 4.0 11.2 - - + -
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU 3.0 15.4 + - - -
284A THR* 2.8 23.7 + - - +
286A PHE* 1.4 75.7 - - - +
288A VAL* 1.3 55.6 + - - +
290A ALA* 3.3 3.5 + - - +
291A ARG* 3.0 49.1 + - - +
473A LEU* 4.1 16.5 - - - +
474A PRO* 3.6 29.6 + - - +
476A ASP 4.8 1.7 + - - -
478A PRO* 5.8 0.5 - - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A THR* 3.3 13.7 + - + +
285A LEU* 3.5 7.9 - - - +
287A SER* 1.3 81.0 + - - +
289A ALA* 1.3 61.5 + - - +
291A ARG* 3.1 25.4 + - + +
292A LEU* 3.1 30.9 + - + +
393A LEU* 5.9 1.3 - - + +
396A ALA* 3.6 21.3 - - + -
397A PHE* 4.4 20.9 - - + -
478A PRO* 3.9 25.4 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LEU 3.3 9.1 + - - +
286A PHE* 3.3 8.9 + - + +
288A VAL* 1.3 74.7 - - - +
290A ALA* 1.3 66.9 + - - +
292A LEU* 3.2 13.2 + - - +
293A TYR* 3.1 27.7 + - - -
304A LEU* 3.7 14.1 - - + -
396A ALA 3.8 17.2 + - - +
399A THR* 4.3 16.2 - - + -
400A ALA* 4.2 10.1 - - + +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A PHE* 2.8 21.0 + - + +
287A SER 3.5 5.6 - - - +
289A ALA* 1.3 74.6 - - - +
291A ARG* 1.3 61.6 + - - +
293A TYR* 3.4 4.3 + - - +
294A LYS* 3.4 29.3 + - - +
302A VAL 4.9 1.4 - - - +
304A LEU* 3.6 31.4 + - + +
473A LEU* 3.8 22.0 - - + -
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER* 3.0 30.2 + - - +
288A VAL* 3.4 32.0 - - - +
289A ALA 3.1 0.4 - - - -
290A ALA* 1.3 74.3 - - - +
292A LEU* 1.3 66.4 + - + +
294A LYS* 3.1 25.9 + - + +
295A HIS* 3.6 5.9 + - - +
474A PRO 3.4 18.4 + - - -
475A GLY* 3.6 11.5 + - - -
476A ASP 3.0 27.0 + - - -
477A LEU* 4.7 13.9 - - - +
478A PRO* 4.3 9.7 - - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 3.1 22.1 + - + +
289A ALA* 3.2 9.4 + - - +
291A ARG* 1.3 76.3 - - + +
293A TYR* 1.3 57.2 + - - +
295A HIS* 3.2 19.9 + - - +
396A ALA 4.6 2.2 - - - +
397A PHE* 3.9 33.9 - - + -
400A ALA* 3.7 25.1 - - + -
429A MET* 4.2 16.4 - - + -
437A LEU* 4.6 3.8 - - + -
442A PRO* 4.6 15.0 - - + +
443A TRP* 2.9 31.9 + - + +
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Residues in contact with TYR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA 3.1 25.1 + - - +
290A ALA 3.8 5.4 - - - +
291A ARG 3.2 0.2 - - - -
292A LEU* 1.3 75.7 - - - +
294A LYS* 1.3 55.8 + - - +
295A HIS 3.4 1.3 - - - -
298A ILE* 3.3 50.6 - - + +
300A ASN 4.5 0.5 - - - +
302A VAL* 3.6 40.7 + - + +
304A LEU* 3.8 21.8 - - + -
400A ALA* 2.7 41.5 + - + -
403A LEU* 3.1 12.9 - - + -
404A GLY* 2.9 22.7 + - - -
407A PHE* 3.8 22.4 - + - -
409A MET* 4.2 3.1 - - + -
443A TRP* 3.4 18.3 - + - +
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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