Contacts of the helix formed by residues 277 - 295 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A HIS 5.2 1.6 + - - -
486A ARG* 3.3 27.0 - - - +
274B HIS* 3.1 14.9 + - - -
276B SER* 1.3 80.6 + - - +
278B LEU* 1.3 65.4 + - - +
279B LYS 3.4 1.2 + - - -
280B HIS* 3.5 5.1 + - - +
281B TYR* 3.1 19.3 + - - +
482B TYR* 4.3 2.1 + - - -
486B ARG* 6.2 2.2 - - - -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 4.0 9.9 - - + -
270B MET* 3.8 20.0 - - + -
271B ALA* 3.6 31.4 - - - +
274B HIS* 3.7 34.4 + - + -
275B GLY 3.1 15.2 + - - +
276B SER 3.1 3.2 - - - -
277B GLY* 1.3 75.4 - - - +
279B LYS* 1.3 67.5 + - + +
281B TYR* 2.8 16.3 + - + +
282B LEU* 2.9 30.4 + - + +
311B VAL* 3.8 27.4 - - + -
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLN* 3.9 14.6 - - - +
494A GLU* 2.9 40.1 + - - -
495A ASP* 3.2 22.4 + - - +
1562A NI 4.0 7.7 - - - +
276B SER 4.3 4.1 + - - -
277B GLY 3.4 0.6 - - - -
278B LEU* 1.3 75.4 - - + +
280B HIS* 1.3 64.5 + - - +
282B LEU* 3.1 9.5 + - + +
283B LEU* 3.0 33.2 + - + +
309B ILE* 4.3 33.7 - - + -
311B VAL* 4.7 16.8 - - + -
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Residues in contact with HIS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A SER 5.2 4.6 + - - -
483A ASP* 3.0 17.7 + - + -
486A ARG* 3.7 32.6 - - + +
489A GLN* 5.5 1.0 + - - -
276B SER 5.2 1.0 + - - -
277B GLY 3.5 6.8 + - - +
278B LEU 3.3 0.4 - - - -
279B LYS* 1.3 76.1 - - - +
281B TYR* 1.3 54.1 + - - +
283B LEU* 3.3 6.7 + - - +
284B THR* 2.6 55.2 + - - -
474B PRO* 4.5 15.1 - - + +
481B SER* 3.5 23.3 + - - -
482B TYR* 3.2 28.5 - + - +
1555B CD 2.2 34.2 - - - -
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Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B MET* 4.3 7.2 - - + -
274B HIS* 3.6 33.0 - + - +
277B GLY 3.1 11.8 + - - +
278B LEU* 2.8 13.4 + - + +
280B HIS* 1.3 77.5 - - - +
282B LEU* 1.3 56.2 + - + -
284B THR* 3.3 5.2 + - - +
285B LEU* 3.0 49.8 + - + +
390B ASP* 2.5 34.8 + - - -
392B GLY* 3.2 23.6 + - - -
393B LEU* 3.8 9.2 - - + -
482B TYR* 3.1 20.1 + + - +
490B PHE* 3.4 46.4 - + - +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.0 21.6 - - + +
266B ALA* 4.0 21.1 - - + +
270B MET* 4.2 14.6 - - + -
278B LEU* 2.9 26.9 + - + +
279B LYS* 3.6 9.6 - - + +
281B TYR* 1.3 73.7 - - + +
283B LEU* 1.3 62.9 + - + +
285B LEU* 3.4 10.8 + - + +
286B PHE* 3.0 26.2 + - - +
309B ILE* 4.3 24.0 - - + -
311B VAL* 5.3 0.4 - - + -
356B PHE* 3.6 44.5 - - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.8 2.2 - - + -
279B LYS* 3.0 25.5 + - + +
280B HIS* 3.9 5.4 - - - +
282B LEU* 1.3 76.4 - - - +
284B THR* 1.3 60.7 + - - +
286B PHE* 3.8 3.5 - - - +
287B SER* 2.9 30.0 + - - -
306B VAL* 3.9 18.8 - - + -
309B ILE* 4.0 15.0 - - + -
471B ILE* 3.7 33.2 - - + -
472B GLN 4.2 8.3 - - - +
473B LEU* 3.4 25.9 - - + +
474B PRO* 3.5 17.6 - - + +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B HIS* 2.6 45.4 + - - -
281B TYR 3.3 7.6 - - - +
283B LEU* 1.3 76.4 - - - +
285B LEU* 1.3 64.6 - - - +
287B SER* 2.7 22.8 + - - +
288B VAL* 3.6 9.7 - - - +
393B LEU* 4.6 6.5 - - + -
474B PRO* 4.2 8.9 - - + +
476B ASP 6.1 0.2 - - - +
478B PRO* 4.0 28.3 - - + +
481B SER* 4.6 4.1 + - - +
482B TYR* 3.9 20.6 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B MET* 5.7 0.2 - - + -
281B TYR* 3.0 45.0 + - + +
282B LEU* 3.5 11.2 - - + +
284B THR* 1.3 77.0 - - - +
286B PHE* 1.3 61.6 + - - +
288B VAL 3.2 10.6 + - - -
289B ALA* 3.5 8.5 + - - +
356B PHE* 3.7 37.5 - - + -
390B ASP* 5.0 0.9 - - - +
392B GLY 4.0 1.6 - - - +
393B LEU* 4.0 25.1 - - + -
395B ALA* 4.0 16.6 - - + -
396B ALA* 3.5 41.1 - - + +
399B THR* 5.2 2.5 - - - +
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Residues in contact with PHE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR* 3.3 30.3 - - + -
264B LEU* 3.7 15.7 - - + -
282B LEU 3.0 14.5 + - - +
283B LEU* 3.8 8.3 - - - +
284B THR 3.4 0.2 - - - -
285B LEU* 1.3 79.8 - - - +
287B SER* 1.3 56.8 + - - +
289B ALA* 3.2 8.3 + - + +
290B ALA* 2.9 28.1 + - + +
304B LEU* 3.7 46.0 - - + -
305B VAL 3.8 2.0 - - - -
306B VAL* 3.3 27.8 - - + -
354B ILE* 3.7 27.1 - - + -
356B PHE* 5.5 1.9 - + - -
399B THR* 4.5 10.1 - - + +
403B LEU* 4.6 2.2 - - + -
473B LEU* 3.8 11.7 - - + -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU 2.9 15.3 + - - -
284B THR* 2.7 26.7 + - - +
286B PHE* 1.3 76.6 - - - +
288B VAL* 1.3 61.7 + - - +
290B ALA* 3.5 8.3 + - - +
291B ARG* 3.1 43.3 + - - +
473B LEU* 4.5 9.8 - - - +
474B PRO* 3.7 29.7 + - - +
476B ASP 5.1 1.0 + - - -
478B PRO* 5.8 0.5 - - - +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B THR 3.6 14.4 - - - +
285B LEU* 3.2 7.2 + - - +
286B PHE 3.2 0.4 - - - -
287B SER* 1.3 75.4 + - - +
289B ALA* 1.3 63.9 + - - +
291B ARG* 3.2 15.9 + - + +
292B LEU* 3.1 35.8 + - + +
393B LEU 5.7 0.4 - - - +
396B ALA* 3.7 21.8 - - + -
397B PHE* 4.5 17.3 - - + -
478B PRO* 3.6 37.0 - - + -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU 3.5 3.8 + - - +
286B PHE* 3.2 14.3 + - + +
288B VAL* 1.3 77.0 - - - +
290B ALA* 1.3 63.1 + - - +
292B LEU* 3.2 5.1 + - - +
293B TYR* 3.0 28.4 + - - -
304B LEU* 4.0 16.4 - - + -
396B ALA 4.0 16.5 + - - +
399B THR* 4.5 9.4 - - + -
400B ALA* 4.1 23.3 - - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 2.9 16.8 + - + +
287B SER* 3.6 9.6 - - - +
289B ALA* 1.3 74.3 - - - +
291B ARG* 1.3 65.7 + - + +
293B TYR* 3.4 3.1 + - - +
294B LYS* 3.1 34.2 + - - +
302B VAL 5.0 1.0 - - - +
304B LEU* 4.0 37.3 + - + +
473B LEU* 4.6 8.7 - - + -
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER* 3.1 31.8 + - - +
288B VAL* 3.2 15.3 + - + +
290B ALA* 1.3 75.6 - - + +
292B LEU* 1.3 59.2 + - + +
294B LYS* 2.9 30.3 + - + +
295B HIS* 3.4 6.2 + - - +
474B PRO 3.1 26.7 + - - -
475B GLY* 3.7 11.6 + - - -
476B ASP 3.1 20.5 + - - -
477B LEU* 3.8 16.0 - - - +
478B PRO* 3.7 28.9 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 3.1 26.6 + - + +
289B ALA* 3.2 6.9 + - - +
291B ARG* 1.3 76.4 - - + +
293B TYR* 1.3 56.7 + - - +
295B HIS* 3.1 22.1 + - + +
397B PHE* 3.8 38.6 - - + -
400B ALA* 4.0 16.2 - - + -
429B MET* 4.0 11.9 - - - -
437B LEU* 4.7 3.6 - - + -
442B PRO* 4.3 22.9 - - + -
443B TRP* 3.0 31.3 + - + +
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA 3.0 26.7 + - - +
290B ALA 3.7 5.8 - - - +
291B ARG 3.4 0.2 - - - -
292B LEU* 1.3 74.6 - - - +
294B LYS* 1.3 59.4 + - - +
295B HIS 3.4 0.2 - - - -
298B ILE* 3.5 42.7 - - + +
300B ASN 4.6 2.1 - - - +
302B VAL* 3.6 35.0 + - + +
304B LEU* 3.9 22.7 - - + -
400B ALA* 3.0 27.4 + - + -
403B LEU* 2.8 15.7 + - + -
404B GLY* 2.8 35.2 + - - -
407B PHE* 3.9 21.3 - + - -
409B MET* 4.4 2.9 - - + -
443B TRP* 3.6 22.4 - + - +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA* 3.1 23.2 + - - +
291B ARG* 2.9 18.0 + - + +
293B TYR* 1.3 76.5 - - - +
295B HIS* 1.3 65.1 + - - +
296B PRO* 3.4 5.5 - - - +
298B ILE* 5.1 0.4 - - - -
300B ASN 5.7 1.5 - - - +
302B VAL 4.3 9.4 + - - +
303B SER* 3.6 28.0 + - - +
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Residues in contact with HIS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG 3.4 5.0 + - - +
292B LEU* 3.1 18.8 + - + +
294B LYS* 1.3 76.4 - - - +
296B PRO* 1.3 85.8 - - + +
297B SER* 3.0 24.3 + - - +
298B ILE* 3.2 23.4 + - - +
439B HIS 3.5 11.8 + - - -
440B SER* 3.2 27.9 + - - -
441B GLN* 3.7 0.7 - - + -
442B PRO* 3.4 31.5 - - + +
443B TRP* 4.5 0.4 - - + -
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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