Contacts of the helix formed by residues 272 - 290 (chain H) in PDB entry 6BCH
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 272 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H ASP* 3.0 22.2 - - - -
62H THR* 5.8 2.7 - - - -
63H ILE* 5.6 4.9 - - - +
271H ILE* 1.3 74.9 - - - +
273H VAL* 1.3 66.3 + - - -
274H LYS 3.1 3.4 - - - -
275H LEU* 3.0 20.0 + - - +
276H GLN 4.3 0.3 + - - -
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Residues in contact with VAL 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LYS* 3.8 33.0 - - + +
60H ASP* 3.1 16.5 + - - +
272H GLY* 1.3 71.6 - - - -
274H LYS* 1.3 56.0 + - - +
276H GLN* 2.9 29.6 + - + +
277H ASP* 3.4 10.2 + - - +
313H ARG* 3.9 27.1 - - - -
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Residues in contact with LYS 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ASP* 5.3 0.8 + - - -
181H THR 6.0 0.7 - - - +
182H ALA* 4.9 11.7 - - - +
187H PHE* 4.9 8.5 - - + -
270H ILE* 3.9 13.7 - - + -
271H ILE 4.4 4.7 - - - +
272H GLY* 3.1 1.0 + - - -
273H VAL* 1.3 77.7 - - - +
275H LEU* 1.3 51.2 + - - +
277H ASP* 3.0 17.2 + - + +
278H TYR* 2.7 34.3 + - - +
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Residues in contact with LEU 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H ILE* 3.5 38.2 - - + +
271H ILE* 4.5 0.7 - - - -
272H GLY 3.0 15.3 + - - +
274H LYS* 1.3 76.5 - - - +
276H GLN* 1.3 51.4 + - - +
278H TYR* 3.0 9.5 + - + +
279H ARG* 2.7 40.5 + - + +
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Residues in contact with GLN 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H GLY 4.3 0.2 + - - -
273H VAL* 2.9 15.8 + - + +
275H LEU* 1.3 77.1 - - - +
277H ASP* 1.3 64.9 + - - +
279H ARG* 3.0 11.2 + - - +
280H ASP* 2.9 25.3 + - - -
313H ARG* 4.4 18.2 - - - +
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Residues in contact with ASP 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H PHE* 5.1 6.3 - - + +
273H VAL* 3.9 9.2 - - - +
274H LYS* 3.0 23.0 + - + +
276H GLN* 1.3 75.7 - - - +
278H TYR* 1.3 52.7 - - - +
280H ASP* 3.0 5.7 + - - +
281H TRP* 2.6 38.0 + - - +
309H MET* 3.7 8.1 - - + +
310H ASN* 3.1 42.0 + - - +
313H ARG* 2.8 37.3 + - - +
17J A 5.6 0.3 + - - -
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Residues in contact with TYR 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H PHE* 3.4 49.1 - + + -
262H ILE* 3.1 37.3 + - + -
265H PHE* 3.3 28.1 - + + +
266H ASN* 3.5 14.3 + - - -
270H ILE* 4.5 11.4 - - + -
274H LYS 2.7 13.5 + - - +
275H LEU* 3.1 16.8 - - + +
277H ASP* 1.3 75.1 - - - +
279H ARG* 1.3 62.3 + - - +
281H TRP* 3.0 16.8 + + - +
282H CYS* 2.7 56.9 + - - -
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Residues in contact with ARG 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266H ASN* 4.3 18.2 + - - +
275H LEU* 2.7 24.2 + - + +
276H GLN* 3.0 11.4 + - - +
278H TYR* 1.3 81.7 - - - +
280H ASP* 1.3 66.9 + - - +
282H CYS* 3.0 27.6 + - - +
283H LYS* 2.9 21.4 + - - +
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Residues in contact with ASP 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H GLN 2.9 14.2 + - - +
277H ASP 3.5 6.7 - - - +
279H ARG* 1.3 76.8 - - - +
281H TRP* 1.3 64.0 + - - +
283H LYS* 3.0 18.4 + - - +
284H VAL* 3.0 17.3 + - - +
305H ILE* 4.3 12.2 - - + +
308H GLY 4.4 1.6 - - - +
309H MET* 3.9 22.5 - - + +
313H ARG* 2.7 27.9 + - - -
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Residues in contact with TRP 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H PHE* 3.4 53.6 - + + -
188H TYR* 3.3 10.2 + - - -
189H ILE* 3.6 20.0 - - + +
205H SER* 4.4 2.0 - - - -
206H VAL 3.1 40.3 + - - +
207H PHE* 3.9 9.2 - - + -
257H ILE* 3.7 43.1 - - + -
261H ILE* 4.5 5.2 - - + -
262H ILE* 4.3 8.5 - - + -
277H ASP 2.6 17.0 + - - +
278H TYR* 3.2 25.8 - + - +
280H ASP* 1.3 71.4 - - - +
282H CYS* 1.3 66.0 + - - +
284H VAL* 3.1 7.5 + - - +
285H VAL* 2.9 31.1 + - + +
309H MET* 3.7 12.5 - - + +
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Residues in contact with CYS 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H ILE* 3.8 24.8 - - + +
266H ASN* 5.0 0.4 - - - -
278H TYR* 2.7 58.9 + - - -
279H ARG* 3.3 25.8 - - - +
281H TRP* 1.3 73.2 - - - +
283H LYS* 1.3 64.6 + - - +
285H VAL* 3.0 11.1 + - - +
286H THR* 2.9 26.0 + - - +
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Residues in contact with LYS 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H ARG 2.9 11.0 + - - +
280H ASP* 3.0 13.2 + - - +
282H CYS* 1.3 75.0 - - - +
284H VAL* 1.3 64.5 + - + +
286H THR* 3.0 18.9 + - - -
287H LEU* 3.0 14.9 + - - +
305H ILE* 5.7 6.7 - - + -
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Residues in contact with VAL 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ILE* 3.7 35.0 - - + -
280H ASP 3.0 17.3 + - - +
281H TRP 3.6 6.3 - - - +
283H LYS* 1.3 74.3 - - - +
285H VAL* 1.3 58.1 + - - +
287H LEU* 3.0 18.0 + - + +
288H ILE* 2.8 41.4 + - + +
302H ILE* 4.3 15.5 - - + +
305H ILE* 3.7 39.9 - - + -
306H LYS 5.5 0.2 - - - +
309H MET* 4.9 0.7 - - - -
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Residues in contact with VAL 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ILE* 5.2 0.2 - - + -
205H SER* 3.6 27.1 - - - +
254H LEU* 4.2 16.1 - - + +
257H ILE* 3.9 28.9 - - + -
258H LYS* 5.2 6.7 - - + +
262H ILE* 4.2 10.5 - - + -
281H TRP* 2.9 30.6 + - + +
282H CYS* 3.3 10.5 - - - +
284H VAL* 1.3 76.3 - - - +
286H THR* 1.3 57.7 + - - +
288H ILE* 3.0 9.9 + - - +
289H ASP* 2.8 30.2 + - + +
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Residues in contact with THR 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282H CYS* 2.9 14.8 + - - +
283H LYS* 3.0 12.0 + - - -
285H VAL* 1.3 77.3 - - - +
287H LEU* 1.3 63.7 + - - +
289H ASP* 3.0 18.9 + - + +
290H ASN* 3.1 28.2 + - - +
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Residues in contact with LEU 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H LYS 3.0 8.8 + - - +
284H VAL* 3.0 27.1 + - + +
286H THR* 1.3 76.8 - - - +
288H ILE* 1.3 61.8 + - - +
290H ASN* 3.3 9.8 + - - +
292H GLU* 3.1 49.9 + - + +
293H HIS* 3.7 8.1 - - - +
298H GLY* 4.5 5.2 - - - +
301H LYS* 5.2 4.0 - - + -
302H ILE* 3.5 44.4 - - + +
305H ILE* 4.2 17.9 - - + -
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Residues in contact with ILE 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H ILE* 5.0 0.2 - - + -
203H VAL* 3.7 29.2 - - + +
204H GLN* 4.5 0.7 - - - -
205H SER* 4.2 28.3 - - - +
254H LEU* 4.0 25.2 - - + +
284H VAL* 2.8 33.2 + - + +
285H VAL* 3.4 8.1 - - - +
287H LEU* 1.3 76.6 - - + +
289H ASP* 1.3 60.7 + - - +
291H LYS* 2.8 17.8 + - - -
293H HIS* 3.2 45.9 - - + +
302H ILE* 4.5 0.2 - - + -
5I T 5.4 0.4 - - - +
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Residues in contact with ASP 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H LEU* 4.6 19.4 - - + +
258H LYS* 5.0 12.0 - - - +
285H VAL* 2.8 18.7 + - + +
286H THR* 3.0 13.7 + - + +
288H ILE* 1.3 74.2 - - - +
290H ASN* 1.3 62.6 + - - +
291H LYS* 3.5 3.3 + - - +
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Residues in contact with ASN 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286H THR* 3.1 31.4 + - - +
287H LEU* 3.3 6.5 + - - +
288H ILE 3.0 1.0 - - - -
289H ASP* 1.3 82.8 - - - +
291H LYS* 1.3 63.1 + - - +
292H GLU* 3.0 15.3 + - + +
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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