Contacts of the helix formed by residues 279 - 290 (chain A) in PDB entry 1O95
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 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A THR* 6.4 0.7 - - - -
258A ILE* 4.5 18.1 - - + +
266A GLU 4.8 0.4 - - - +
267A ASP* 4.7 5.6 - - - +
277A GLY 2.9 1.0 + - - -
278A HIS* 1.3 109.2 - - + +
280A ILE* 1.3 67.4 + - - +
281A PRO 3.3 0.7 - - - -
282A TRP* 2.9 16.8 + - - +
283A VAL* 2.8 28.1 + - - +
297A VAL* 2.5 31.3 + - + +
298A GLY* 3.5 7.2 - - - -
300A TYR* 3.9 5.4 + - - -
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Residues in contact with ILE 280 (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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277A GLY* 2.6 36.6 + - - +
279A THR* 1.3 70.7 + - - +
281A PRO* 1.4 66.8 - - + +
283A VAL* 2.3 32.7 + - + -
284A LYS* 2.7 23.9 + - + +
300A TYR* 3.2 16.4 - - + +
305A LYS* 4.4 13.7 - - - +
308A GLU* 5.1 3.8 - - - +
309A ILE* 3.5 32.1 - - + -
314A TYR* 3.4 36.6 - - + -
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Residues in contact with PRO 281 (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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277A GLY 4.1 1.8 - - - +
278A HIS* 3.7 9.2 - - - +
279A THR 3.4 4.0 - - - -
280A ILE* 1.4 96.6 - - + +
282A TRP* 1.3 72.8 + - + +
284A LYS* 2.8 33.5 - - - +
285A LEU* 3.2 13.2 - - - +
616B TYR* 3.7 32.3 - - + +
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Residues in contact with TRP 282 (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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225A VAL* 3.6 20.5 - - + +
226A ASP* 3.7 35.8 + - + -
228A VAL* 3.9 9.8 - - + +
236A ALA* 4.6 3.8 - - + -
256A ILE* 4.7 0.7 - - - +
258A ILE* 3.9 25.6 - - + -
278A HIS 3.5 18.4 - - - -
279A THR 2.9 14.4 + - - +
281A PRO* 1.3 94.4 - - + +
283A VAL* 1.3 64.6 + - - +
285A LEU* 4.1 16.4 - - - +
286A VAL* 4.7 0.9 - - - +
614B ARG* 2.9 44.9 - - + -
615B THR 3.8 4.0 - - - -
616B TYR* 3.3 61.8 - + + -
623B PRO* 4.6 5.5 - - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 4.3 20.8 - - + +
257A THR* 5.6 0.9 - - - -
258A ILE* 5.6 4.5 - - + -
279A THR* 2.8 35.6 + - - +
280A ILE* 2.3 28.5 + - + +
282A TRP* 1.3 69.9 - - - +
284A LYS* 1.4 61.6 + - + +
286A VAL* 3.2 23.9 + - - +
287A LYS 4.5 0.9 + - - -
294A VAL* 4.7 5.4 - - + +
295A LEU 5.0 2.0 - - - -
296A GLY* 4.0 36.6 - - - +
297A VAL 4.2 1.3 - - - +
300A TYR* 5.7 1.3 - - - +
309A ILE* 6.5 0.4 - - + -
314A TYR* 4.2 16.6 - - + +
315A ALA* 5.4 3.4 - - + -
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Residues in contact with LYS 284 (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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280A ILE* 2.7 16.7 + - + +
281A PRO* 2.8 39.3 - - - +
283A VAL* 1.4 69.2 - - - +
285A LEU* 1.3 63.4 + - + +
286A VAL 2.7 16.8 + - - -
287A LYS* 3.3 16.1 + - - +
288A GLN* 3.5 13.6 + - - +
314A TYR* 2.7 77.2 + - + +
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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
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225A VAL* 6.0 1.1 - - + -
236A ALA* 3.8 28.0 - - + -
237A GLU* 4.0 19.3 - - + +
241A GLN* 3.9 15.6 - - + +
281A PRO 3.2 20.2 - - - +
282A TRP* 4.1 10.3 - - - +
283A VAL 3.4 0.2 - - - -
284A LYS* 1.3 86.2 - - + +
286A VAL* 1.4 61.7 + - + +
288A GLN* 3.3 34.9 - - - +
289A VAL* 3.5 10.9 - - - +
616B TYR* 3.9 26.0 - - + -
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Residues in contact with VAL 286 (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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225A VAL* 4.4 16.2 - - + -
241A GLN* 6.2 0.7 - - + -
244A VAL* 4.2 25.6 - - + -
254A TRP* 4.3 2.5 - - + -
256A ILE* 3.4 44.9 - - + -
282A TRP 4.7 2.7 - - - +
283A VAL 3.4 13.9 - - - +
284A LYS 2.7 4.6 + - - -
285A LEU* 1.4 75.8 - - + +
287A LYS* 1.3 67.7 + - - +
288A GLN 3.2 0.4 - - - -
289A VAL* 2.8 11.7 + - + +
290A SER* 2.8 19.3 + - - -
294A VAL* 3.5 20.6 - - + -
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Residues in contact with LYS 287 (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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284A LYS 3.3 9.9 + - - +
286A VAL* 1.3 72.4 - - - +
288A GLN* 1.4 55.1 - - - +
289A VAL 2.2 21.3 + - - -
290A SER* 2.6 28.5 + - - +
292A LYS 4.8 3.9 + - - +
294A VAL* 4.1 15.3 - - + +
313A GLY* 3.6 32.1 - - - +
314A TYR 3.6 22.9 - - - +
315A ALA 4.3 4.7 - - - -
316A ASP* 2.7 41.0 + - - +
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Residues in contact with GLN 288 (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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241A GLN* 3.7 17.4 - - - +
284A LYS* 3.5 10.3 + - - +
285A LEU* 3.3 30.8 + - - +
286A VAL 3.2 1.6 - - - -
287A LYS* 1.4 76.0 - - - +
289A VAL* 1.3 64.0 + - + +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN* 2.9 63.0 - - + +
244A VAL* 4.3 10.2 - - + +
245A GLU* 4.2 34.0 - - + +
248A ASP* 4.3 5.0 - - - +
285A LEU 3.5 9.9 - - - +
286A VAL* 2.8 18.4 + - - +
287A LYS 2.2 16.0 + - - -
288A GLN* 1.3 79.2 - - + +
290A SER* 1.3 58.3 - - - +
291A LYS* 4.0 8.4 + - - +
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Residues in contact with SER 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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244A VAL* 4.0 10.5 - - - -
248A ASP* 2.7 21.4 + - - -
254A TRP* 4.1 1.8 - - - -
286A VAL 2.8 13.1 + - - -
287A LYS* 2.6 28.1 + - - +
289A VAL* 1.3 75.6 - - - +
291A LYS* 1.4 60.7 + - - +
292A LYS* 2.4 36.6 + - - +
294A VAL* 4.2 17.3 - - - -
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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
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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