Contacts of the helix formed by residues 270 - 285 (chain N) in PDB entry 1OCR
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 TYR 270 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N TYR* 3.2 32.3 - - - -
180N GLN 4.5 0.2 - - - -
181N THR 2.8 28.8 + - - -
182N PRO* 4.8 1.3 - - + -
183N LEU* 3.8 25.8 - - + -
186N TRP* 3.1 18.7 + - - -
266N GLU* 4.3 11.0 - - + +
267N PRO* 3.9 18.2 + - + +
268N PHE 3.4 3.5 - - - -
269N GLY* 1.3 73.8 - - - +
271N MET* 1.3 81.8 + - + +
273N MET* 3.2 9.7 - - - +
274N VAL* 3.0 33.2 + - + +
67S SER* 3.5 32.5 - - - +
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Residues in contact with MET 271 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ARG* 3.9 29.2 - - + +
18G PHE* 3.7 36.4 - - + -
179N TYR* 3.9 30.3 - - + -
269N GLY 2.9 2.0 + - - -
270N TYR* 1.3 96.4 - - + +
272N GLY* 1.3 61.6 + - - +
273N MET 3.0 1.3 - - - -
274N VAL* 3.8 5.8 - - - +
275N TRP* 2.9 28.6 + - - +
59O GLN* 6.0 3.1 - - - +
67S SER* 5.3 2.7 - - - +
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Residues in contact with GLY 272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N GLY* 2.7 12.7 + - - -
271N MET* 1.3 74.1 - - - +
273N MET* 1.3 57.4 + - - +
275N TRP* 3.4 14.2 + - - +
276N ALA* 2.9 30.1 + - - +
318N VAL* 3.9 6.9 - - - +
322N SER* 5.7 0.7 - - - -
59O GLN* 5.4 8.3 - - - +
62O GLU* 4.3 19.7 - - - -
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Residues in contact with MET 273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N LEU* 3.5 26.9 - - + -
255N SER* 3.7 7.4 - - - +
267N PRO* 5.2 4.7 - - + -
268N PHE 4.3 7.6 - - - +
269N GLY 2.8 7.9 + - - +
270N TYR* 3.2 13.7 - - - +
272N GLY* 1.3 77.2 - - - +
274N VAL* 1.3 63.2 - - - +
276N ALA* 3.5 2.3 + - - +
277N MET* 3.3 19.8 + - - +
318N VAL 4.7 0.7 - - - +
319N LYS* 3.4 41.9 + - - +
322N SER* 3.4 33.2 - - - -
323N TRP* 3.3 42.4 - - + +
326N THR* 5.6 0.4 - - - +
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Residues in contact with VAL 274 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G PHE* 4.3 14.8 - - + -
179N TYR* 5.1 3.6 - - + -
183N LEU* 3.8 10.3 - - + -
186N TRP* 3.7 63.0 - - + +
190N ILE* 4.7 0.8 - - - +
270N TYR* 3.0 26.4 + - + +
271N MET* 3.3 9.8 + - - +
273N MET* 1.3 72.3 - - - +
275N TRP* 1.3 69.6 + - - +
277N MET* 3.2 8.9 + - - +
278N MET* 3.1 25.3 + - + +
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Residues in contact with TRP 275 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 6.1 1.3 - - - -
18G PHE* 3.9 24.8 - + + -
22G GLY* 3.0 41.4 + - - -
26G PRO* 5.9 5.2 - - + -
271N MET 2.9 18.2 + - - +
272N GLY* 3.5 12.6 - - - +
274N VAL* 1.3 75.9 - - - +
276N ALA* 1.3 77.5 + - + +
278N MET* 3.1 8.5 + - + +
279N SER* 2.9 41.5 + - - -
314N ILE* 4.7 8.5 - - + -
315N PRO* 3.9 27.6 - - + -
318N VAL* 3.9 28.0 - - + -
62O GLU* 6.0 1.1 - - - -
66O THR* 5.1 7.6 - - + -
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Residues in contact with ALA 276 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272N GLY 2.9 18.5 + - - +
273N MET 3.7 2.9 - - - +
274N VAL 3.2 0.2 - - - -
275N TRP* 1.3 83.0 - - + +
277N MET* 1.3 62.1 + - - +
279N SER* 3.4 1.7 + - - -
280N ILE* 2.9 31.1 + - - +
315N PRO* 3.4 28.9 - - - +
318N VAL* 3.8 7.6 - - + -
319N LYS* 3.6 21.1 - - + -
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Residues in contact with MET 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N LEU* 4.7 10.8 - - - +
186N TRP* 4.8 4.5 - - - -
187N SER* 3.2 44.4 - - - -
190N ILE* 3.6 24.7 - - + +
248N LEU* 3.6 21.7 - - + +
251N PHE* 3.4 30.3 - - + -
252N GLY* 3.9 4.3 - - - +
273N MET 3.3 6.9 + - - +
274N VAL* 3.2 6.9 + - - +
276N ALA* 1.3 75.9 - - - +
278N MET* 1.3 57.7 + - - +
280N ILE* 3.7 6.5 - - - +
281N GLY* 2.8 26.2 + - - -
319N LYS* 3.4 26.5 - - + +
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Residues in contact with MET 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 3.1 60.9 - - + +
7G ASP 3.4 22.0 - - - +
8G HIS* 4.6 8.7 - - + +
18G PHE* 3.1 36.8 - - + -
19G LEU* 4.7 3.4 - - + -
186N TRP* 4.5 10.8 - - - -
190N ILE* 4.0 12.1 - - + -
274N VAL* 3.1 20.2 + - + +
275N TRP* 3.1 7.2 + - + +
277N MET* 1.3 74.8 - - - +
279N SER* 1.3 58.0 + - - +
281N GLY 3.2 1.3 + - - +
282N PHE 2.8 24.9 + - - -
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Residues in contact with SER 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 4.4 7.5 + - - +
22G GLY 4.9 1.6 + - - -
275N TRP* 2.9 41.0 + - - -
276N ALA 3.6 4.3 - - - -
278N MET* 1.3 74.4 - - - +
280N ILE* 1.3 60.2 + - - +
282N PHE* 4.4 4.7 - - - -
283N LEU* 2.9 42.3 + - - +
315N PRO* 3.8 20.4 - - - -
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Residues in contact with ILE 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244N TYR* 3.5 38.8 - - + -
248N LEU* 4.5 10.8 - - + -
251N PHE* 3.9 24.9 - - + -
276N ALA 2.9 25.3 + - - +
277N MET* 3.7 5.4 - - - +
279N SER* 1.3 74.1 - - - +
281N GLY* 1.3 65.1 + - - +
283N LEU* 4.2 3.7 - - - +
284N GLY* 2.9 24.1 + - - -
312N ILE* 4.4 6.7 - - + +
315N PRO* 4.1 14.1 - - + -
316N THR* 3.5 33.2 - - - +
319N LYS* 4.5 6.1 - - + -
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Residues in contact with GLY 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ALA 3.2 12.5 - - - +
190N ILE* 4.5 5.2 - - - -
194N LEU* 4.0 27.8 - - - +
248N LEU* 5.0 0.9 - - - -
277N MET 2.8 16.4 + - - -
278N MET 3.6 3.4 - - - -
280N ILE* 1.3 80.5 - - - +
282N PHE* 1.3 61.7 + - - +
284N GLY* 3.4 6.6 + - - -
285N PHE* 3.4 15.2 - - - -
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Residues in contact with PHE 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G SER 4.3 4.9 - - - -
3G ALA* 3.6 26.2 - - + -
4G ALA 3.2 22.6 + - - -
5G LYS* 3.6 29.6 - - + +
23G LEU* 4.9 16.8 - - + -
278N MET 2.8 16.4 + - - +
279N SER* 3.7 4.3 - - - +
281N GLY* 1.3 72.8 - - - +
283N LEU* 1.3 88.5 + - + +
284N GLY 3.0 1.6 - - - -
285N PHE* 3.1 19.9 + - - +
286N ILE* 4.2 17.0 + - + +
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Residues in contact with LEU 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279N SER* 2.9 25.5 + - - +
282N PHE* 1.3 83.4 - - + +
284N GLY* 1.3 58.3 + - - +
285N PHE 2.9 10.9 + - - -
286N ILE* 3.1 34.5 + - + +
287N VAL* 3.4 16.7 - - + +
308N ALA* 5.1 1.6 - - + +
311N ILE* 4.1 32.5 - - + +
312N ILE* 3.6 39.9 - - + +
315N PRO* 4.5 11.0 - - + -
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Residues in contact with GLY 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194N LEU* 6.3 0.9 - - - -
240N HIS* 3.3 36.2 - - - +
241N PRO* 3.4 18.1 - - - +
244N TYR* 4.3 5.2 - - - -
280N ILE 2.9 19.2 + - - -
281N GLY 3.8 5.2 - - - -
282N PHE 3.0 1.4 - - - -
283N LEU* 1.3 76.0 - - - +
285N PHE* 1.3 60.1 + - - +
286N ILE 3.5 0.4 - - - -
287N VAL* 4.2 2.1 + - - +
288N TRP 5.5 0.2 + - - -
312N ILE* 4.2 6.1 - - - -
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Residues in contact with PHE 285 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G SER* 4.3 9.2 + - - -
3G ALA* 4.5 12.3 - - - +
4G ALA* 3.4 26.9 - - + -
194N LEU* 3.8 34.5 - - + -
197N LEU* 3.7 31.9 - - + -
198N SER* 4.3 7.9 - - - -
237N PHE* 3.9 40.7 - + - -
241N PRO* 3.9 21.8 - - + -
281N GLY 3.4 17.3 - - - -
282N PHE 3.1 9.1 + - - +
283N LEU 2.9 1.6 + - - -
284N GLY* 1.3 79.5 - - - +
286N ILE* 1.3 65.9 + - + +
287N VAL 3.7 2.0 - - - -
288N TRP* 3.8 15.5 - - - -
92P LEU* 5.7 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
------------------------------------------------------------
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