Contacts of the helix formed by residues 269 - 284 (chain B) in PDB entry 1OFD
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 SER 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ARG* 6.2 2.0 - - - -
217B LEU* 4.7 17.3 - - - +
233B LEU* 4.5 0.7 - - - -
267B ALA 4.3 0.2 + - - -
268B ASN* 1.3 75.6 - - - +
270B ASP* 1.3 68.4 + - - +
271B SER* 3.5 6.9 + - - -
272B TYR* 3.2 23.9 + - - +
273B ASN* 3.0 25.9 + - - -
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Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 4.1 4.6 - - - -
228B GLY 4.1 0.9 - - - +
229B GLU* 3.4 26.7 - - - +
230B ILE* 3.0 52.1 + - + +
233B LEU* 3.8 25.5 - - + +
269B SER* 1.3 74.1 - - - +
271B SER* 1.3 86.5 + - - +
273B ASN* 3.3 3.1 + - - +
274B LEU* 3.0 25.7 + - - +
326B TRP* 4.8 1.2 - - - -
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 3.2 30.3 + - - -
221B MET* 3.0 15.9 - - - +
224B LEU* 4.2 2.1 - - - +
226B HIS* 2.9 31.3 + - - -
228B GLY 5.4 0.3 + - - -
269B SER* 3.3 6.5 + - - -
270B ASP* 1.3 85.3 + - - +
272B TYR* 1.3 66.7 + - - +
274B LEU* 3.3 4.2 + - - +
275B ASP* 2.9 20.4 + - - +
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Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLY* 5.2 6.9 + - - -
159B LEU* 3.7 27.2 - - + +
164B TYR* 4.2 28.3 - + - -
216B PRO* 5.5 4.0 - - + -
217B LEU* 5.1 14.6 - - + -
221B MET* 3.3 21.2 - - + +
222B ARG* 4.8 12.6 + - - -
263B ILE 6.0 0.7 - - - -
268B ASN* 3.5 32.5 - - + -
269B SER* 3.2 25.5 + - - +
271B SER* 1.3 80.8 - - - +
273B ASN* 1.3 63.4 + - - +
275B ASP* 3.5 3.1 + - - +
276B SER* 3.1 28.2 + - - -
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Residues in contact with ASN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 4.6 4.4 - - + +
237B ILE* 3.7 9.0 - - - +
263B ILE 4.2 0.7 - - - +
264B VAL* 2.8 34.7 - - + +
265B ASN* 2.9 30.3 + - - +
268B ASN* 3.1 14.3 + - - +
269B SER 3.0 24.2 + - - +
270B ASP 3.3 4.2 + - - +
272B TYR* 1.3 78.2 - - - +
274B LEU* 1.3 60.1 + - - +
276B SER* 3.7 5.0 - - - -
277B ALA* 2.9 32.4 + - - +
326B TRP* 3.8 18.6 - - + -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 4.0 13.2 - - + -
226B HIS* 4.1 14.4 - - + +
230B ILE* 4.1 18.4 - - + -
270B ASP 3.0 14.5 + - - +
271B SER* 3.6 5.4 - - - +
272B TYR 3.3 0.2 - - - -
273B ASN* 1.3 73.3 - - - +
275B ASP* 1.3 61.5 + - - +
277B ALA* 4.7 0.2 - - - -
278B LEU* 2.9 38.6 + - + +
295B LEU* 4.2 20.9 - - + -
296B VAL* 4.8 8.1 - - + -
326B TRP* 3.9 33.6 - - + -
332B LEU* 3.7 31.9 - - + -
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B MET* 3.3 24.0 - - + +
222B ARG* 3.2 30.0 + - - +
223B LEU* 2.9 31.0 + - - +
224B LEU* 3.0 22.6 + - + +
271B SER 2.9 17.3 + - - +
272B TYR 3.6 5.2 - - - +
274B LEU* 1.3 77.7 - - - +
276B SER* 1.3 56.8 + - - +
278B LEU* 3.8 3.0 - - - +
279B GLU* 2.9 32.3 + - - +
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 4.5 4.0 + - - -
262B PRO 5.0 0.2 + - - -
263B ILE* 2.6 36.8 + - - +
272B TYR* 3.1 26.9 + - - -
273B ASN* 3.7 3.6 - - - -
274B LEU 3.2 0.2 - - - -
275B ASP* 1.3 75.8 - - - +
277B ALA* 1.3 65.1 + - - +
279B GLU* 3.3 5.6 + - - +
280B LEU* 3.0 23.0 + - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B MET* 4.1 14.8 - - + +
263B ILE* 3.9 14.9 - - + +
264B VAL* 4.6 1.3 - - + -
273B ASN 2.9 20.6 + - - +
274B LEU 4.1 1.1 - - - +
276B SER* 1.3 73.7 + - - +
278B LEU* 1.3 62.3 + - - +
280B LEU* 3.3 5.6 + - - +
281B LEU* 3.3 25.1 + - - +
295B LEU* 3.8 18.8 - - + -
326B TRP* 3.9 20.6 - - + -
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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
----------------------------------------------------------
223B LEU* 3.5 31.2 - - + -
224B LEU* 4.0 30.3 - - + -
274B LEU* 2.9 22.4 + - + +
275B ASP 3.9 1.3 - - - +
277B ALA* 1.3 77.0 - - - +
279B GLU* 1.3 56.0 + - - +
281B LEU* 3.3 7.4 + - - +
282B VAL* 3.0 29.9 + - + +
288B PRO* 3.8 7.9 - - + +
291B ALA* 3.5 27.1 - - + +
292B ALA* 3.6 21.8 - - + +
295B LEU* 3.8 12.7 - - + +
332B LEU* 5.7 4.3 - - + -
334B PHE* 4.7 9.6 - - + -
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 3.5 16.3 - - + -
152B ARG* 2.6 45.3 + - - -
222B ARG* 3.8 15.4 + - - +
223B LEU* 3.7 21.4 - - + +
275B ASP* 2.9 20.5 + - - +
276B SER* 3.9 5.3 - - - +
277B ALA 3.3 0.2 - - - -
278B LEU* 1.3 73.2 - - - +
280B LEU* 1.3 60.2 + - - +
282B VAL* 4.2 1.3 - - + -
283B ARG* 2.8 67.1 + - + +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 3.3 13.3 + - + +
240B MET* 4.7 14.6 - - + -
247B LEU* 4.5 16.4 - - + -
257B LEU* 5.1 0.9 - - + -
260B LEU* 3.7 28.5 - - + -
263B ILE* 4.2 29.8 - - + -
276B SER 3.0 12.4 + - - +
277B ALA* 3.4 11.4 - - - +
278B LEU 3.3 0.4 - - - -
279B GLU* 1.3 76.4 - - - +
281B LEU* 1.3 56.8 + - + +
283B ARG* 4.0 0.3 - - - +
284B THR* 2.7 51.8 + - + +
528B LEU* 5.5 1.1 - - + -
529B LEU* 4.1 25.1 - - + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B MET* 5.8 1.1 - - + -
277B ALA 3.3 11.2 + - - +
278B LEU 3.3 7.2 + - - +
280B LEU* 1.3 78.5 - - + +
282B VAL* 1.3 61.9 + - - +
284B THR* 3.5 12.2 + - - -
285B GLY 3.5 0.2 + - - -
286B ARG* 3.2 37.9 + - - +
291B ALA* 3.6 37.2 - - + +
294B ILE* 4.4 15.5 - - + -
295B LEU* 3.8 26.2 - - + -
528B LEU* 4.0 21.3 - - + -
529B LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU* 3.7 17.9 - - + -
278B LEU* 3.0 18.3 + - + +
279B GLU* 3.2 9.6 + - - +
281B LEU* 1.3 75.6 - - - +
283B ARG* 1.3 76.8 + - + +
285B GLY* 3.2 10.4 + - - -
286B ARG 3.2 23.7 + - - +
287B SER 4.1 0.9 - - - -
288B PRO* 3.5 34.8 - - + -
291B ALA* 4.1 4.7 - - + -
336B ASP* 3.8 24.0 - - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP* 5.2 3.4 + - - +
145B ASP* 3.7 39.3 + - - +
146B ARG* 4.3 15.2 - - + +
149B TYR* 3.4 43.7 - - + +
152B ARG* 4.5 4.0 - - - +
169B SER* 5.4 2.2 + - - -
171B ARG* 4.9 6.9 - - - +
172B THR* 6.0 3.4 - - - +
222B ARG 5.8 2.0 + - - -
223B LEU* 5.7 5.7 - - - +
252B TRP* 3.2 20.2 + - + -
279B GLU* 2.8 52.0 + - + +
280B LEU 4.3 0.7 - - - +
282B VAL* 1.3 82.7 - - - +
284B THR* 1.3 59.6 + - - +
285B GLY 3.4 1.9 + - - -
336B ASP* 4.4 22.2 + - - +
338B LYS* 6.1 0.4 - - - +
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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
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249B VAL* 4.0 37.7 - - + +
250B SER 5.3 2.6 - - - +
252B TRP* 3.7 30.9 - - + +
257B LEU* 4.7 2.0 - - + -
280B LEU* 2.7 38.9 + - + +
281B LEU* 3.5 6.7 + - - -
282B VAL 3.2 0.4 - - - -
283B ARG* 1.3 77.8 - - + +
285B GLY* 1.3 57.3 + - - +
286B ARG* 5.7 0.8 - - - +
529B LEU* 3.6 24.0 + - + +
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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