Contacts of the strand formed by residues 266 - 277 (chain B) in PDB entry 5O67
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B ARG 3.8 1.2 - - - +
230B VAL* 3.4 4.7 - - - -
231B LYS* 3.0 56.7 + - - +
265B TRP* 1.3 78.3 - - - +
267B ILE* 1.3 69.0 + - - +
268B THR* 4.8 2.6 + - - -
289B THR* 3.9 13.6 - - - +
290B HIS 3.4 10.8 - - - -
291B ASN* 3.3 21.3 + - - -
292B LEU* 4.8 1.6 - - - -
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Residues in contact with ILE 267 (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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228B VAL* 4.5 15.7 - - + -
229B ARG 3.6 4.5 - - - +
230B VAL* 3.6 30.3 - - + -
265B TRP* 5.8 1.6 - - + -
266B SER* 1.3 81.9 - - - +
268B THR* 1.3 67.3 + - - +
269B PRO* 4.0 13.3 - - + +
288B TYR 3.9 0.3 - - - +
289B THR* 3.5 0.3 - - - -
290B HIS* 2.9 37.4 + - + +
292B LEU* 4.6 21.3 - - + -
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B SER* 4.6 0.5 + - - -
228B VAL* 3.4 3.1 - - - -
229B ARG* 2.9 46.4 + - + +
266B SER* 4.8 3.1 + - - -
267B ILE* 1.3 77.9 + - - +
269B PRO* 1.3 67.9 - - - +
270B GLY 3.8 0.5 + - - -
287B SER* 4.1 15.0 - - - +
288B TYR 3.2 15.0 - - - +
289B THR* 2.9 28.8 + - - +
318B GLN* 4.3 2.2 - - - +
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Residues in contact with PRO 269 (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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226B VAL* 6.4 1.1 - - + -
227B SER 3.2 10.3 - - - +
228B VAL* 4.0 11.2 - - + -
267B ILE* 4.0 13.2 - - + +
268B THR* 1.3 88.0 - - - +
270B GLY* 1.3 57.5 + - - +
287B SER* 3.2 3.1 - - - -
288B TYR* 3.2 72.6 + - + +
290B HIS* 6.2 0.2 - - + -
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Residues in contact with GLY 270 (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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225B VAL 3.9 0.2 - - - +
226B VAL* 3.5 6.5 - - - +
227B SER* 2.9 41.8 + - - +
268B THR 3.8 0.6 + - - -
269B PRO* 1.3 74.0 - - - +
271B LEU* 1.3 60.8 + - - +
286B VAL 3.2 12.8 - - - -
287B SER* 3.6 7.2 - - - -
501B LDA 5.3 5.8 - - - -
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Residues in contact with LEU 271 (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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214B PHE* 3.7 34.1 - - + -
224B ALA* 4.6 2.2 - - + -
225B VAL 3.5 7.0 - - - +
226B VAL* 4.7 5.8 - - + +
270B GLY* 1.3 73.7 - - - +
272B SER* 1.3 79.4 + - - +
273B MET* 5.6 4.0 - - + -
285B SER* 3.2 6.9 - - - -
286B VAL* 2.8 51.6 + - + +
501B LDA 4.5 4.7 + - - -
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Residues in contact with SER 272 (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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99B ALA 4.6 2.3 + - - -
100B SER* 3.6 39.7 + - - -
223B ASP 4.2 0.8 + - - -
224B ALA* 3.4 5.0 - - - -
225B VAL* 3.2 38.4 + - - +
271B LEU* 1.3 83.9 - - - +
273B MET* 1.3 61.2 + - - +
274B VAL* 3.9 6.9 - - - +
284B GLY 3.5 10.4 + - - -
285B SER* 4.3 2.9 - - - +
501B LDA 4.5 8.3 - - - -
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Residues in contact with MET 273 (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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222B PRO* 4.6 16.2 - - + -
223B ASP 3.3 6.7 - - - +
224B ALA* 5.3 2.9 - - + -
271B LEU* 5.6 4.9 - - + -
272B SER* 1.3 73.7 + - - +
274B VAL* 1.3 65.9 + - - +
283B PHE* 3.4 2.2 - - - -
284B GLY* 3.2 33.4 + - - +
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Residues in contact with VAL 274 (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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96B TYR* 3.4 32.3 - - + -
99B ALA* 4.7 6.3 - - + +
100B SER* 4.0 22.9 - - - +
217B GLU* 3.8 4.6 - - - +
222B PRO* 3.5 2.8 - - - +
223B ASP* 3.0 39.7 + - + +
225B VAL* 6.5 0.2 - - + -
272B SER* 3.9 14.6 - - - +
273B MET* 1.3 80.2 - - - +
275B LYS* 1.3 64.5 + - - +
281B VAL* 3.9 19.5 - - + -
282B LEU 3.7 6.3 - - - +
283B PHE* 4.3 11.4 - - + -
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Residues in contact with LYS 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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217B GLU* 3.8 8.9 + - - +
218B SER 2.9 27.3 + - - -
219B ALA* 4.1 8.8 + - - +
220B THR* 4.1 19.3 - - - +
221B MET 4.0 14.5 + - - +
222B PRO* 4.0 16.6 - - + -
274B VAL* 1.3 76.3 - - - +
276B THR* 1.3 71.8 + - - +
277B PHE* 3.6 42.5 - - + -
281B VAL* 3.7 4.4 - - - -
282B LEU* 3.2 32.9 + - + +
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Residues in contact with THR 276 (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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92B VAL* 5.9 0.5 - - - +
96B TYR* 2.6 29.0 + - - -
217B GLU* 3.0 15.2 + - - +
275B LYS* 1.3 87.0 + - - +
277B PHE* 1.3 69.0 + - - +
278B ASP* 3.7 25.8 - - + +
279B PRO 5.6 0.4 - - - -
280B ALA 4.1 3.1 - - - -
281B VAL* 3.8 17.6 - - + +
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Residues in contact with PHE 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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275B LYS* 3.6 49.8 - - + -
276B THR* 1.3 73.9 - - - +
278B ASP* 1.3 67.9 + - - +
280B ALA* 3.1 25.0 + - - +
282B LEU* 4.0 24.5 - - + -
328C ASN* 3.4 10.3 + - - +
330C ARG* 6.5 0.9 - - + -
331C MET* 3.4 33.4 - - + -
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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
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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