Contacts of the strand formed by residues 266 - 277 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ARG 4.0 0.7 + - - +
230A VAL* 3.5 6.1 - - - +
231A LYS* 2.9 63.0 + - - +
264A VAL* 5.2 0.9 - - - -
265A TRP* 1.3 78.1 - - - +
267A ILE* 1.3 61.6 + - - +
268A THR* 4.7 2.4 + - - -
289A THR* 4.0 12.9 - - - +
290A HIS 3.3 6.7 - - - -
291A ASN* 3.4 21.8 - - - -
292A LEU* 4.8 1.3 - - - +
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Residues in contact with ILE 267 (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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228A VAL* 3.9 25.1 - - + -
229A ARG 3.5 4.7 - - - +
230A VAL* 4.3 16.2 - - + -
266A SER* 1.3 77.0 - - - +
268A THR* 1.3 64.7 + - - +
269A PRO* 3.7 9.7 - - + +
289A THR* 3.6 0.3 - - - -
290A HIS* 2.9 53.0 + - + +
292A LEU* 4.7 15.0 - - + -
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A SER 4.6 0.2 - - - -
228A VAL* 3.4 3.4 - - - -
229A ARG* 2.8 46.9 + - + +
266A SER* 4.7 2.6 + - - -
267A ILE* 1.3 70.5 - - - +
269A PRO* 1.3 65.5 - - - +
270A GLY* 4.1 0.4 + - - -
287A SER* 3.9 22.4 - - - +
288A TYR 3.3 11.0 - - - +
289A THR* 2.7 35.0 + - - +
318A GLN* 4.6 0.4 - - - +
501A LDA 6.3 0.9 - - + -
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Residues in contact with PRO 269 (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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226A VAL* 6.1 1.8 - - + -
227A SER 3.3 11.4 - - - +
228A VAL* 4.2 10.5 - - + -
267A ILE* 3.7 13.9 - - + +
268A THR* 1.3 90.8 - - - +
270A GLY* 1.3 58.5 + - - +
287A SER* 3.5 2.8 - - - -
288A TYR* 3.3 74.8 + - + +
290A HIS* 6.3 0.2 - - + -
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Residues in contact with GLY 270 (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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226A VAL* 3.4 9.6 - - - +
227A SER* 2.9 42.0 + - - -
268A THR* 5.5 0.2 - - - -
269A PRO* 1.3 74.8 - - - +
271A LEU* 1.3 61.8 + - - -
286A VAL 3.4 11.4 - - - -
287A SER* 3.8 7.2 - - - -
501A LDA 5.1 2.9 - - - -
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Residues in contact with LEU 271 (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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214A PHE* 3.8 31.0 - - + -
224A ALA* 5.1 1.6 - - + -
225A VAL 3.4 17.3 - - - +
226A VAL* 4.5 6.1 - - + -
227A SER* 4.2 0.6 + - - -
270A GLY* 1.3 73.4 - - - +
272A SER* 1.3 68.5 + - - +
273A MET* 5.1 4.9 - - + +
285A SER* 3.1 8.5 - - - -
286A VAL* 3.0 51.3 + - + +
501A LDA 4.6 5.9 - - - +
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Residues in contact with SER 272 (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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99A ALA 4.5 0.8 + - - -
100A SER* 3.4 43.9 - - - -
223A ASP 3.5 1.6 + - - +
224A ALA* 3.4 5.4 - - - +
225A VAL* 3.0 40.4 + - - +
271A LEU* 1.3 77.0 - - - +
273A MET* 1.3 59.5 + - - +
274A VAL* 4.0 6.4 - - - +
284A GLY 3.5 8.1 - - - -
285A SER* 4.3 0.4 - - - -
501A LDA 4.6 14.1 - - - -
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Residues in contact with MET 273 (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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222A PRO* 4.7 13.9 - - + -
223A ASP 3.5 5.4 - - - +
224A ALA* 5.2 4.5 - - + -
271A LEU* 5.1 7.2 - - + +
272A SER* 1.3 73.1 - - - +
274A VAL* 1.3 65.0 + - - +
283A PHE* 3.3 1.8 - - - -
284A GLY* 3.0 34.5 + - - +
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Residues in contact with VAL 274 (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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96A TYR* 3.3 38.8 - - + -
99A ALA* 4.4 9.2 - - + +
100A SER* 4.0 19.5 - - - -
217A GLU* 3.8 2.1 - - - +
222A PRO* 3.5 2.0 - - - +
223A ASP* 3.0 39.8 + - + +
272A SER* 4.0 15.0 - - - +
273A MET* 1.3 77.7 - - - +
275A LYS* 1.3 65.9 + - - +
281A VAL* 3.8 14.8 - - + -
282A LEU 3.6 6.5 - - - +
283A PHE* 3.9 13.5 - - + -
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Residues in contact with LYS 275 (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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217A GLU* 3.8 11.3 + - - +
218A SER 2.9 24.9 + - - -
219A ALA* 3.2 19.5 + - - +
220A THR 3.7 13.9 - - - -
221A MET 3.3 19.5 + - - +
222A PRO* 3.5 16.8 - - + -
274A VAL* 1.3 76.0 - - - +
276A THR* 1.3 71.9 + - - +
277A PHE* 3.5 37.3 - - + -
281A VAL* 3.5 3.1 - - - -
282A LEU* 3.1 34.1 + - + +
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Residues in contact with THR 276 (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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92A VAL* 6.0 0.2 - - - +
96A TYR* 2.6 31.7 + - - -
217A GLU* 3.0 16.0 + - - +
275A LYS* 1.3 81.2 + - - +
277A PHE* 1.3 66.3 + - - +
278A ASP* 3.8 24.2 + - + +
279A PRO 5.5 1.3 - - - -
280A ALA 3.6 11.4 - - - +
281A VAL* 3.8 11.2 - - + +
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Residues in contact with PHE 277 (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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275A LYS* 3.5 45.3 - - + -
276A THR* 1.3 75.7 - - - +
278A ASP* 1.3 58.8 + - - +
280A ALA* 2.8 21.2 + - + +
282A LEU* 4.4 15.3 - - + -
328B ASN* 2.8 23.1 + - - +
330B ARG* 6.4 2.7 - - + -
331B MET* 3.2 38.6 - - + -
373B ILE* 6.3 0.4 - - + -
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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