Contacts of the strand formed by residues 245 - 252 (chain B) in PDB entry 2O07
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 GLN 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A THR* 3.1 34.9 + - + +
209B CYS* 3.7 19.5 - - - +
210B GLN* 2.9 43.2 - - - +
211B TRP* 3.3 14.3 - - + -
233B TYR* 5.1 0.8 + - - -
235B TYR* 3.4 15.6 - - - +
236B CYS 3.1 17.9 - - - +
237B THR* 4.1 6.7 - - + -
238B ILE* 3.5 10.3 + - - +
241B TYR* 4.1 5.2 + - - +
242B PRO* 3.4 14.6 + - - +
243B SER 4.1 6.6 - - - +
244B GLY* 1.3 81.2 - - - +
246B ILE* 1.3 66.0 + - - +
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Residues in contact with ILE 246 (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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79B TYR* 3.7 22.2 - - + -
206B GLN* 3.1 39.5 - - + +
208B GLU* 3.6 20.0 - - - +
209B CYS* 4.2 3.8 - - + +
233B TYR* 4.5 0.7 - - - -
235B TYR* 3.3 4.7 - - - -
236B CYS* 2.9 32.4 + - - +
238B ILE* 4.4 5.2 - - + -
241B TYR* 3.7 26.2 - - + -
242B PRO* 5.9 0.9 - - + -
245B GLN* 1.3 78.3 - - - +
247B GLY* 1.3 66.8 + - - +
248B PHE* 4.0 4.9 - - + -
601B SPD 3.8 25.8 - - + -
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Residues in contact with GLY 247 (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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206B GLN* 3.8 1.2 - - - -
207B GLY* 2.8 29.1 + - - -
208B GLU 2.8 20.2 + - - -
233B TYR* 3.4 9.4 + - - -
234B ALA 3.0 15.3 - - - -
235B TYR* 3.8 1.1 - - - -
246B ILE* 1.3 79.4 - - - +
248B PHE* 1.3 67.7 + - - -
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Residues in contact with PHE 248 (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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79B TYR* 3.7 33.9 - + - -
82B MET* 3.8 20.9 - - + -
83B ILE* 3.6 35.7 - - + -
86B LEU* 3.6 23.8 - - + -
204B CYS* 3.8 15.5 - - - -
205B CYS 3.2 8.5 - - - -
206B GLN* 4.4 1.3 - - - -
207B GLY 4.0 0.2 - - - +
233B TYR* 3.3 13.9 - - - -
234B ALA 2.8 40.9 + - - +
235B TYR* 4.3 0.4 - - - -
236B CYS* 3.8 30.1 - - + -
246B ILE* 4.0 9.2 - - + -
247B GLY* 1.3 79.9 - - - -
249B MET* 1.3 61.1 + - - +
250B LEU* 3.7 4.5 + - + +
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Residues in contact with MET 249 (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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190B TYR* 3.8 33.2 - - + +
203B LEU* 3.8 1.6 - - - +
204B CYS* 3.2 4.7 - - - -
205B CYS 2.8 34.1 + - - +
207B GLY* 4.0 5.3 - - - -
217B ILE* 5.0 1.3 - - + +
220B MET* 3.5 53.2 - - + +
221B ARG* 3.5 13.9 - - + +
224B CYS* 3.8 7.4 - - + -
231B VAL* 3.6 23.1 - - - -
232B ALA 3.8 5.4 - - - +
233B TYR* 4.9 6.1 - - + +
248B PHE* 1.3 72.5 - - - +
250B LEU* 1.3 66.0 + - - +
251B CYS* 3.7 11.4 - - - -
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Residues in contact with LEU 250 (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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86B LEU* 4.1 12.1 - - + -
87B PRO* 4.0 16.8 - - + -
203B LEU 3.3 5.8 - - - +
204B CYS* 3.7 30.5 - - + -
231B VAL* 3.3 4.7 - - - +
232B ALA* 2.8 40.3 + - + +
234B ALA* 4.2 13.2 - - + +
248B PHE* 4.6 5.2 - - + +
249B MET* 1.3 76.1 - - - +
251B CYS* 1.3 63.2 + - - +
259B PHE* 3.7 35.2 - - + -
288B PHE* 3.5 37.7 - - + -
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Residues in contact with CYS 251 (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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190B TYR* 4.6 0.2 - - - -
197B LEU* 5.1 0.9 - - - +
202B VAL* 3.3 3.1 - - - -
203B LEU* 2.9 49.5 + - + +
224B CYS* 3.6 36.1 - - - -
228B PHE* 3.6 32.5 - - + -
230B VAL 3.3 5.8 - - - +
231B VAL* 4.1 3.4 - - - -
249B MET* 3.7 12.1 - - - -
250B LEU* 1.3 78.6 - - - +
252B SER* 1.3 60.8 + - - +
259B PHE* 3.5 5.2 - - - -
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Residues in contact with SER 252 (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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201B GLY 3.7 4.7 + - - -
202B VAL* 3.6 9.4 - - - +
228B PHE* 3.5 11.1 - - - +
229B PRO* 3.2 21.7 - - - +
230B VAL* 2.9 14.0 + - - -
251B CYS* 1.3 75.6 - - - +
253B LYS* 1.3 57.2 + - - +
254B ASN* 3.0 16.5 + - - +
257B THR* 2.5 39.6 + - - -
259B PHE* 3.6 13.4 - - - -
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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