Contacts of the strand formed by residues 241 - 250 (chain G) in PDB entry 3BZE
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 PHE 241 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G ASP* 3.9 23.3 - - + -
207G GLY* 3.0 10.6 + - - -
208G PHE* 2.8 51.8 + - + +
209G TYR* 3.9 14.6 - + - -
210G PRO 4.2 0.7 - - - -
211G ALA* 3.8 34.1 - - + -
233G THR* 4.0 15.7 - - + -
234G ARG* 3.3 18.2 - - - +
235G PRO* 3.9 21.5 - - + -
236G ALA 4.2 0.2 - - - +
239G GLY 3.9 16.4 - - - -
240G THR* 1.3 76.6 - - - +
242G GLN* 1.3 63.5 + - - +
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Residues in contact with GLN 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G ALA 3.2 14.8 - - - +
206G LEU* 3.5 23.1 - - + +
207G GLY 4.6 2.2 - - - +
208G PHE* 3.3 4.3 - - - -
233G THR* 3.6 1.9 - - - +
234G ARG* 2.9 71.7 + - + +
236G ALA* 3.2 34.6 - - - +
241G PHE* 1.3 77.6 - - - +
243G LYS* 1.3 65.1 + - - +
10H TYR* 3.5 16.4 - - + -
11H SER 3.8 9.6 + - - +
12H ARG 3.7 14.4 + - - +
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Residues in contact with LYS 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G TRP* 3.8 2.5 - - - +
205G ALA* 2.9 34.9 + - - +
206G LEU* 5.1 0.4 - - - +
208G PHE* 4.3 9.6 - - + -
213G ILE* 3.8 21.5 - - + +
215G LEU* 3.7 22.3 - - + +
230G LEU* 3.5 26.1 - - + +
231G VAL* 2.8 36.1 + - - +
232G GLU* 3.9 3.8 + - - +
233G THR* 2.9 36.0 + - - +
234G ARG* 5.2 2.2 - - - +
242G GLN* 1.3 78.3 - - - +
244G TRP* 1.3 77.7 + - - +
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Residues in contact with TRP 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G ARG* 3.6 35.4 - - + -
203G CYS 3.0 21.1 - - - +
204G TRP* 3.4 34.2 - + + -
215G LEU* 3.6 6.5 - - - -
229G GLU* 3.5 49.1 - - + -
230G LEU* 3.2 6.4 - - - +
231G VAL* 3.2 59.3 + - + +
234G ARG* 4.0 10.3 - - - +
243G LYS* 1.3 80.8 - - - +
245G ALA* 1.3 64.6 + - - +
246G ALA* 3.9 6.1 - - + -
99H MET* 3.2 32.1 + - + -
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Residues in contact with ALA 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G CYS* 2.8 37.0 + - + -
215G LEU* 3.9 21.2 - - + +
216G THR 5.1 0.2 - - - +
217G TRP* 2.9 18.5 + - + +
228G THR* 3.6 20.2 - - + -
229G GLU 3.2 5.2 - - - -
230G LEU* 3.8 14.1 - - + -
244G TRP* 1.3 77.6 - - - +
246G ALA* 1.3 58.5 + - - +
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Residues in contact with ALA 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G THR* 3.9 23.6 - - + -
201G LEU 3.6 5.8 - - - +
202G ARG* 4.4 9.0 - - - +
228G THR* 3.2 7.0 - - - -
229G GLU* 2.7 49.8 + - + +
244G TRP* 3.9 19.0 - - + -
245G ALA* 1.3 74.8 - - - +
247G VAL* 1.3 62.2 + - - +
248G VAL* 4.3 0.9 - - + +
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Residues in contact with VAL 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G THR* 5.2 0.7 - - - -
201G LEU* 3.5 17.3 + - + +
217G TRP* 3.3 51.6 - - + +
226G GLN* 3.4 43.5 - - + +
227G ASP 4.5 6.3 - - - +
228G THR* 4.7 6.3 - - - +
246G ALA* 1.3 77.1 - - - +
248G VAL* 1.3 63.7 + - - +
249G VAL* 2.9 17.5 + - + +
257G TYR* 4.2 4.7 - - + -
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Residues in contact with VAL 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G ILE* 3.6 33.7 - - + -
198G GLU* 3.7 28.7 - - + +
199G ALA 4.7 4.0 - - - -
200G THR* 4.0 11.6 - - + +
226G GLN* 3.5 20.9 + - - +
227G ASP 5.2 2.0 + - - -
246G ALA 4.3 0.4 - - - -
247G VAL* 1.3 70.3 - - - +
249G VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G GLU* 4.7 1.1 - - - -
199G ALA* 2.8 30.2 + - - +
201G LEU* 4.4 8.3 - - + -
226G GLN* 4.8 0.4 - - - +
247G VAL* 2.9 26.0 + - + +
248G VAL* 1.3 82.0 - - - +
250G PRO* 1.3 106.1 - - + +
253G GLU 4.2 7.4 - - - +
254G GLU* 4.5 5.8 - - + +
257G TYR* 3.2 57.7 - - + -
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Residues in contact with PRO 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G HIS 3.2 11.9 - - - +
198G GLU* 4.2 7.8 - - + +
249G VAL* 1.3 113.2 - - + +
251G SER* 1.3 72.4 + - - +
253G GLU* 2.5 40.1 + - - +
254G GLU* 4.0 2.9 + - - +
257G TYR* 4.1 7.2 - - - +
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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
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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