Contacts of the strand formed by residues 235 - 243 (chain B) in PDB entry 2EF1
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 VAL 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B ALA* 3.5 26.9 - - + +
201B CYS 3.9 0.2 - - - +
202B ASP 3.6 7.4 - - - +
204B VAL* 3.6 25.1 - - + -
230B LEU* 4.3 8.3 - - + -
231B GLN 2.7 29.3 + - - +
232B PRO* 2.9 24.9 - - - +
233B GLU 4.0 1.1 - - - +
234B LYS* 1.3 72.6 - - - +
236B GLN* 1.3 63.1 + - - +
237B THR 3.5 26.5 - - - +
238B LEU* 5.3 0.2 - - - -
270B ASN 5.1 0.5 - - - +
271B ILE* 4.0 23.3 - - + +
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Residues in contact with GLN 236 (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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78A ARG* 5.6 1.3 + - - -
202B ASP* 2.9 36.5 + - - +
203B VAL* 4.0 10.2 - - - +
234B LYS 3.9 1.5 + - - +
235B VAL* 1.3 75.5 - - - +
237B THR* 1.3 74.9 + - - +
270B ASN 5.8 0.2 - - - -
271B ILE* 3.3 6.2 - - - +
272B GLN* 2.8 49.7 + - - +
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Residues in contact with THR 237 (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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202B ASP 3.2 0.8 + - - -
203B VAL* 3.4 18.5 - - + +
204B VAL 2.8 30.7 + - - -
235B VAL* 3.5 6.5 - - - +
236B GLN* 1.3 101.4 + - - +
238B LEU* 1.3 68.7 + - - +
239B GLU* 4.0 2.2 - - + +
271B ILE* 4.0 4.0 - - - -
272B GLN* 3.2 29.2 + - + +
273B PHE 4.6 0.2 - - - -
274B SER* 4.1 18.8 - - - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.1 0.2 - - + -
204B VAL* 3.2 27.6 - - + +
206B VAL* 3.7 27.4 - - + -
222B PHE* 4.2 16.6 - - + -
227B VAL* 4.4 1.6 - - + -
230B LEU* 4.4 12.8 - - + -
235B VAL* 5.5 0.4 - - + -
237B THR* 1.3 74.5 - - - +
239B GLU* 1.3 58.4 + - - +
262B LEU* 3.8 16.6 - - + -
266B ILE* 3.3 43.7 - - + -
271B ILE* 3.9 4.2 - - + +
272B GLN 3.0 9.5 + - - +
273B PHE* 3.3 9.6 - - + -
274B SER 3.0 21.7 + - - -
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Residues in contact with GLU 239 (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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203B VAL* 4.3 11.8 - - + +
204B VAL 2.7 10.0 + - - +
205B HIS* 3.1 32.0 + - + +
206B VAL* 3.0 24.4 + - - -
237B THR* 4.0 2.4 - - + -
238B LEU* 1.3 73.2 - - - +
240B ALA* 1.3 63.9 + - - +
241B TRP* 3.6 15.3 + - - +
274B SER* 3.0 28.8 + - - +
275B CYS* 5.1 1.1 - - - -
276B LYS* 3.2 36.0 + - - +
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Residues in contact with ALA 240 (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 VAL* 3.3 18.4 - - + +
208B LEU* 4.3 16.6 - - + -
238B LEU 3.8 1.4 + - - -
239B GLU* 1.3 73.9 - - - +
241B TRP* 1.3 67.4 + - - +
242B VAL* 5.2 0.4 - - + -
259B ILE* 5.6 0.4 - - + -
262B LEU* 4.4 1.3 - - + -
273B PHE* 3.6 29.8 - - + -
274B SER 2.6 9.3 + - - +
275B CYS* 3.5 9.5 - - - -
276B LYS* 3.1 24.7 + - - +
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Residues in contact with TRP 241 (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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123B LEU* 4.3 10.8 - - + -
135B PHE* 3.8 40.6 - + - -
142B MET* 4.3 7.6 - - + -
205B HIS* 3.3 30.0 - + + -
206B VAL 2.8 13.6 + - - +
207B MET* 3.6 34.9 - - + +
208B LEU* 2.5 35.7 + - - +
239B GLU* 3.3 25.4 + - + -
240B ALA* 1.3 85.7 - - - +
242B VAL* 1.3 59.3 + - - +
276B LYS* 3.5 31.5 - - + +
278B ILE* 3.7 22.7 - - + -
284B PHE* 4.3 5.4 - + - -
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Residues in contact with VAL 242 (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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208B LEU* 3.5 6.5 - - + -
210B GLY* 3.7 12.6 - - - -
215B ILE* 3.6 34.5 - - + -
240B ALA 5.1 0.4 - - - -
241B TRP* 1.3 75.7 - - - +
243B ILE* 1.3 59.0 + - - +
244B HIS* 3.5 4.4 + - + -
253B LEU* 3.8 19.5 - - + +
254B CYS* 4.3 2.0 - - - -
259B ILE* 4.4 17.9 - - + -
275B CYS* 3.7 27.8 - - - -
276B LYS 3.1 7.9 + - - +
277B ASN* 4.4 7.6 - - - +
278B ILE* 2.8 31.9 + - - +
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Residues in contact with ILE 243 (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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128B ILE* 3.3 24.0 - - + -
131B LEU* 3.8 26.0 - - + -
207B MET* 3.8 18.2 - - + -
208B LEU 2.7 21.9 + - - +
209B ASN* 4.1 3.8 - - - +
210B GLY* 2.6 33.1 + - - +
211B SER* 4.5 0.3 + - - -
241B TRP 4.6 0.7 - - - +
242B VAL* 1.3 73.0 - - - +
244B HIS* 1.3 66.6 + - - +
278B ILE* 3.5 40.2 - - + +
281B PRO* 3.7 22.7 - - + -
284B PHE* 5.1 1.3 - - + -
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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