Contacts of the strand formed by residues 241 - 248 (chain B) in PDB entry 1EKF
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 MET 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B TYR* 6.3 0.4 - - + -
182B VAL* 5.4 3.1 - - + -
184B LEU* 6.0 0.2 - - + -
224B GLN* 3.2 39.5 - - - +
237B GLU* 3.3 6.8 - - - +
238B VAL* 2.7 56.7 + - + +
239B GLY 3.5 0.4 + - - -
240B THR* 1.3 81.7 - - - +
242B ASN* 1.3 58.9 + - - +
310B GLY* 4.1 4.7 - - - -
311B SER 3.1 21.3 - - - +
312B GLY* 4.4 4.7 - - - +
314B ALA* 6.5 0.9 - - + -
315B CYS* 4.1 21.3 - - + +
318B CYS* 3.9 32.5 - - + -
370B PLP 3.8 6.7 + - - -
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Residues in contact with ASN 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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236B THR 5.0 0.4 - - - -
237B GLU* 3.8 12.5 - - - +
238B VAL* 3.9 0.6 - - - +
241B MET* 1.3 75.8 - - - +
243B ILE* 1.3 60.3 + - - +
244B PHE* 4.6 2.5 - - + -
258B THR* 4.9 1.6 - - - +
265B ILE* 3.6 15.6 - - + +
266B LEU 2.9 18.2 + - - +
268B GLY* 3.2 33.7 - - - +
271B ARG* 3.4 25.1 - - + +
310B GLY* 3.0 6.4 - - - -
311B SER* 2.8 43.3 + - - +
370B PLP 3.6 12.9 + - - -
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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
----------------------------------------------------------
184B LEU* 5.3 1.8 - - + -
226B LEU* 3.7 17.3 - - + -
235B LEU* 3.9 24.0 - - + +
236B THR 3.5 26.8 + - - +
237B GLU* 4.4 1.1 - - - +
238B VAL* 3.6 28.9 - - + -
241B MET 3.9 0.2 + - - -
242B ASN* 1.3 76.4 - - - +
244B PHE* 1.3 68.5 + - - +
245B VAL* 5.0 3.8 - - + -
258B THR* 2.6 27.2 + - - -
259B PRO* 3.4 19.3 - - + +
291B ILE* 5.2 3.1 - - + +
308B VAL* 4.3 15.5 - - + -
309B PHE 3.5 9.0 - - - +
320B VAL* 6.0 0.2 - - + -
323B ILE* 5.9 0.4 - - + -
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Residues in contact with PHE 244 (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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242B ASN* 4.6 2.0 - - + -
243B ILE* 1.3 79.6 - - - +
245B VAL* 1.3 68.3 + - - +
256B LEU* 3.8 25.4 - - + -
257B VAL 3.5 4.5 - - - -
258B THR* 3.7 22.7 - - + -
271B ARG* 3.6 37.5 - - + -
274B LEU* 3.9 15.0 - - + -
275B LEU* 3.9 18.8 - - + -
308B VAL* 3.5 6.2 - - - +
309B PHE* 2.9 65.7 + + + +
311B SER* 3.5 31.9 - - - -
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Residues in contact with VAL 245 (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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235B LEU* 5.2 4.9 - - + -
243B ILE* 5.0 8.1 - - + -
244B PHE* 1.3 80.1 - - - +
246B TYR* 1.3 63.2 + - - +
247B TRP* 3.5 41.8 + - + -
255B GLU 3.7 0.7 - - - +
256B LEU* 3.5 4.4 - - - +
257B VAL* 2.9 44.8 + - + +
291B ILE* 3.9 24.9 - - + -
296B LEU* 5.7 7.0 - - + -
305B VAL* 4.9 3.8 - - + -
307B GLU 3.6 5.8 - - - +
308B VAL* 4.3 20.6 - - + -
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Residues in contact with TYR 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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245B VAL* 1.3 71.8 - - - +
247B TRP* 1.3 61.5 + - - +
254B LEU* 3.6 31.0 - - + +
255B GLU 3.4 16.2 - - - -
256B LEU* 4.2 6.5 - - + -
284B PHE* 3.9 26.5 - + - -
305B VAL* 4.2 1.6 - - - +
306B ARG* 2.9 69.7 + - + +
307B GLU* 2.7 41.2 + - + +
309B PHE* 4.7 2.0 - - + -
340B GLU* 5.5 0.4 - - + -
341B LEU* 3.5 42.6 - - + +
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Residues in contact with TRP 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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245B VAL* 3.5 19.3 - - + -
246B TYR* 1.3 78.5 - - - +
248B THR* 1.3 61.4 + - - +
249B HIS* 4.1 21.1 - + - +
250B GLU* 6.2 1.1 - - + -
254B LEU* 3.5 10.7 - - - +
255B GLU* 2.7 72.5 + - + +
257B VAL* 3.6 21.6 - - + +
289B ARG* 4.6 2.9 - - - -
291B ILE* 4.2 13.5 - - + -
295B GLN* 3.9 39.5 - - + -
296B LEU* 4.3 7.9 - - + -
299B ALA* 3.5 31.6 - - + -
304B ARG* 3.2 18.4 - - - +
305B VAL* 3.8 11.4 - - + -
306B ARG* 4.1 2.9 - - - +
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Residues in contact with THR 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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247B TRP* 1.3 74.6 - - - +
249B HIS* 1.3 67.6 + - - +
252B GLY* 4.1 21.2 + - - +
253B VAL 3.7 4.5 - - - -
254B LEU* 4.2 14.5 + - - +
304B ARG* 2.9 58.0 + - + +
306B ARG* 5.4 2.8 - - - +
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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