Contacts of the strand formed by residues 255 - 261 (chain C) in PDB entry 3F78
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 ILE 255 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C THR* 3.6 28.0 - - + -
232C LYS 3.0 15.3 + - - +
233C VAL* 3.4 14.7 - - + +
234C LEU 2.8 28.9 + - - +
253C ASP 3.9 2.4 + - - +
254C ILE* 1.3 69.7 - - - +
256C ARG* 1.3 61.8 + - - +
257C TYR* 5.9 1.1 - - + -
279C SER* 3.4 7.4 - - - +
285C PHE* 3.7 30.1 - - + -
305C LYS 4.4 13.2 - - - +
308C GOL 3.5 34.5 - - - +
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ILE* 5.0 2.0 - - - -
234C LEU* 3.5 26.2 - - + -
236C ILE* 4.7 6.1 - - + -
248C ILE* 3.7 21.1 - - - +
251C ALA* 3.3 22.4 + - - -
252C LYS* 3.4 37.8 + - - +
254C ILE* 2.7 20.1 + - + +
255C ILE* 1.3 75.1 - - - +
257C TYR* 1.3 59.8 + - - +
258C ILE 4.1 0.2 - - - -
276C LYS 4.4 1.4 + - - -
277C PHE 3.0 38.5 + - - +
278C ALA* 3.4 20.1 + - - -
279C SER* 2.8 46.8 + - - +
285C PHE* 3.5 12.9 - - - +
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Residues in contact with TYR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C VAL* 5.7 1.6 - - + -
234C LEU 2.9 10.4 + - - +
235C ILE* 3.3 16.9 - - + -
236C ILE* 2.9 26.0 + - - +
255C ILE* 4.1 1.3 + - + -
256C ARG* 1.3 73.1 - - - +
258C ILE* 1.3 60.3 + - - +
259C ILE* 3.6 30.1 - - + -
284C GLU 3.4 19.5 - - - -
285C PHE* 3.4 31.2 - + + -
286C VAL 5.4 0.2 - - - -
287C LYS* 3.4 31.6 - - + +
298C LEU* 4.3 5.0 - - + +
301C GLU* 4.3 6.6 + - - +
302C LEU* 3.4 30.5 - - + +
305C LYS* 3.9 24.3 + - + -
306C ILE* 5.2 7.2 - - + -
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Residues in contact with ILE 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C THR* 5.1 2.7 - - + -
236C ILE* 3.3 35.4 - - + +
238C THR* 4.3 6.1 - - + -
256C ARG 4.1 0.4 - - - -
257C TYR* 1.3 75.3 - - - +
259C ILE* 1.3 71.8 + - - +
260C GLY 4.1 0.4 + - - -
274C LEU* 3.9 38.6 - - + +
277C PHE* 4.0 24.9 - - + -
278C ALA* 3.8 11.0 - - + -
285C PHE 2.9 8.4 + - - +
286C VAL* 3.5 30.1 - - + +
287C LYS* 2.8 27.0 + - - +
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Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE* 4.0 15.0 - - + -
235C ILE* 3.9 25.1 - - + -
236C ILE 2.7 11.9 + - - +
237C ILE* 4.2 8.8 - - + +
238C THR* 2.9 29.6 + - - +
257C TYR* 3.6 26.5 - - + -
258C ILE* 1.3 74.9 - - - +
260C GLY* 1.3 59.8 + - - +
261C ILE* 3.8 14.8 - - + -
287C LYS* 3.2 10.3 - - + +
289C LEU* 3.7 30.7 - - + -
295C LEU* 4.3 3.4 - - + -
298C LEU* 3.5 24.0 - - + -
302C LEU* 5.2 0.4 - - + -
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Residues in contact with GLY 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C THR* 3.4 6.3 - - - -
258C ILE 4.1 0.8 - - - -
259C ILE* 1.3 74.0 - - - +
261C ILE* 1.3 59.9 + - - +
265C PHE* 3.6 21.5 - - - -
274C LEU* 3.9 15.5 - - - +
287C LYS 2.9 8.3 + - - -
288C ILE* 3.3 8.5 - - - +
289C LEU 2.9 25.3 + - - +
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ILE* 3.9 18.8 - - + -
238C THR 2.9 13.8 + - - +
239C ASP* 3.5 26.5 - - - +
259C ILE* 3.8 13.0 - - + +
260C GLY* 1.3 79.0 - - - +
262C GLY* 1.3 66.7 + - - +
265C PHE* 3.6 5.3 - - - -
289C LEU* 3.3 9.0 - - + +
291C THR 3.6 30.1 - - - +
292C PHE* 3.7 32.5 - - + +
295C LEU* 3.6 40.6 - - + -
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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