Contacts of the strand formed by residues 242 - 247 (chain C) in PDB entry 3F7F
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 HIS 242 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559B GLU* 5.6 2.4 + - - -
560B ASN* 3.2 38.1 + - - -
221C ASP* 4.4 8.7 - - - +
236C VAL 3.4 2.9 - - - +
237C LEU* 3.6 2.2 - - - -
238C THR* 2.9 38.1 + - - +
240C ASN* 3.7 32.6 + - + +
241C CYS* 1.3 74.9 - - - +
243C LEU* 1.3 59.6 + - - +
244C LYS* 3.4 13.4 + - - -
256C ASP* 3.4 20.2 + - - +
257C TYR 3.2 17.6 + - - +
258C ASP* 3.8 20.2 + - + -
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Residues in contact with LEU 243 (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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235C ILE* 3.4 28.5 - - + -
236C VAL 3.2 17.7 - - - +
237C LEU* 4.8 3.4 - - + -
241C CYS 4.0 1.6 + - - -
242C HIS* 1.3 70.7 - - - +
244C LYS* 1.3 58.2 + - - +
245C ILE* 3.5 7.0 + - + +
256C ASP* 3.9 0.3 - - - -
257C TYR* 3.0 39.6 + - + -
259C MET* 3.7 24.8 - - + +
280C LEU* 4.3 15.7 - - + -
287C LEU* 4.4 9.9 - - + -
289C THR* 5.2 0.4 - - - +
303C LEU* 5.6 0.9 - - + -
313C TYR* 3.5 45.8 - - + -
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Residues in contact with LYS 244 (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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203C SER* 4.1 24.0 + - - +
206C LYS* 4.8 9.0 - - - +
221C ASP* 3.6 26.9 + - - +
234C LEU 3.9 1.0 - - - +
236C VAL* 2.8 48.4 + - + +
238C THR* 4.2 13.8 - - + +
242C HIS* 3.4 12.0 + - + +
243C LEU* 1.3 71.3 - - - +
245C ILE* 1.3 60.0 + - - +
246C TRP* 4.0 10.9 + - + +
253C LEU* 3.7 22.7 - - + -
255C GLN 3.5 6.1 - - - -
256C ASP* 3.7 32.5 - - - +
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Residues in contact with ILE 245 (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 TYR* 4.2 5.2 - - + -
234C LEU 4.1 3.1 - - - +
235C ILE* 4.5 21.5 - - + -
243C LEU* 3.5 10.3 + - + +
244C LYS* 1.3 74.4 - - - +
246C TRP* 1.3 69.8 + - - +
253C LEU* 3.6 1.8 - - - +
254C ILE* 2.8 29.7 + - + +
255C GLN* 3.3 27.9 + - + -
257C TYR* 3.9 22.9 - - + +
303C LEU* 4.5 10.1 - - + -
311C LEU* 3.2 38.4 - - + -
313C TYR* 4.4 13.2 - - + +
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Residues in contact with TRP 246 (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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183C LEU* 3.1 39.7 - - + +
199C PHE* 4.3 14.8 - + + -
200C ASN* 3.4 30.7 - - - -
201C ASP* 4.6 13.2 - - + -
203C SER* 6.0 1.6 - - - -
233C TYR* 3.1 6.4 - - - +
234C LEU* 2.7 56.3 + - + +
236C VAL* 4.2 16.9 - - + +
244C LYS* 4.0 17.0 - - + +
245C ILE* 1.3 77.3 - - - +
247C ASP* 1.3 62.8 + - - +
248C LEU* 3.7 7.5 + - + -
251C PHE 4.1 5.2 - - - -
252C THR* 3.5 11.4 - - - -
253C LEU* 3.1 57.2 - - + +
254C ILE* 4.5 0.2 - - - -
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Residues in contact with ASP 247 (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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232C ARG* 3.4 15.5 + - - -
233C TYR* 3.2 31.4 - - + -
246C TRP* 1.3 72.2 - - - +
248C LEU* 1.3 51.4 + - - +
249C THR* 3.0 27.6 + - - -
250C SER* 3.9 13.0 + - - +
251C PHE* 2.5 36.5 + - - -
252C THR 3.2 8.1 + - - +
254C ILE* 3.1 31.2 - - + +
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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