Contacts of the strand formed by residues 242 - 247 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ASP* 4.4 8.1 - - - +
236B VAL 3.4 3.1 - - - +
237B LEU* 3.6 2.2 - - - -
238B THR* 2.9 38.3 + - - +
240B ASN* 3.7 32.8 + - + +
241B CYS* 1.3 74.0 - - - +
243B LEU* 1.3 61.2 + - - +
244B LYS* 3.4 13.7 + - - -
256B ASP* 3.3 20.7 + - - +
257B TYR 3.1 18.2 + - - +
258B ASP* 3.8 29.0 + - + -
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Residues in contact with LEU 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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235B ILE* 3.4 28.0 - - + -
236B VAL 3.2 18.4 - - - +
237B LEU* 4.8 3.4 - - + -
241B CYS 4.0 1.6 + - - -
242B HIS* 1.3 69.9 - - - +
244B LYS* 1.3 59.5 + - - +
245B ILE* 3.5 8.1 + - + +
256B ASP* 3.9 0.3 - - - -
257B TYR* 3.0 39.0 + - + -
259B MET* 3.7 26.0 - - + +
280B LEU* 4.2 15.0 - - + -
287B LEU* 4.4 9.9 - - + -
289B THR* 5.3 0.9 - - + +
303B LEU* 5.6 0.7 - - + -
313B TYR* 3.6 44.4 - - + -
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Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B SER* 4.1 25.0 + - - +
206B LYS* 4.8 9.0 - - - +
221B ASP* 3.6 27.5 + - - +
234B LEU 3.9 1.2 - - - +
236B VAL* 2.8 48.3 + - + +
238B THR* 4.2 14.5 - - + +
242B HIS* 3.4 11.1 + - - +
243B LEU* 1.3 71.6 - - - +
245B ILE* 1.3 61.3 + - - +
246B TRP* 4.0 11.1 + - + +
253B LEU* 3.6 22.2 - - + -
255B GLN 3.5 5.8 - - - -
256B ASP* 3.8 31.6 - - - +
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Residues in contact with ILE 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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233B TYR* 4.2 5.4 - - + -
234B LEU 4.1 3.4 - - - +
235B ILE* 4.5 21.3 - - + +
243B LEU* 3.5 10.3 + - + +
244B LYS* 1.3 73.8 - - - +
246B TRP* 1.3 70.9 + - - +
253B LEU* 3.6 2.2 - - - +
254B ILE* 2.9 30.2 + - + +
255B GLN* 3.3 27.4 + - + -
257B TYR* 4.0 22.4 - - + +
303B LEU* 4.5 8.7 - - + -
311B LEU* 3.2 40.2 - - + -
313B TYR* 4.4 13.7 - - + +
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Residues in contact with TRP 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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183B LEU* 3.1 38.1 - - + +
199B PHE* 4.3 15.5 - + + -
200B ASN* 3.4 26.7 - - - -
201B ASP* 4.6 13.7 - - + -
203B SER* 6.0 1.8 - - - -
233B TYR* 3.1 7.1 - - - +
234B LEU* 2.7 57.3 + - + +
236B VAL* 4.1 17.3 - - + +
244B LYS* 4.0 16.8 - - + +
245B ILE* 1.3 77.6 - - - +
247B ASP* 1.3 62.8 + - - +
248B LEU* 3.7 6.1 + - + -
251B PHE 4.0 11.4 - - - -
252B THR* 3.5 8.5 - - - -
253B LEU* 3.1 56.6 - - + +
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Residues in contact with ASP 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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232B ARG* 3.4 11.8 + - - -
233B TYR* 3.2 31.3 - - + -
246B TRP* 1.3 71.7 - - - +
248B LEU* 1.3 52.7 + - - +
249B THR* 3.0 28.9 + - - -
250B SER* 3.9 13.0 + - - +
251B PHE* 2.5 37.8 + - - -
252B THR 3.4 7.3 + - - +
254B ILE* 3.2 30.7 - - + +
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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