Contacts of the strand formed by residues 235 - 242 (chain B) in PDB entry 4JF7
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 GLY 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 4.8 0.2 - - - -
173B HIS* 2.8 28.1 + - - -
175B CYS* 3.3 2.6 - - - -
197B MET* 4.5 6.5 - - - -
232B VAL* 2.9 24.0 + - - +
233B PRO 3.4 1.4 + - - -
234B GLY* 1.3 80.9 - - - +
236B CYS* 1.3 65.9 + - - -
264B MET 3.2 11.9 - - - -
265B TYR* 4.1 2.0 - - - -
266B TYR 4.4 1.3 - - - -
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Residues in contact with CYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B CYS* 2.0 43.5 - - - -
195B VAL* 5.1 1.6 - - - -
196B SER 4.4 2.0 - - - -
197B MET* 3.7 29.8 - - - -
229B ILE* 3.9 17.3 - - + -
230B SER 3.3 7.2 - - - +
232B VAL* 3.6 7.4 - - - +
235B GLY* 1.3 74.9 - - - -
237B MET* 1.3 60.4 + - - +
262B ILE 3.8 0.5 - - - +
263B ILE* 3.3 4.7 - - - +
264B MET* 2.7 48.4 + - + +
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Residues in contact with MET 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.6 1.8 - - - +
230B SER 2.8 32.2 + - - +
232B VAL* 3.9 17.9 - - + +
236B CYS* 1.3 74.7 - - - +
238B MET* 1.3 63.3 + - - +
261B ILE* 3.6 28.7 - - + -
262B ILE 3.4 3.8 - - - +
263B ILE* 3.8 29.4 - - + +
301B VAL* 3.8 34.8 - - + -
303B PHE* 3.5 23.0 - - + -
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Residues in contact with MET 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 3.4 31.0 - - - -
193B GLN* 3.9 9.2 - - + -
195B VAL* 4.0 9.4 - - + -
218B LEU* 3.7 31.2 - - + -
224B ARG* 5.0 0.4 - - - -
227B CYS* 3.8 12.8 - - + -
228B SER 3.4 14.6 - - - +
229B ILE* 4.2 6.1 - - + -
236B CYS 4.2 0.2 - - - -
237B MET* 1.3 76.3 - - - +
239B TYR* 1.3 62.8 + - - +
240B CYS* 3.8 24.0 - - - -
261B ILE* 3.3 6.8 - - - +
262B ILE* 2.7 47.9 + - + +
264B MET* 4.0 12.1 - - + -
303B PHE* 4.3 1.3 - - - -
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Residues in contact with TYR 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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227B CYS* 3.1 4.3 - - - -
228B SER 2.9 30.9 + - - -
238B MET* 1.3 74.4 - - - +
240B CYS* 1.3 77.9 + - - +
259B GLN* 2.7 38.1 + - + +
260B ARG 3.4 11.7 - - - -
261B ILE* 3.5 20.6 - - + -
275B ILE* 4.6 8.2 - - + +
287B LEU* 3.7 21.1 - - - +
289B PRO* 3.4 31.8 - - + +
303B PHE* 3.8 35.7 - + + -
305B ILE* 3.6 25.7 - - + +
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Residues in contact with CYS 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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224B ARG* 4.0 18.6 - - + -
225B LYS 3.6 6.7 - - - +
227B CYS* 2.0 47.6 - - - -
238B MET* 3.8 20.6 - - - -
239B TYR* 1.3 81.4 - - - +
241B PHE* 1.3 68.0 + - - +
259B GLN* 3.7 0.2 - - - -
260B ARG* 2.9 33.9 + - + +
262B ILE* 4.2 8.3 - - + -
289B PRO* 3.8 7.6 - - - -
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Residues in contact with PHE 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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224B ARG* 3.6 3.8 - - - -
225B LYS* 2.8 58.2 + - + +
226B SER* 3.5 19.3 - - - -
240B CYS* 1.3 75.9 - - - +
242B VAL* 1.3 67.3 + - - +
243B SER* 3.8 22.7 - - - -
250B ASP* 4.1 18.4 - - - -
257B PRO* 3.6 21.8 - - + -
258B GLU 3.2 11.2 - - - +
259B GLN* 3.6 19.5 - - - +
287B LEU 3.8 2.7 - - - +
288B ASN* 3.3 38.1 - - - -
289B PRO* 4.0 4.6 - - + +
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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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222B VAL* 3.7 23.1 - - + -
223B ASN* 3.5 12.8 - - + +
224B ARG* 5.0 2.2 - - + -
241B PHE* 1.3 84.3 - - - +
243B SER* 1.3 63.3 + - - +
244B THR* 3.8 21.0 + - + +
257B PRO* 3.7 12.3 - - - +
258B GLU* 2.8 36.3 + - + +
260B ARG* 3.6 34.1 - - + +
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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