Contacts of the strand formed by residues 224 - 232 (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 ARG 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ASN* 3.2 23.4 + - - -
191B SER* 3.8 2.8 + - - -
192B ASN 5.7 0.2 - - - -
193B GLN* 3.6 14.1 - - + +
218B LEU* 3.9 38.7 + - - +
220B ASP* 2.5 45.6 + - - +
222B VAL* 3.0 36.2 + - + +
223B ASN* 1.3 68.9 + - - +
225B LYS* 1.3 60.3 + - - +
227B CYS* 4.1 3.4 - - - -
238B MET* 5.0 0.4 - - - -
240B CYS* 4.0 20.9 - - + -
241B PHE 3.6 6.5 - - - +
242B VAL* 5.0 0.9 - - + -
260B ARG* 4.8 4.9 - - - -
262B ILE* 4.1 14.8 - - - +
272B GLU* 2.7 49.2 + - - +
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Residues in contact with LYS 225 (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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179B ASN* 3.4 23.3 + - - +
181B ILE* 3.4 18.6 - - - +
187B ASP 3.3 25.7 + - - +
191B SER* 3.9 6.2 - - - -
193B GLN* 5.4 0.2 - - - -
223B ASN* 3.3 25.6 - - - +
224B ARG* 1.3 78.6 - - - +
226B SER* 1.3 69.6 - - - +
227B CYS* 3.2 4.1 + - - -
240B CYS* 3.6 2.3 - - - +
241B PHE* 2.8 52.4 + - + +
243B SER* 3.5 21.5 - - - -
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 4.5 10.0 - - - +
179B ASN* 6.1 1.8 - - - +
193B GLN* 5.8 0.4 + - - -
225B LYS* 1.3 77.0 - - - +
227B CYS* 1.3 64.7 + - - +
241B PHE* 3.5 22.4 - - - -
288B ASN* 3.9 7.7 + - - +
289B PRO* 2.8 40.6 + - - +
291B THR* 3.3 21.9 - - - +
306B TYR* 4.7 3.6 + - - -
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Residues in contact with CYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 4.9 8.8 + - - +
166B SER* 3.6 13.2 - - - -
177B THR* 4.5 1.4 - - + +
193B GLN* 3.7 41.2 - - - +
224B ARG* 4.1 5.6 - - - -
225B LYS 4.0 6.7 - - - -
226B SER* 1.3 76.3 - - - +
228B SER* 1.3 60.2 + - - +
238B MET* 3.8 11.0 - - - -
239B TYR 3.1 6.5 - - - +
240B CYS* 2.0 46.4 - - - -
291B THR* 3.6 11.7 - - - -
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 3.4 4.5 - - - -
226B SER 3.4 1.8 + - - -
227B CYS* 1.3 73.9 - - - +
229B ILE* 1.3 59.7 + - - +
238B MET* 3.4 5.7 - - - +
239B TYR 2.9 31.8 + - - -
289B PRO* 4.1 6.7 - - - -
290B GLY 3.5 7.8 + - - -
291B THR 2.7 28.1 + - - -
292B GLY 2.8 20.6 + - - -
303B PHE* 3.6 22.9 - - - -
304B PRO* 4.0 2.4 - - - +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 2.8 42.9 + - - +
167B PHE* 3.9 2.5 - - - +
168B SER* 3.6 2.3 - - - +
175B CYS* 3.7 35.2 - - + +
176B TYR 4.1 8.3 - - - +
177B THR* 3.9 13.2 - - + -
195B VAL* 4.0 22.2 - - + -
228B SER* 1.3 75.8 - - - +
230B SER* 1.3 63.1 + - - +
236B CYS* 3.9 15.5 - - + -
237B MET 3.6 10.1 - - - +
238B MET* 4.2 6.5 - - + -
264B MET* 4.5 4.9 - - + -
293B SER* 3.3 9.2 - - - -
294B GLY 3.0 19.5 + - - -
303B PHE* 4.0 1.1 - - - -
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Residues in contact with SER 230 (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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168B SER* 3.6 7.5 + - - -
175B CYS* 4.4 4.0 - - - -
229B ILE* 1.3 76.6 - - - +
231B THR* 1.3 74.6 + - - +
236B CYS* 3.3 3.6 - - - +
237B MET* 2.8 36.0 + - - +
294B GLY* 3.6 21.7 + - - -
295B VAL* 3.7 18.0 - - - -
296B TYR 3.8 0.5 + - - -
301B VAL* 3.8 20.5 - - - +
303B PHE* 4.2 1.6 - - - -
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Residues in contact with THR 231 (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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168B SER* 3.0 34.6 + - - +
170B THR* 2.9 34.6 + - - +
173B HIS* 3.7 29.8 - - - +
175B CYS* 3.8 15.3 - - - +
230B SER* 1.3 88.8 + - - +
232B VAL* 1.3 65.3 + - - +
235B GLY 3.5 6.1 - - - -
296B TYR* 3.7 12.5 + - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B HIS* 3.3 7.6 - - - -
230B SER* 4.3 0.4 - - - +
231B THR* 1.3 81.2 - - - +
233B PRO* 1.3 79.0 - - + +
234B GLY 2.9 4.5 + - - -
235B GLY* 2.9 18.2 + - - +
236B CYS 3.6 26.5 - - - +
237B MET* 3.9 20.0 - - + -
263B ILE* 4.6 5.4 - - + -
265B TYR* 4.2 18.4 - - + +
296B TYR* 4.8 5.2 - - + -
301B VAL* 3.7 28.9 - - + -
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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