Contacts of the strand formed by residues 238 - 247 (chain B) in PDB entry 5J63
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 GLN 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP* 3.1 43.9 + - - +
61A ASN* 3.6 19.6 + - + +
234B TYR* 3.3 4.5 - - - -
235B VAL* 2.9 40.2 + - + +
236B GLY 3.4 0.2 - - - -
237B ASN* 1.3 72.9 - - - +
239B LYS* 1.3 84.1 + - - +
240B PHE* 3.4 2.8 + - - -
281B ALA* 4.3 6.4 - - + -
282B GLY* 3.6 12.0 - - - +
296B LEU* 4.2 22.9 - - + -
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Residues in contact with LYS 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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60A ASP* 5.4 0.4 - - - +
203B PRO* 5.8 5.1 - - - +
204B ASP* 4.6 5.3 + - - -
232B PHE* 3.6 43.5 - - + -
233B SER 3.4 11.7 - - - +
234B TYR* 3.5 31.0 + - + +
237B ASN 3.2 7.0 + - - +
238B GLN* 1.3 80.7 + - - +
240B PHE* 1.3 64.2 + - - +
241B THR* 5.0 6.5 - - - +
282B GLY* 2.9 28.1 + - - -
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Residues in contact with PHE 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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210B TRP* 4.9 0.2 - + - -
232B PHE* 3.1 6.8 - - - +
233B SER* 2.9 55.5 + - - -
234B TYR 3.6 19.7 - - - -
235B VAL* 3.5 31.6 - - + -
238B GLN 3.9 3.8 - - - -
239B LYS* 1.3 75.9 - - - +
241B THR* 1.3 69.7 + - - +
242B VAL* 4.1 10.1 - - + -
265B LEU* 5.7 0.7 - - + -
276B ILE* 4.0 23.1 - - + -
280B GLN 3.3 14.8 - - - +
281B ALA* 4.1 7.0 - - - -
282B GLY 4.2 1.3 - - - +
292B LEU* 4.2 11.7 - - + -
296B LEU* 3.9 21.3 - - + -
298B LEU* 5.8 1.1 - - + -
304B LEU* 3.9 19.7 - - + -
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Residues in contact with THR 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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229B PRO 4.6 3.3 + - - +
230B GLY* 3.8 19.3 - - - -
231B ALA 3.5 12.3 - - - +
232B PHE* 4.5 5.2 - - - +
239B LYS* 5.0 7.1 - - - +
240B PHE* 1.3 77.0 + - - +
242B VAL* 1.3 65.0 + - - +
243B TRP* 3.7 32.6 - - + -
279B GLY* 3.1 25.1 - - - -
280B GLN* 2.9 31.5 + - - +
282B GLY 4.8 3.8 + - - -
292B LEU* 4.2 5.2 - - - +
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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
----------------------------------------------------------
208B LEU* 3.5 25.4 - - + -
210B TRP* 5.1 0.4 - - + -
221B VAL* 3.4 34.1 - - + +
225B ALA* 5.7 0.7 - - - -
230B GLY* 4.9 0.2 - - - -
231B ALA 2.8 25.9 + - - +
232B PHE* 5.2 0.2 - - - -
240B PHE* 4.1 11.9 - - + +
241B THR* 1.3 74.6 - - - +
243B TRP* 1.3 60.9 + - - +
244B SER 3.8 19.1 - - - +
245B SER* 4.2 5.6 - - - -
274B LEU* 5.3 2.2 - - + -
276B ILE* 3.9 36.8 - - + -
278B THR 3.9 4.0 - - - +
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Residues in contact with TRP 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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39B LYS* 5.9 2.0 - - - -
221B VAL* 3.5 9.0 - - - +
225B ALA* 3.6 20.6 - - - +
226B ASP* 3.6 27.4 - - + -
228B TRP 3.5 16.4 - - - -
229B PRO* 3.9 15.5 - - + -
230B GLY* 3.5 20.6 - - - -
241B THR* 3.7 18.1 - - + +
242B VAL* 1.3 73.6 - - - +
244B SER* 1.3 62.2 + - - +
278B THR* 3.0 16.9 + - - +
279B GLY* 3.6 23.1 - - - -
280B GLN* 2.6 39.2 + - - +
286B THR* 3.1 22.1 + - + -
47D ARG* 3.3 27.6 - - - +
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Residues in contact with SER 244 (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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221B VAL* 3.7 5.6 - - - -
242B VAL* 3.5 5.3 - - - +
243B TRP* 1.3 82.0 - - - +
245B SER* 1.3 65.3 - - - +
277B VAL* 2.8 36.3 + - - +
278B THR* 2.6 34.5 + - - +
51D GLU* 6.0 1.0 - - - +
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Residues in contact with SER 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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218B HIS* 2.9 38.8 + - - -
221B VAL* 3.4 30.6 - - - +
242B VAL* 4.2 4.3 - - - -
244B SER* 1.3 76.4 - - - +
246B ARG* 1.3 65.5 + - - +
274B LEU* 3.7 13.9 - - - -
275B GLU 3.1 16.8 - - - -
277B VAL* 3.9 6.3 - - - +
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Residues in contact with ARG 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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218B HIS* 3.6 5.6 + - - -
245B SER* 1.3 81.0 + - - +
247B VAL* 1.3 65.0 + - - +
248B HIS* 3.5 28.2 + - + +
274B LEU* 3.7 3.6 - - - -
275B GLU* 2.9 67.2 + - + +
277B VAL* 3.8 21.4 - - + +
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Residues in contact with VAL 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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214B ALA* 4.4 9.9 - - + +
215B SER* 4.2 18.8 - - - +
218B HIS* 3.5 40.4 + - + -
246B ARG* 1.3 74.7 - - - +
248B HIS* 1.3 70.2 + - - +
249B PRO* 4.0 21.3 - - + +
272B GLY* 6.1 0.4 - - - -
273B ALA 4.1 11.9 - - - +
274B LEU* 4.3 2.5 - - + -
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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