Contacts of the strand formed by residues 226 - 235 (chain B) in PDB entry 5JSJ
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 SER 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ALA* 3.3 6.1 - - - -
222B LYS* 2.7 49.6 + - - +
223B GLU 4.9 3.1 - - - -
224B ASP 3.2 5.7 + - - -
225B GLY* 1.3 80.6 - - - +
227B LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 227 (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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219B GLU* 5.6 9.9 - - + +
220B TYR 3.3 10.1 - - - +
221B ALA* 4.7 7.2 - - + -
222B LYS* 5.4 0.4 - - - -
225B GLY 3.6 18.9 + - - +
226B SER* 1.3 84.9 + - - +
228B ARG* 1.3 65.8 + - - +
229B THR* 5.4 1.0 + - + -
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Residues in contact with ARG 228 (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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219B GLU* 3.3 7.1 - - - +
220B TYR* 2.8 44.2 + - - +
221B ALA 6.0 0.4 - - - -
222B LYS* 4.5 33.3 - - + +
226B SER 4.4 0.2 + - - -
227B LYS* 1.3 77.1 - - - +
229B THR* 1.3 64.4 + - - +
247B PHE* 3.3 54.6 - - + -
248B ASP 5.6 4.0 - - - +
250B ASP* 4.5 4.7 + - - -
254B TYR* 3.5 25.8 + - - -
256B TYR* 3.3 18.8 + - - -
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Residues in contact with THR 229 (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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217B GLN* 5.4 7.4 - - + +
218B VAL 3.6 3.6 - - - +
219B GLU* 3.3 37.5 - - + +
227B LYS* 5.4 0.6 + - + -
228B ARG* 1.3 76.2 - - - +
230B GLY* 1.3 58.7 + - - +
247B PHE* 3.1 14.4 - - - +
248B ASP* 2.8 42.0 + - - +
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Residues in contact with GLY 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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217B GLN* 3.3 10.0 - - - +
218B VAL 3.0 33.7 + - - +
229B THR* 1.3 77.0 - - - +
231B MET* 1.3 60.9 + - - -
245B ILE* 4.5 4.5 - - - -
246B LYS 2.9 15.0 - - - -
247B PHE* 3.7 9.8 - - - -
248B ASP* 4.8 3.1 - - - -
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Residues in contact with MET 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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82B VAL* 4.2 22.4 - - - +
83B ASN* 3.7 35.4 - - + +
86B LEU* 5.6 1.6 - - + -
215B GLY 4.2 9.2 - - - +
216B LYS 3.7 10.1 - - - +
217B GLN* 4.5 5.8 - - + +
230B GLY* 1.3 75.6 - - - -
232B VAL* 1.3 75.1 + - - +
233B ILE* 3.6 15.5 + - + +
245B ILE* 3.3 7.0 - - - +
246B LYS* 2.9 37.1 + - + +
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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
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82B VAL* 4.5 1.0 - - - +
213B LEU* 3.6 16.4 - - + +
214B VAL* 3.5 14.5 - - + +
215B GLY* 2.8 28.4 + - - -
216B LYS* 3.0 13.7 + - + +
218B VAL* 3.5 31.0 - - + -
231B MET* 1.3 74.3 - - - +
233B ILE* 1.3 60.1 + - - +
234B HIS 4.5 0.2 - - - +
243B TYR* 3.5 43.5 - - + -
244B PHE 3.6 3.4 - - - +
245B ILE* 4.3 4.7 - - + -
258B LEU* 3.8 13.9 - - + -
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Residues in contact with ILE 233 (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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80B VAL* 3.6 46.4 - - + +
81B PRO* 4.5 5.5 - - - +
82B VAL* 3.8 5.7 - - + +
86B LEU* 4.2 8.5 - - + -
88B LEU* 4.7 4.5 - - + -
214B VAL* 3.7 12.5 - - - +
231B MET* 4.0 32.8 - - + +
232B VAL* 1.3 77.0 - - - +
234B HIS* 1.3 67.6 + - + +
244B PHE* 3.1 30.6 + - + +
245B ILE* 4.3 1.8 - - - +
246B LYS* 4.3 13.9 - - + +
253B ILE* 4.1 27.1 - - + -
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Residues in contact with HIS 234 (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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78B ASP* 6.0 1.8 - - - -
81B PRO* 6.0 5.6 - - + -
167B TYR* 6.1 2.5 - + - -
214B VAL* 3.7 9.5 - - - +
232B VAL 3.7 1.6 - - - -
233B ILE* 1.3 86.2 - - + +
235B GLN* 1.3 84.3 + - - +
236B VAL* 4.1 7.7 + - + -
237B GLU* 4.7 15.3 + - + +
243B TYR* 3.1 8.1 - - - +
244B PHE* 2.8 68.6 + + + -
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Residues in contact with GLN 235 (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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211B ASP* 3.3 19.7 + - - +
212B SER* 3.7 13.6 + - - +
214B VAL* 3.6 10.0 - - + +
234B HIS* 1.3 92.4 + - - +
236B VAL* 1.3 66.4 + - - +
237B GLU* 3.1 9.9 + - - +
240B PRO* 3.1 38.2 - - + +
243B TYR* 2.9 39.9 + - + -
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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