Contacts of the strand formed by residues 238 - 247 (chain B) in PDB entry 5IZL
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 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B SER* 3.1 5.4 - - - -
234B ILE* 2.6 40.5 + - - +
235B LYS 4.9 0.2 + - - -
236B GLY 3.6 1.0 - - - -
237B GLN* 1.3 81.8 - - - +
239B THR* 1.3 60.5 + - - -
289B CYS* 4.7 1.8 - - - -
290B VAL 3.7 6.3 - - - -
292B GLN* 3.9 22.8 - - - +
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Residues in contact with THR 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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231B CYS* 3.6 9.6 - - - -
232B PHE* 3.3 19.1 - - - +
233B SER* 4.0 1.6 - - - +
238B GLY* 1.3 73.1 + - - -
240B VAL* 1.3 62.1 + - - +
288B ILE 3.8 0.2 - - - +
289B CYS* 3.5 1.5 - - - -
290B VAL* 3.1 37.8 + - - +
292B GLN* 3.2 4.8 - - - +
293B PHE* 2.9 79.9 + - + +
295B PRO* 4.8 2.0 - - + -
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS 3.7 0.9 - - - +
231B CYS* 3.2 6.4 - - - -
232B PHE* 2.6 60.8 + - + -
234B ILE* 3.5 33.9 - - + -
237B GLN* 5.2 0.2 - - - +
239B THR* 1.3 77.2 - - - +
241B MET* 1.3 66.5 + - - +
242B THR* 4.1 14.8 - - + -
287B GLY* 4.7 2.7 - - - -
288B ILE 3.3 11.7 - - - +
289B CYS* 4.1 19.1 - - + -
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Residues in contact with MET 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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226B MET* 3.7 9.5 - - + +
228B VAL* 4.1 18.8 - - + -
230B HIS 3.3 5.4 - - - +
231B CYS* 3.8 19.3 - - + -
239B THR 5.1 0.7 - - - +
240B VAL* 1.3 74.6 - - - +
242B THR* 1.3 63.4 + - - +
256B VAL* 4.7 12.6 - - + -
258B ILE* 4.0 25.6 - - + -
287B GLY* 3.3 0.5 - - - -
288B ILE* 2.8 56.0 + - + +
290B VAL* 4.3 19.3 - - + -
293B PHE* 4.4 10.1 - - + -
298B LEU* 5.1 4.0 - - - -
303B VAL* 4.1 24.5 - - + -
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Residues in contact with THR 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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226B MET* 3.8 2.5 - - - -
228B VAL* 3.7 1.6 - - - -
229B ASP* 2.5 52.9 + - - +
230B HIS* 3.0 22.8 + - - +
232B PHE* 4.6 13.5 - - + -
240B VAL* 4.1 13.7 - - + -
241B MET* 1.3 76.8 - - - +
243B GLY* 1.3 55.9 + - - +
285B ARG* 4.5 9.6 + - - -
286B LEU 3.2 14.1 - - - +
287B GLY* 4.0 8.5 - - - -
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Residues in contact with GLY 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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226B MET* 3.3 15.3 - - - +
227B SER 3.0 14.1 - - - -
229B ASP* 4.1 9.6 - - - -
242B THR* 1.3 74.9 - - - +
244B THR* 1.3 63.5 + - - -
245B ILE 4.2 0.2 + - - -
284B ASP 4.1 0.5 - - - +
285B ARG* 3.5 7.8 - - - +
286B LEU* 3.1 32.7 + - - +
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Residues in contact with THR 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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9B ASN* 3.2 34.2 + - - +
53B PHE* 4.8 5.5 - - - -
109B ILE* 4.8 19.3 - - + +
226B MET* 4.4 1.3 - - - -
227B SER* 2.8 37.0 + - - -
243B GLY* 1.3 74.9 - - - -
245B ILE* 1.3 73.2 + - - +
246B LEU* 3.4 6.8 + - + +
283B GLY* 4.2 8.5 - - - +
284B ASP 3.5 12.3 - - - +
285B ARG* 3.8 11.8 + - - +
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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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224B PHE* 3.8 24.2 - - + -
225B LEU 3.4 16.2 - - - +
226B MET* 4.2 6.7 - - + +
244B THR* 1.3 75.9 - - - +
246B LEU* 1.3 59.3 + - - +
247B SER 3.6 14.8 - - - +
248B GLY 3.9 12.8 - - - +
250B ILE* 4.3 1.6 - - + +
280B ALA* 3.4 33.7 - - + -
281B MET 3.5 18.2 - - - +
282B GLN* 3.9 5.4 - - - +
283B GLY* 3.1 22.2 + - - -
284B ASP 3.0 12.4 + - - +
286B LEU* 3.6 17.0 - - + -
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Residues in contact with LEU 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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108B GLN* 3.8 23.8 - - + +
109B ILE* 4.2 17.5 - - + -
225B LEU* 3.0 36.2 + - + +
227B SER* 4.0 18.6 - - - +
244B THR* 4.0 14.6 - - + +
245B ILE* 1.3 77.0 - - - +
247B SER* 1.3 62.8 + - - +
282B GLN* 3.7 17.0 + - - +
302B LEU* 4.3 8.1 - - + -
341B HIS* 4.5 6.5 - - + +
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Residues in contact with SER 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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221B SER 5.1 4.0 - - - -
222B GLY* 6.0 0.2 - - - -
223B PRO* 2.8 23.0 + - - +
224B PHE* 3.4 0.3 - - - -
225B LEU* 2.9 39.8 + - - +
245B ILE* 3.5 5.3 - - - +
246B LEU* 1.3 82.1 - - - +
248B GLY* 1.3 65.5 + - - +
282B GLN* 4.1 11.2 - - - -
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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