Contacts of the strand formed by residues 227 - 234 (chain B) in PDB entry 1IAS
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 GLU 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B THR* 3.3 19.8 - - - +
177B LEU* 2.4 42.6 + - + +
178B LYS* 3.0 49.2 + - - +
223B LYS* 3.1 2.5 - - - -
224B TRP* 2.8 42.0 + - - +
225B ARG* 3.2 8.2 + - - +
226B GLY* 1.3 73.8 - - - +
228B GLU* 1.3 63.8 + - - +
229B VAL* 4.5 0.3 - - - +
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Residues in contact with GLU 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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11B SO4 4.8 2.2 + - - -
177B LEU* 3.8 10.4 - - - +
221B ARG* 2.6 35.0 + - + +
222B GLY 3.4 5.4 - - - +
223B LYS* 4.1 20.4 - - + -
226B GLY 4.8 0.7 - - - +
227B GLU* 1.3 73.3 - - - +
229B VAL* 1.3 68.5 + - - +
281B ASP* 5.6 0.2 - - - -
282B TYR* 3.4 41.9 + - + +
284B GLU* 5.4 2.9 - - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.8 12.8 - - + -
201B ILE* 6.3 0.4 - - + -
205B ILE* 4.0 18.6 - - + -
221B ARG* 3.6 3.3 - - - -
222B GLY 2.7 45.9 + - - +
223B LYS* 4.6 1.6 - - - +
224B TRP* 4.9 4.5 - - + +
227B GLU 4.5 1.8 - - - +
228B GLU* 1.3 79.4 - - - +
230B ALA* 1.3 55.0 + - - +
231B VAL* 4.1 5.6 - - + -
263B ILE* 3.5 22.9 - - + -
279B VAL* 3.6 20.9 - - + -
280B SER 2.9 21.5 - - - +
281B ASP* 4.6 1.1 - - - -
282B TYR* 3.5 12.6 - - - +
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Residues in contact with ALA 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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211B ILE* 5.4 1.3 - - + -
219B VAL* 4.6 12.6 - - + -
220B TRP 3.4 8.1 - - - +
229B VAL* 1.3 73.3 - - - +
231B VAL* 1.3 61.7 + - - +
232B LYS 4.2 0.6 + - - -
260B LEU* 6.1 0.4 - - + -
278B LEU 3.9 0.2 - - - +
279B VAL* 3.4 6.2 - - - +
280B SER* 2.9 40.4 + - - +
281B ASP 3.5 17.9 - - - +
282B TYR* 3.8 13.3 - - + +
283B HIS 5.6 0.2 - - - +
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Residues in contact with VAL 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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205B ILE* 3.9 29.2 - - + -
207B LEU* 4.1 20.0 - - + -
219B VAL* 3.4 2.9 - - - -
220B TRP* 2.7 45.5 + - + +
222B GLY 4.8 2.0 - - - +
229B VAL* 4.1 8.7 - - + +
230B ALA* 1.3 79.4 - - - +
232B LYS* 1.3 60.7 + - - +
233B ILE* 3.6 16.3 + - + -
277B TRP* 3.5 35.9 - - + -
278B LEU 3.4 9.0 - - - +
279B VAL* 4.4 1.6 - - + -
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Residues in contact with LYS 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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216B PHE* 3.6 40.2 - - + +
218B GLU 3.4 5.2 - - - +
219B VAL* 4.3 12.3 - - + +
230B ALA 4.2 0.6 - - - -
231B VAL* 1.3 70.7 - - - +
233B ILE* 1.3 61.1 + - - +
234B PHE* 3.2 38.7 - - + -
245B GLU* 2.8 31.4 + - - +
277B TRP* 3.6 1.7 - - - -
278B LEU* 2.9 37.7 + - + +
351B ASP* 3.8 25.8 + - - +
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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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207B LEU* 3.7 31.2 - - + -
217B GLY* 3.6 2.6 - - - -
218B GLU* 2.8 33.9 + - + +
220B TRP* 3.8 26.0 - - + +
231B VAL* 3.8 13.5 - - + -
232B LYS* 1.3 75.0 - - - +
234B PHE* 1.3 71.7 + - - +
275B GLN* 5.9 3.4 - - + -
276B LEU 3.7 3.4 - - - +
277B TRP* 3.6 34.8 - - + +
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Residues in contact with PHE 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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216B PHE* 3.6 32.3 - - + +
217B GLY* 4.5 0.2 - - - -
232B LYS* 3.2 42.4 - - + -
233B ILE* 1.3 84.4 - - - +
235B SER* 1.3 69.5 + - - +
236B SER 3.8 1.2 + - - -
238B GLU 3.9 9.4 - - - +
241B SER* 3.7 9.2 - - - -
242B TRP* 3.4 46.2 - + + -
245B GLU* 4.1 7.0 - - - -
274B THR 5.2 1.4 - - - +
275B GLN* 5.3 1.0 - - - -
276B LEU* 2.9 37.8 + - + +
278B LEU* 3.6 24.9 - - + -
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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