Contacts of the strand formed by residues 224 - 232 (chain Y) in PDB entry 1IRA
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 ILE 224 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Y MET* 4.4 6.1 - - - -
218Y VAL* 3.8 39.7 - - + -
222Y SER* 4.7 2.2 - - - +
223Y GLN* 1.3 83.0 - - - +
225Y GLN* 1.3 66.8 + - - +
226Y LEU* 4.0 13.0 - - + -
276Y LEU 3.8 0.3 - - - +
277Y ASN 3.9 0.2 - - - -
278Y ILE* 3.0 46.5 + - + +
281Y ILE* 3.7 26.9 - - + -
307Y LEU* 3.9 15.3 - - + -
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Residues in contact with GLN 225 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Y MET* 5.3 3.5 - - - +
223Y GLN* 6.1 2.2 - - + +
224Y ILE* 1.3 79.6 - - - +
226Y LEU* 1.3 68.2 + - - +
227Y ILE* 3.7 15.3 + - + +
275Y VAL* 3.9 17.4 - - + +
276Y LEU 3.3 3.8 - - - -
277Y ASN* 2.8 29.3 + - + +
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Residues in contact with LEU 226 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216Y MET* 4.0 25.1 - - + -
224Y ILE* 4.0 10.8 - - + -
225Y GLN* 1.3 75.9 - - - +
227Y ILE* 1.3 61.7 + - - +
240Y TRP* 3.5 21.2 + - + -
275Y VAL* 3.5 1.3 - - - -
276Y LEU* 2.8 44.6 + - + +
278Y ILE* 4.3 15.3 - - + -
290Y PHE* 3.6 46.2 - - + -
305Y ILE* 3.8 30.5 - - + -
307Y LEU* 4.8 1.6 - - + -
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Residues in contact with ILE 227 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y SER* 3.8 14.4 + - - +
211Y PRO* 3.9 8.7 - - - +
225Y GLN* 3.7 16.0 + - + +
226Y LEU* 1.3 75.4 - - - +
228Y CYS* 1.3 66.1 + - - +
229Y ASN 4.0 0.6 + - - +
240Y TRP* 4.0 1.6 - - - -
259Y TYR* 5.5 2.0 - - - +
273Y ILE* 3.8 17.7 - - + -
274Y THR 3.9 2.7 - - - -
275Y VAL* 3.8 22.7 - - + +
305Y ILE* 5.3 4.0 - - - +
403Y NAG 3.6 39.7 - - + +
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Residues in contact with CYS 228 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Y ILE* 4.1 6.1 - - - -
210Y SER 3.3 12.8 - - - -
211Y PRO* 4.1 1.3 - - - -
227Y ILE* 1.3 74.3 - - - +
229Y ASN* 1.3 59.0 + - - +
230Y VAL* 3.9 15.9 - - - -
240Y TRP* 3.8 11.0 - - + +
272Y LEU 3.5 1.6 - - - +
273Y ILE* 3.3 10.4 - - - +
274Y THR* 3.0 42.2 + - - +
292Y CYS* 2.0 50.0 - - - -
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Residues in contact with ASN 229 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Y ILE* 3.7 1.0 - - - -
209Y VAL* 2.9 40.0 + - + +
210Y SER* 2.7 20.6 + - - +
227Y ILE* 4.0 0.6 + - + -
228Y CYS* 1.3 71.0 - - - +
230Y VAL* 1.3 63.8 + - - +
271Y THR* 3.9 18.9 - - - +
272Y LEU 3.9 1.3 - - - -
273Y ILE* 4.1 5.8 - - - +
403Y NAG 1.5 82.8 + - - +
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Residues in contact with VAL 230 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206Y PRO* 4.0 6.1 - - + -
207Y VAL 3.3 14.6 - - - +
208Y ILE* 3.9 13.2 - - + -
228Y CYS* 3.9 22.2 - - - +
229Y ASN* 1.3 77.8 + - - +
231Y THR* 1.3 73.9 - - - +
232Y GLY 4.1 0.7 - - - +
238Y ALA* 4.0 19.5 - - + -
270Y SER 3.5 0.5 - - - +
271Y THR* 3.2 7.4 - - - -
272Y LEU* 2.8 55.3 + - + +
292Y CYS* 4.6 0.2 - - - -
294Y ALA* 3.9 21.1 - - + -
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Residues in contact with THR 231 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Y THR* 5.6 0.7 - - - +
205Y ARG 4.4 1.6 - - - +
206Y PRO* 3.6 4.0 - - - +
207Y VAL* 2.8 45.4 + - - +
209Y VAL* 4.5 14.0 - - - +
230Y VAL* 1.3 76.0 + - - +
232Y GLY* 1.3 61.2 + - - +
269Y ARG* 3.6 49.1 + - + +
270Y SER 3.2 7.6 - - - +
271Y THR* 4.8 7.9 - - + +
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Residues in contact with GLY 232 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204Y THR* 5.1 5.6 - - - -
206Y PRO* 4.9 1.8 - - - -
230Y VAL* 4.1 1.3 + - - +
231Y THR* 1.3 77.4 - - - +
233Y GLN* 1.3 68.7 + - - -
236Y ASP* 3.5 9.9 - - - -
267Y LYS 3.9 0.2 - - - +
268Y ARG 3.3 17.4 - - - +
270Y SER* 2.8 34.2 + - - +
272Y LEU* 4.7 3.4 - - - +
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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