Contacts of the strand formed by residues 225 - 232 (chain I) in PDB entry 3IXS
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 225 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224I SER* 1.3 77.7 - - - +
226I ILE* 1.3 59.9 + - - +
227I GLU* 4.4 3.1 + - + +
249I LYS* 3.9 30.3 + - + +
250I THR 3.4 11.9 - - - +
251I SER* 4.9 5.2 - - - -
147J ARG* 5.3 5.4 + - - +
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Residues in contact with ILE 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224I SER 4.1 0.2 + - - -
225I GLU* 1.3 75.4 - - - +
227I GLU* 1.3 76.1 + - - +
228I LEU* 4.9 3.8 - - + +
248I ILE 3.9 0.5 - - - +
249I LYS* 3.4 2.5 - - - -
250I THR* 2.8 43.8 + - + +
251I SER 4.1 9.4 - - - +
252I GLY* 4.5 4.5 - - - -
311I LEU* 3.9 42.4 - - + +
312I GLU* 5.4 5.2 - - - +
315I SER* 4.0 15.0 - - - +
325I MET* 3.6 34.1 - - + +
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Residues in contact with GLU 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I GLU* 4.4 2.4 + - + +
226I ILE* 1.3 84.3 - - - +
228I LEU* 1.3 62.2 + - - +
248I ILE 3.2 4.5 - - - +
249I LYS* 3.5 21.6 - - + +
324I PRO* 3.5 8.8 - - + +
325I MET 3.2 18.7 + - - -
147J ARG* 3.0 28.9 + - - +
148J LEU* 2.6 51.3 + - + +
153J ARG* 2.9 34.5 + - - -
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Residues in contact with LEU 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226I ILE* 4.9 5.6 - - + +
227I GLU* 1.3 76.7 - - - +
229I VAL* 1.3 66.4 + - - +
230I PHE* 3.7 33.0 - - + -
246I ARG 3.9 0.2 - - - +
247I TYR* 3.8 0.3 - - - -
248I ILE* 2.8 56.8 + - + -
250I THR* 5.2 0.7 - - + -
259I LEU* 4.3 6.1 - - + -
311I LEU* 4.0 27.4 - - + -
324I PRO 4.6 0.2 - - - -
325I MET* 3.1 31.2 - - + +
327I LEU* 4.2 20.6 - - + -
148J LEU* 3.8 7.5 - - - +
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Residues in contact with VAL 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228I LEU* 1.3 75.9 - - - +
230I PHE* 1.3 61.4 + - - +
231I ARG* 3.9 27.5 - - - +
245I THR* 4.1 9.0 - - - +
246I ARG 3.7 1.8 - - - -
247I TYR* 3.6 29.6 - - + +
324I PRO* 4.4 7.9 - - + -
325I MET 2.8 12.9 + - - +
326I GLU* 3.5 19.4 - - + +
327I LEU 2.9 27.5 + - - +
148J LEU* 3.7 18.8 - - + -
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Residues in contact with PHE 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228I LEU* 3.7 12.3 - - + -
229I VAL* 1.3 72.8 - - - +
231I ARG* 1.3 61.9 + - - +
245I THR* 3.4 2.8 - - - -
246I ARG* 2.8 48.7 + - + +
248I ILE* 3.5 24.5 - - + -
259I LEU* 4.1 23.6 - - + -
262I TYR* 4.3 3.1 - + - -
263I LEU* 3.5 45.5 - - + -
293I ILE* 3.8 18.4 - - + -
327I LEU* 3.7 25.4 - - + -
328I TYR 3.9 20.9 - - - -
329I TYR* 3.9 10.6 - + + -
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Residues in contact with ARG 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229I VAL* 4.0 25.0 + - + +
230I PHE* 1.3 77.7 - - - +
232I PRO* 1.3 69.3 - - + +
245I THR* 4.1 16.4 + - - +
326I GLU* 3.2 44.7 + - - +
327I LEU 2.9 8.7 + - - +
328I TYR* 3.0 41.6 + - + -
329I TYR* 2.9 28.4 + - - -
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Residues in contact with PRO 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231I ARG* 1.3 90.3 - - + +
233I HIS* 1.3 66.1 + - - +
234I PRO* 3.1 8.1 - - - +
237I MET* 3.6 27.1 - - + +
238I GLU 6.5 0.2 - - - -
243I ALA* 4.0 16.8 - - + +
244I GLN 3.8 20.9 - - - +
245I THR* 4.1 6.1 - - - +
328I TYR* 3.9 2.9 - - - -
329I TYR* 3.6 25.1 - - + +
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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