Contacts of the strand formed by residues 289 - 295 (chain C) in PDB entry 4IXU
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 LEU 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C SER* 3.4 15.1 + - - -
246C ILE* 3.7 11.9 - - + +
248C LEU* 3.9 14.6 - - + +
283C ILE* 3.8 28.0 + - + +
284C HIS* 5.4 1.6 - - - -
286C THR* 4.0 3.6 + - - -
287C GLY 3.7 2.1 - - - +
288C LEU* 1.3 76.4 - - - +
290C SER* 1.3 59.8 + - - +
291C ALA 3.4 28.0 - - - +
292C LEU* 4.2 4.9 - - + -
322C SER* 3.5 34.8 - - - +
323C PHE* 3.6 34.6 - - + -
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Residues in contact with SER 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 4.6 7.3 - - - +
111C TYR 4.0 2.9 + - - +
112C SER* 3.2 11.2 - - - +
113C CYS* 2.9 21.4 + - - +
130C HIS* 2.8 32.1 + - - -
134C CYS* 4.3 6.1 - - - -
245C PRO* 3.7 20.1 - - - +
246C ILE 2.9 8.0 + - - -
288C LEU 3.2 1.5 + - - -
289C LEU* 1.3 74.8 - - - +
291C ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C VAL* 5.5 1.8 - - + -
113C CYS* 3.1 24.0 - - + +
126C THR* 6.0 0.7 - - - -
130C HIS* 3.4 28.7 - - + +
246C ILE 3.3 2.8 + - - -
247C HIS* 3.4 17.3 - - + +
248C LEU 2.9 23.6 + - - -
289C LEU* 3.4 8.5 - - - +
290C SER* 1.3 79.7 - - - +
292C LEU* 1.3 60.9 + - - +
293C ASP* 5.6 0.2 - - - +
323C PHE* 6.1 1.3 - - - -
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C CYS 2.8 11.0 + - - +
114C VAL* 3.3 17.8 - - + -
115C THR 2.8 32.1 + - - -
248C LEU* 3.1 23.1 - - + +
250C PHE* 5.5 0.4 - - + -
289C LEU* 4.2 13.2 - - + -
291C ALA* 1.3 75.8 - - - +
293C ASP* 1.3 77.4 + - - +
294C LEU* 4.0 6.7 - - + +
318C VAL* 5.3 2.0 - - + -
319C ILE* 3.9 29.2 - - + -
322C SER* 3.5 36.1 - - - +
323C PHE* 4.2 8.0 - - + -
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C CYS 5.5 0.2 - - - +
115C THR* 3.4 7.2 - - - +
122C LEU* 4.3 7.4 - - + -
123C ALA* 4.0 5.0 - - - +
126C THR* 2.8 36.9 + - - +
247C HIS* 2.7 24.7 + - - -
248C LEU 2.8 7.6 + - - +
249C SER* 2.8 25.4 + - - +
250C PHE* 2.9 30.0 + - - +
292C LEU* 1.3 80.5 + - - +
294C LEU* 1.3 59.5 + - - +
295C VAL* 3.9 17.3 - - + -
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 4.0 5.4 - - + +
115C THR 2.9 11.5 + - - +
116C LEU* 3.8 5.4 - - + -
117C GLY* 3.0 22.2 + - - +
250C PHE* 3.4 30.1 - - + +
252C ILE* 4.3 7.6 - - + -
292C LEU* 4.0 4.0 - - + +
293C ASP* 1.3 72.1 - - - +
295C VAL* 1.3 64.7 + - - +
297C VAL* 3.9 17.4 - - + +
315C ALA* 3.6 32.8 - - + +
318C VAL* 4.0 24.5 - - + -
319C ILE* 4.0 25.6 - - + -
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLY* 4.3 1.6 - - - +
118C GLY 3.5 9.0 - - - +
120C HIS* 3.4 42.6 - - + +
122C LEU* 3.9 39.0 - - + -
250C PHE 3.0 6.1 + - - +
251C ASP* 3.7 13.7 - - - -
252C ILE* 3.1 27.9 + - - +
293C ASP* 4.0 13.0 - - + -
294C LEU* 1.3 81.3 - - - +
296C GLU* 1.3 70.9 + - + +
297C VAL 3.3 4.5 + - - -
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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