Contacts of the strand formed by residues 292 - 302 (chain C) in PDB entry 4IRQ
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 TYR 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C VAL* 3.6 46.9 - - + -
150C LEU* 3.6 33.8 - - + +
151C GLU* 2.3 39.8 + - + +
290C VAL* 3.8 17.7 - - + -
291C LYS* 1.3 76.5 - - - +
293C HIS* 1.3 83.9 + - - +
294C VAL* 3.9 7.9 - - + -
312C ILE* 4.3 3.1 - - + -
313C MET 3.3 13.2 - - - +
314C LEU* 3.9 7.6 - - + -
315C ASP* 4.4 2.0 - - - +
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Residues in contact with HIS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C TYR* 1.3 83.1 - - - +
294C VAL* 1.3 88.3 + - - +
295C ALA* 3.5 12.7 + - + -
312C ILE* 3.7 2.4 - - - -
313C MET* 2.9 67.3 + - + +
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Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 3.7 35.2 - - + +
292C TYR* 3.9 12.1 - - + -
293C HIS* 1.3 84.1 + - - +
295C ALA* 1.3 63.6 + - - +
296C SER* 3.3 27.7 + - - +
297C ARG* 4.0 22.2 - - + +
310C LEU* 4.7 6.7 - - + -
311C ASN 3.5 7.0 - - - +
312C ILE* 4.7 10.3 - - + -
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Residues in contact with ALA 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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134C VAL* 4.6 3.6 - - + -
293C HIS* 3.5 15.2 + - + -
294C VAL* 1.3 72.8 - - - +
296C SER* 1.3 62.5 + - - +
311C ASN* 3.0 21.5 + - + +
313C MET* 3.6 28.3 - - + -
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Residues in contact with SER 296 (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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294C VAL* 3.2 12.6 - - - +
295C ALA* 1.3 81.0 - - - +
297C ARG* 1.3 66.5 + - - +
298C THR* 4.7 6.3 - - - +
309C VAL 4.5 0.2 - - - -
310C LEU* 3.7 0.3 - - - -
311C ASN* 3.0 55.5 + - - +
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Residues in contact with ARG 297 (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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129C TYR* 5.5 3.0 - - - -
151C GLU* 2.2 55.6 + - - +
294C VAL* 4.0 14.9 - - + +
296C SER* 1.3 78.5 - - - +
298C THR* 1.3 64.5 + - - +
308C THR* 5.0 8.8 - - + +
309C VAL 3.3 5.6 - - - +
310C LEU* 3.4 32.1 - - + +
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Residues in contact with THR 298 (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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296C SER* 4.7 10.8 - - - +
297C ARG* 1.3 79.0 - - - +
299C ALA* 1.3 69.5 + - - +
300C LEU* 3.5 8.5 + - - +
308C THR* 3.8 4.3 - - - +
309C VAL* 2.9 54.4 + - + +
311C ASN* 5.0 3.4 - - - +
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Residues in contact with ALA 299 (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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298C THR* 1.3 79.0 + - - +
300C LEU* 1.3 61.7 + - - +
301C SER 4.4 0.2 + - - -
307C CYS 3.9 6.7 - - - +
308C THR* 5.0 3.1 - - - +
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Residues in contact with LEU 300 (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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105C PHE* 6.0 4.3 - - + -
108C LEU* 4.2 21.5 - - + -
109C LEU* 6.5 0.2 - - + -
298C THR* 3.5 7.7 + - - +
299C ALA* 1.3 79.2 - - - +
301C SER* 1.3 66.0 + - - +
302C VAL* 4.2 14.1 - - + -
306C PRO* 3.4 3.1 - - - +
307C CYS* 2.8 52.4 + - - +
309C VAL* 3.8 27.8 - - + -
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Residues in contact with SER 301 (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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300C LEU* 1.3 81.1 - - - +
302C VAL* 1.3 62.4 + - - +
303C GLY 3.9 2.4 + - - -
304C GLY* 3.5 30.7 + - - -
305C ALA 3.4 4.7 + - - -
306C PRO* 4.4 3.4 - - - +
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Residues in contact with VAL 302 (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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108C LEU* 4.8 3.4 - - + +
109C LEU* 3.3 54.3 - - + +
112C VAL* 4.1 23.6 - - + -
113C PRO* 3.4 20.4 - - + +
300C LEU* 4.5 20.4 - - + -
301C SER* 1.3 75.7 - - - +
303C GLY* 1.3 67.1 + - - +
305C ALA* 2.8 21.0 + - - +
307C CYS* 5.1 1.3 - - - -
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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