Contacts of the helix formed by residues 289 - 295 (chain A) in PDB entry 2RIO
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 THR 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ILE* 3.9 4.3 - - - -
287A ARG 5.4 0.2 - - - +
288A PRO* 1.3 74.8 - - - +
290A ALA* 1.3 65.0 + - - +
291A MET* 3.1 8.5 + - - +
292A LYS* 3.1 45.2 + - - +
293A VAL* 2.9 22.0 + - - +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA* 4.7 3.4 - - - +
128A VAL* 4.5 2.2 - - + -
129A ALA* 3.5 36.7 - - + +
132A HIS* 4.0 22.8 - - + -
222A ILE* 3.5 17.3 - - + +
225A MET* 6.2 1.1 - - - -
289A THR* 1.3 73.4 - - - +
291A MET* 1.3 61.3 + - + +
293A VAL* 3.4 7.4 + - - +
294A LEU* 3.3 26.5 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 4.0 19.3 - - + +
133A SER* 5.6 3.4 - - - +
289A THR* 3.0 8.1 + - - +
290A ALA* 1.3 76.7 - - + +
292A LYS* 1.3 65.2 + - - +
294A LEU* 3.4 12.4 + - - +
295A ARG* 3.3 59.1 + - - +
157B ASP* 5.0 2.0 - - - +
158B GLN* 5.1 2.7 - - + +
159B GLN* 3.6 45.5 - - + +
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 5.1 0.9 - - - +
285A LEU 5.6 2.2 + - - -
286A LYS 6.0 0.4 - - - -
287A ARG 3.7 7.3 + - - -
288A PRO* 3.6 21.5 - - + +
289A THR* 3.1 54.8 + - - +
291A MET* 1.3 75.6 - - - +
293A VAL* 1.3 67.0 + - - +
295A ARG* 3.3 24.6 + - - +
296A HIS* 3.4 11.8 + - - +
419A LYS* 6.3 2.2 - - - +
433A TYR* 6.1 5.6 - - + -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA* 3.7 24.7 - - + -
222A ILE* 4.5 10.8 - - + -
225A MET* 5.1 4.0 - - - -
229A PHE* 3.9 22.4 - - + -
275A LEU* 4.2 11.9 - - + -
279A MET* 4.1 15.5 - - + -
288A PRO* 4.1 18.6 - - + +
289A THR 2.9 21.6 + - - +
290A ALA* 3.4 11.4 - - - +
291A MET 3.4 0.2 - - - -
292A LYS* 1.3 74.7 - - - +
294A LEU* 1.3 62.6 + - - +
296A HIS* 3.1 19.6 + - - +
299A PHE* 3.3 16.8 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 4.0 26.9 - - + +
125A ALA* 3.8 24.7 - - + +
126A SER* 4.2 4.9 - - - +
129A ALA* 3.6 25.8 - - + -
290A ALA 3.3 9.5 + - - +
291A MET* 3.6 15.7 - - - +
292A LYS 3.3 0.4 - - - -
293A VAL* 1.3 78.2 - - - +
295A ARG* 1.3 61.8 + - + +
296A HIS 3.6 0.5 + - - -
299A PHE* 3.8 22.7 - - + +
300A TRP* 5.4 1.4 - - - -
159B GLN* 3.5 33.0 - - + +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A MET* 3.3 47.9 + - - +
292A LYS* 3.9 16.7 - - - +
293A VAL 3.1 1.2 - - - -
294A LEU* 1.3 76.7 - - + +
296A HIS* 1.3 65.3 + - - +
297A PRO* 3.6 2.1 - - - +
300A TRP* 3.1 22.2 + - - +
415A TYR* 4.5 5.4 + - - +
431A PHE 4.9 0.8 - - - +
432A LEU 3.8 23.0 - - - +
433A TYR* 3.6 38.4 + - - +
434A SER 3.6 20.9 - - - +
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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