Contacts of the helix formed by residues 302 - 312 (chain A) in PDB entry 1O94
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 ASP 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLN* 2.8 24.1 + - - +
301A THR* 1.3 79.2 + - - +
303A PRO* 1.3 71.9 - - - +
304A GLU* 2.9 38.1 + - - +
305A LYS* 3.0 16.4 + - + +
306A MET* 3.1 14.9 + - - +
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Residues in contact with PRO 303 (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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6A HIS* 3.6 35.7 - - + +
9A LEU* 4.1 5.4 - - + -
301A THR 3.7 7.6 - - - +
302A ASP* 1.3 91.1 - - - +
304A GLU* 1.3 57.2 + - + +
306A MET* 3.4 14.2 - - + +
307A ILE* 2.9 34.5 + - - +
334A VAL* 4.0 24.5 - - + -
339A TYR* 3.8 20.0 - - + -
342A ILE* 4.9 4.7 - - + -
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Residues in contact with GLU 304 (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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3A ASP* 4.2 9.4 - - - +
5A LYS* 5.3 0.7 - - - +
6A HIS* 2.7 31.6 + - + +
302A ASP* 2.9 20.9 + - - +
303A PRO* 1.3 78.5 - - + +
305A LYS* 1.3 59.9 + - - +
307A ILE* 3.3 29.1 - - - +
308A GLU* 3.3 10.6 + - - +
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Residues in contact with LYS 305 (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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276A GLN* 3.7 36.9 + - + +
277A GLY* 4.5 0.4 - - - -
280A ILE* 3.7 26.8 - - + +
300A TYR* 3.8 21.8 - - + -
302A ASP* 3.0 15.2 + - + +
304A GLU* 1.3 77.9 - - - +
306A MET* 1.3 63.4 + - - +
308A GLU* 3.1 34.4 + - - +
309A ILE* 3.3 22.2 + - - +
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Residues in contact with MET 306 (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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9A LEU* 4.0 9.0 - - + -
24A PHE* 3.4 28.5 - - + -
300A TYR* 3.4 41.1 - - + +
301A THR* 3.8 17.0 - - - +
302A ASP 3.1 6.9 + - - +
303A PRO* 3.2 19.5 + - + +
305A LYS* 1.3 74.6 - - - +
307A ILE* 1.3 65.1 + - - +
309A ILE* 3.3 17.4 + - - +
310A VAL* 3.3 15.2 + - - +
318A ILE* 3.6 34.5 - - + +
320A CYS* 4.7 3.4 - - - -
330A LEU* 4.3 17.0 - - + -
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Residues in contact with ILE 307 (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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5A LYS* 3.4 40.8 - - + +
6A HIS* 4.0 5.6 - - + -
8A ILE* 3.5 21.1 - - + -
9A LEU* 3.8 20.0 - - + -
303A PRO 2.9 19.7 + - - +
304A GLU* 3.3 37.5 - - - +
306A MET* 1.3 72.6 - - - +
308A GLU* 1.3 63.9 + - - +
310A VAL* 4.6 2.0 - - - +
311A THR* 2.8 37.3 + - + +
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Residues in contact with GLU 308 (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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280A ILE* 5.8 1.1 - - - +
304A GLU 3.3 10.4 + - - +
305A LYS* 3.1 44.0 + - - +
306A MET 3.2 1.0 - - - -
307A ILE* 1.3 82.8 - - - +
309A ILE* 1.3 66.8 + - + +
311A THR* 3.4 5.1 + - - -
312A LYS* 2.7 66.5 + - + +
314A TYR* 5.1 3.7 - - + -
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Residues in contact with ILE 309 (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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280A ILE* 3.5 34.8 - - + -
296A GLY 5.1 2.7 - - - +
300A TYR* 3.9 32.1 - - + +
305A LYS* 3.3 12.5 + - + +
306A MET 3.3 13.9 + - - +
308A GLU* 1.3 82.0 - - + +
310A VAL* 1.3 59.4 + - + +
313A GLY 3.5 1.6 + - - -
314A TYR* 3.0 48.3 + - + -
315A ALA* 3.2 23.8 + - + -
317A ILE 4.6 2.7 - - - +
318A ILE* 3.8 22.7 - - + -
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Residues in contact with VAL 310 (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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8A ILE* 3.8 29.1 - - + +
9A LEU* 4.5 10.3 - - + -
23A ARG* 4.6 10.1 - - + +
306A MET 3.3 16.4 + - - +
307A ILE* 4.1 5.4 - - - +
308A GLU 3.2 0.4 - - - -
309A ILE* 1.3 77.5 - - + +
311A THR* 1.3 63.2 + - - +
313A GLY* 3.1 13.3 + - - -
315A ALA 3.3 19.2 - - - +
316A ASP* 3.9 21.8 - - - +
318A ILE* 3.8 19.1 - - + -
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Residues in contact with THR 311 (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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8A ILE* 4.3 21.1 - - + -
307A ILE* 2.8 33.6 + - + +
308A GLU* 3.4 6.9 + - - -
310A VAL* 1.3 76.6 - - - +
312A LYS* 1.3 65.4 + - - +
313A GLY* 3.2 1.1 + - - -
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Residues in contact with LYS 312 (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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308A GLU* 2.7 48.9 + - + +
311A THR* 1.3 80.1 + - - +
313A GLY* 1.4 60.0 + - - +
314A TYR* 3.5 49.2 + - + +
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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