Contacts of the helix formed by residues 298 - 307 (chain A) in PDB entry 2OR4
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 GLY 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A TYR* 4.8 0.2 - - - -
229A SER* 4.7 4.7 - - - -
250A GLY 3.7 6.5 - - - -
251A GLY* 4.9 1.1 - - - -
252A GLY 3.1 23.1 - - - -
253A VAL* 3.6 8.8 - - - +
297A ILE* 1.3 79.3 - - - +
299A TYR* 1.3 61.8 + - - -
300A TYR 3.4 2.9 - - - -
301A ASP* 3.5 8.0 + - - +
302A ALA* 2.9 26.1 + - - +
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Residues in contact with TYR 299 (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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228A TYR* 4.7 0.4 - - + -
229A SER 3.3 26.7 + - - +
231A PRO* 3.7 39.9 - - + -
234A TYR 5.6 0.2 - - - -
235A PHE* 3.6 18.1 - + + -
241A SER* 4.3 0.9 + - - -
248A LEU* 2.6 42.0 + - + -
249A PRO* 3.5 10.3 - - - +
250A GLY* 3.3 24.5 + - - -
298A GLY* 1.3 70.1 - - - -
300A TYR* 1.3 77.2 - + - +
302A ALA* 3.9 6.3 - - - -
303A GLN* 2.9 29.8 + - - +
323A LEU* 4.1 16.8 - - + +
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Residues in contact with TYR 300 (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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249A PRO* 5.8 0.2 - - - +
250A GLY* 3.1 44.2 + - - +
251A GLY* 3.8 7.6 - - - -
299A TYR* 1.3 91.4 - + - +
301A ASP* 1.3 65.8 + - - +
303A GLN* 3.4 18.7 + - - +
304A LYS* 3.5 15.3 + - - +
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Residues in contact with ASP 301 (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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139A PHE* 3.3 21.9 - - - -
140A ASN 4.4 0.5 - - - +
141A THR* 3.3 29.4 - - + -
142A SER* 2.9 35.3 + - - -
250A GLY 4.6 0.4 + - - -
297A ILE* 3.9 13.0 - - + +
298A GLY 3.5 11.3 + - - +
299A TYR 3.3 0.2 - - - -
300A TYR* 1.3 78.8 - - - +
302A ALA* 1.3 67.1 + - - +
304A LYS* 3.2 13.3 + - - +
305A LEU* 3.3 16.5 + - - +
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Residues in contact with ALA 302 (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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202A ILE* 4.9 1.1 - - + -
228A TYR* 3.3 47.8 - - + -
297A ILE* 3.6 9.6 - - + +
298A GLY 2.9 18.2 + - - +
299A TYR* 3.8 4.3 - - - +
301A ASP* 1.3 72.7 - - - +
303A GLN* 1.3 59.1 - - - +
305A LEU* 3.0 5.0 + - - +
306A LEU* 2.9 39.3 + - + +
323A LEU* 4.5 1.1 - - + -
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Residues in contact with GLN 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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299A TYR 2.9 16.9 + - - +
300A TYR* 3.4 10.1 - - - +
302A ALA* 1.3 75.3 - - - +
304A LYS* 1.3 65.5 + - + +
306A LEU* 4.6 2.7 - - - +
307A GLU* 2.8 48.2 + - - +
323A LEU* 3.7 29.3 - - + +
324A LYS* 3.2 25.9 + - - +
325A VAL* 3.0 24.5 - - + +
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Residues in contact with LYS 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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130A ILE* 3.5 16.3 - - + +
139A PHE* 3.6 40.4 - - + -
300A TYR 3.5 15.7 + - - +
301A ASP 3.2 7.8 + - - +
302A ALA 3.1 0.6 - - - -
303A GLN* 1.3 84.5 - - - +
305A LEU* 1.3 59.9 + - - +
307A GLU* 3.7 37.6 + - - +
308A LYS* 4.8 3.8 + - - +
333A PHE* 5.7 0.2 - - - -
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Residues in contact with LEU 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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128A ILE* 4.4 17.3 - - + -
130A ILE* 3.7 30.1 - - + +
139A PHE* 4.0 14.4 - - + -
141A THR* 4.6 4.5 - - + -
174A LEU* 3.6 13.6 - - + +
202A ILE* 4.2 13.0 - - + -
226A ILE* 4.1 24.5 - - + -
297A ILE* 3.5 28.3 - - + -
301A ASP 3.3 9.2 + - - +
302A ALA 3.0 7.3 + - - +
304A LYS* 1.3 77.3 - - - +
306A LEU* 1.3 60.5 - - - +
308A LYS 4.5 0.7 + - - -
309A MET* 3.7 1.0 - - - +
333A PHE* 3.5 24.6 - - - -
342A VAL* 4.5 10.8 - - + -
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Residues in contact with LEU 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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176A TYR* 4.2 15.9 - - + -
202A ILE* 3.9 26.2 - - + -
228A TYR* 3.8 30.5 - - + +
302A ALA 2.9 18.9 + - - +
303A GLN 4.1 1.8 - - - +
305A LEU* 1.3 74.9 - - - +
307A GLU* 1.3 66.3 + - - +
308A LYS 3.2 2.7 - - - -
309A MET* 3.0 41.8 + - + +
323A LEU* 4.0 17.3 - - + -
325A VAL* 4.2 19.3 - - + +
326A PRO* 4.6 3.8 - - - +
327A TYR* 4.3 17.5 + - + +
328A ASN 5.8 0.4 - - - +
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Residues in contact with GLU 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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303A GLN* 2.8 30.5 + - + +
304A LYS* 3.7 39.2 + - - +
305A LEU 3.5 0.2 - - - -
306A LEU* 1.3 77.3 - - - +
308A LYS* 1.3 79.7 + - + +
309A MET 3.3 1.3 + - - +
324A LYS 5.5 0.7 - - - +
325A VAL* 3.6 17.9 - - + -
326A PRO* 4.3 12.7 - - - +
334A THR* 6.0 0.2 - - - +
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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