Contacts of the helix formed by residues 242 - 255 (chain B) in PDB entry 1ORR
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 ALA 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B PHE* 4.0 22.4 - - + -
16B ASN* 4.0 21.8 - - + +
195B MET* 6.1 0.9 - - - -
196B TYR 2.8 18.3 + - - +
197B GLY* 4.1 7.2 - - - -
198B GLY 4.7 1.3 - - - +
240B LEU 3.7 0.4 + - - -
241B HIS* 1.3 78.1 + - + +
243B GLU* 1.3 62.6 + - + +
245B MET* 3.1 13.5 + - + +
246B ILE* 2.9 28.5 + - + +
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B HIS* 3.0 26.0 + - + +
242B ALA* 1.3 78.0 - - + +
244B ASP* 1.3 62.4 + - - +
246B ILE* 3.4 18.6 + - + +
247B SER* 3.5 12.3 + - - -
323B VAL* 3.9 16.2 - - + +
331B LYS* 3.0 32.8 + - - +
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B LEU* 3.6 19.5 - - + +
241B HIS* 2.8 11.4 + - - +
243B GLU* 1.3 75.7 - - - +
245B MET* 1.3 65.2 + - - +
247B SER* 2.5 23.2 + - - -
248B LEU* 3.0 2.6 + - - +
319B TRP* 2.8 21.7 + - + -
320B SER 4.1 2.6 - - - +
321B PRO* 3.5 11.0 - - - +
322B LYS* 2.8 32.5 + - - +
323B VAL* 3.0 35.8 + - - +
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.3 0.7 - - + -
13B LEU* 3.0 63.9 - - + +
16B ASN* 4.7 6.5 - - + -
17B LEU* 3.8 19.3 - - + -
192B HIS* 4.8 1.8 - - + -
195B MET* 3.6 22.0 - - + -
240B LEU* 4.2 14.5 - - + +
241B HIS 3.2 8.6 + - - +
242B ALA* 3.1 17.0 + - - +
244B ASP* 1.3 81.8 - - - +
246B ILE* 1.3 64.6 + - - +
248B LEU* 3.2 7.2 + - + +
249B TYR* 3.1 45.8 + - + -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASN* 3.6 47.6 - - + +
17B LEU* 3.8 9.6 - - + -
20B PHE* 3.7 41.1 - - + +
242B ALA 2.9 20.3 + - - +
243B GLU* 3.7 11.9 - - + +
244B ASP 3.3 0.2 - - - -
245B MET* 1.3 77.4 - - - +
247B SER* 1.3 64.2 + - - +
249B TYR* 3.5 0.3 + - - -
250B PHE* 3.1 30.1 + - + -
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU 3.5 5.0 + - - -
244B ASP* 2.5 32.7 + - - -
246B ILE* 1.3 79.6 - - - +
248B LEU* 1.3 52.3 + - - +
250B PHE* 4.3 3.1 - - - +
251B THR* 2.6 46.1 + - - -
319B TRP* 3.2 14.3 + - - -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE* 3.7 35.0 - - + -
192B HIS* 4.5 2.0 - - + -
244B ASP 3.0 10.2 + - - +
245B MET* 3.2 11.9 + - - +
247B SER* 1.3 81.3 + - - +
249B TYR* 1.3 65.5 + - + +
251B THR* 3.9 1.2 - - - -
252B ALA* 2.7 34.5 + - - +
266B ILE* 3.5 33.2 - - + -
313B ILE* 4.0 21.1 - - + -
317B ILE* 4.1 4.5 - - + -
319B TRP* 3.4 35.2 - - + +
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.2 3.5 - - + +
17B LEU* 3.5 25.1 - - + -
78B PHE* 3.8 27.8 - + + -
80B LEU* 3.9 18.5 - - + +
121B ILE* 3.2 39.1 - - + +
123B SER* 3.4 19.4 - - - -
190B PHE* 3.5 21.1 - + - -
192B HIS* 2.7 33.9 + + - -
245B MET* 3.1 34.4 + - + -
248B LEU* 1.3 82.6 - - + +
250B PHE* 1.3 58.3 + - - +
252B ALA* 4.5 0.9 - - - -
253B LEU* 3.0 28.8 + - - +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.2 13.7 - - + -
17B LEU* 3.7 40.6 - - + -
20B PHE* 3.4 45.8 - + + -
21B ALA 4.2 4.9 - - - -
26B ILE* 4.0 21.3 - - + -
78B PHE* 3.8 21.3 - + - -
246B ILE* 3.1 25.4 + - + +
247B SER* 4.3 2.7 - - - +
249B TYR* 1.3 75.3 - - - +
251B THR* 1.4 67.0 + - - +
253B LEU* 3.4 14.4 + - + +
254B ALA* 3.0 23.0 + - - +
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B SER* 2.6 35.9 + - - -
248B LEU* 3.9 2.5 - - - -
250B PHE* 1.4 69.8 - - - +
252B ALA* 1.4 64.2 + - - +
254B ALA* 3.3 9.8 + - - +
255B ASN* 2.8 36.5 + - - +
317B ILE* 3.8 32.3 - - + +
319B TRP* 5.0 7.7 - - + +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 4.1 7.0 - - + -
188B VAL* 6.2 0.2 - - - -
190B PHE* 3.7 26.0 - - + -
248B LEU 2.7 23.0 + - - +
249B TYR 3.8 3.8 - - - +
251B THR* 1.4 74.1 - - - +
253B LEU* 1.3 56.4 + - - +
255B ASN* 2.9 20.6 + - - +
256B VAL* 3.0 12.6 + - - +
259B ILE* 3.8 21.5 - - + +
313B ILE* 5.2 0.2 - - + -
317B ILE* 3.8 14.5 - - + +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.7 4.9 - - + -
76B SER* 3.3 38.4 - - - +
78B PHE* 4.1 26.0 - - + -
119B ASN* 3.9 20.3 + - + +
121B ILE* 4.2 10.2 - - + +
249B TYR 3.0 18.6 + - - +
250B PHE* 3.5 17.5 - - + +
252B ALA* 1.3 75.3 - - - +
254B ALA* 1.3 62.3 + - - +
255B ASN 3.1 1.0 + - - -
256B VAL* 3.2 24.4 + - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B PHE 3.0 16.8 + - - +
251B THR* 3.5 9.2 - - - +
252B ALA 3.2 0.2 - - - -
253B LEU* 1.3 75.6 - - - +
255B ASN* 1.4 65.4 + - - +
256B VAL* 3.6 0.4 - - - -
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Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B THR* 2.8 34.4 + - - +
252B ALA 2.9 9.8 + - - +
254B ALA* 1.4 82.9 - - - +
256B VAL* 1.3 66.9 + - - +
257B SER* 3.2 4.5 - - - -
258B LYS* 2.9 24.7 + - + +
259B ILE* 3.2 11.3 + - + +
316B ALA 5.1 2.2 - - - +
317B ILE* 3.8 27.2 + - + +
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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