Contacts of the helix formed by residues 242 - 255 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.0 19.7 - - + -
16D ASN* 3.9 23.3 - - - +
195D MET* 6.0 0.2 - - - -
196D TYR 2.8 18.3 + - - +
197D GLY* 4.1 4.3 - - - -
198D GLY 4.7 1.6 - - - +
240D LEU 4.8 0.2 - - - -
241D HIS* 1.3 82.7 + - + +
243D GLU* 1.3 62.8 + - + +
245D MET* 3.1 13.8 + - + +
246D ILE* 2.9 30.1 + - + +
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Residues in contact with GLU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D HIS* 2.9 22.1 + - + +
242D ALA* 1.3 76.7 - - + +
244D ASP* 1.3 61.2 + - - +
246D ILE* 3.5 13.6 + - + +
247D SER* 3.3 19.6 + - - -
323D VAL* 3.9 19.3 - - + +
331D LYS* 3.1 29.3 + - - +
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Residues in contact with ASP 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D LEU* 3.6 22.6 - - + +
241D HIS* 3.1 6.4 + - - +
243D GLU* 1.3 76.0 - - - +
245D MET* 1.3 59.6 + - - +
247D SER* 2.9 7.2 + - - -
248D LEU* 2.9 12.6 + - - +
319D TRP* 2.8 29.9 + - + +
320D SER 4.1 2.6 - - - +
321D PRO* 3.5 13.5 - - + +
322D LYS* 2.8 35.6 + - - +
323D VAL* 3.0 36.3 + - - +
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Residues in contact with MET 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 5.0 2.9 - - + -
13D LEU* 3.8 30.5 - - + +
16D ASN* 3.7 31.0 - - + -
17D LEU* 3.6 25.1 - - - -
192D HIS* 5.0 0.4 - - + -
195D MET* 3.7 30.5 - - + -
240D LEU* 4.4 8.6 - - + +
241D HIS 3.3 9.2 + - - +
242D ALA* 3.1 24.3 + - + +
244D ASP* 1.3 75.1 - - - +
246D ILE* 1.3 67.4 + - + +
248D LEU* 3.3 6.8 + - - +
249D TYR* 3.0 42.9 + - + -
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Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ASN* 3.8 37.9 - - + +
17D LEU* 3.9 7.0 - - + -
20D PHE* 3.7 41.5 - - + -
242D ALA* 2.9 20.5 + - + +
243D GLU* 3.7 14.6 - - + +
244D ASP 3.3 0.2 - - - -
245D MET* 1.3 89.1 - - + +
247D SER* 1.3 65.1 + - - +
249D TYR* 3.3 0.3 + - - -
250D PHE* 3.2 28.9 + - + +
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Residues in contact with SER 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D GLU 3.3 6.3 + - - -
244D ASP* 2.9 24.9 + - - -
246D ILE* 1.3 82.1 - - - +
248D LEU* 1.3 61.8 + - - +
250D PHE* 5.1 2.2 - - - -
251D THR* 2.9 34.5 + - - -
319D TRP* 3.2 15.0 + - - -
320D SER 5.5 0.3 + - - -
322D LYS* 5.9 3.8 + - - +
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PHE* 3.7 35.2 - - + -
192D HIS* 4.3 5.6 - - + -
240D LEU* 5.2 0.2 - - + -
244D ASP 2.9 19.2 + - - +
245D MET* 3.4 7.2 - - - +
247D SER* 1.3 77.6 + - - +
249D TYR* 1.3 61.5 + - + +
251D THR* 3.8 1.1 - - - -
252D ALA* 2.8 34.1 + - - +
266D ILE* 3.5 35.2 - - + -
313D ILE* 4.1 19.7 - - + -
317D ILE* 4.2 5.6 - - + -
319D TRP* 3.4 34.1 - - + +
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Residues in contact with TYR 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.9 3.2 - - + +
17D LEU* 3.4 30.1 - - + -
78D PHE* 3.8 28.7 - + + -
80D LEU* 3.8 19.9 - - + +
121D ILE* 3.6 30.5 - - + +
123D SER* 3.4 19.6 - - - -
190D PHE* 3.6 18.4 - + - -
192D HIS* 2.7 38.2 + + - -
245D MET* 3.0 39.7 + - + +
248D LEU* 1.3 78.5 - - + +
250D PHE* 1.3 58.0 + - - +
253D LEU* 2.9 30.0 + - - +
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Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.1 14.6 - - + -
17D LEU* 3.6 43.5 - - + -
20D PHE* 3.4 46.0 - + + -
21D ALA* 4.0 8.3 - - + -
26D ILE* 4.2 20.9 - - + -
78D PHE* 3.8 17.0 - + - -
246D ILE* 3.2 20.9 + - + +
247D SER* 4.4 2.5 - - - +
249D TYR* 1.3 77.5 - - - +
251D THR* 1.3 58.3 + - - +
253D LEU* 3.5 11.3 + - + +
254D ALA* 3.0 28.4 + - - +
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Residues in contact with THR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D SER* 2.9 24.6 + - - -
248D LEU* 3.8 2.5 - - - -
250D PHE* 1.3 75.1 - - - +
252D ALA* 1.3 65.5 + - - +
254D ALA* 3.2 5.8 + - - +
255D ASN* 2.9 36.7 + - - +
317D ILE* 3.5 39.0 - - + +
319D TRP* 4.9 5.9 - - + -
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ILE* 4.2 6.1 - - + -
188D VAL* 5.4 0.7 - - + -
190D PHE* 3.5 27.1 - - + -
248D LEU 2.8 19.8 + - - +
249D TYR 3.8 2.7 - - - +
251D THR* 1.3 78.5 - - - +
253D LEU* 1.3 57.1 + - - +
255D ASN* 3.0 5.4 + - - -
256D VAL* 2.9 28.1 + - - +
259D ILE* 3.7 20.2 - - + +
317D ILE* 3.9 15.0 - - + +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.5 5.8 - - + -
76D SER* 3.5 35.4 - - - +
77D CYS 5.5 0.7 - - - +
78D PHE* 3.8 29.2 - - + -
119D ASN* 3.7 25.1 + - + +
121D ILE* 4.0 10.2 - - + +
249D TYR 2.9 18.0 + - - +
250D PHE* 3.6 16.4 - - + +
252D ALA* 1.3 75.5 - - - +
254D ALA* 1.4 65.1 + - - +
256D VAL* 3.2 26.6 + - + +
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Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D PHE 3.0 18.7 + - - +
251D THR* 3.2 6.9 + - - +
253D LEU* 1.4 77.2 - - - +
255D ASN* 1.3 64.6 + - - +
256D VAL* 3.3 2.3 + - - +
257D SER 5.2 0.3 + - - -
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Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D THR* 2.9 40.1 + - - +
252D ALA 3.0 4.9 + - - +
254D ALA* 1.3 83.3 - - - +
256D VAL* 1.3 65.1 + - - +
257D SER* 3.2 5.4 - - - -
258D LYS* 3.0 36.6 + - + +
259D ILE* 3.4 9.7 + - + +
317D ILE* 3.7 25.6 - - + +
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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