Contacts of the helix formed by residues 242 - 255 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C PHE* 4.1 16.8 - - + -
16C ASN* 4.1 19.5 - - - +
195C MET* 6.0 0.4 - - - -
196C TYR 2.8 17.7 + - - +
197C GLY* 4.0 13.0 - - - -
198C GLY 4.8 1.1 - - - +
240C LEU 3.6 0.4 + - - -
241C HIS* 1.3 77.4 - - + +
243C GLU* 1.3 65.1 + - + +
245C MET* 3.1 14.6 + - + +
246C ILE* 3.0 30.2 + - + +
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C HIS* 2.9 19.8 + - + +
242C ALA* 1.3 78.1 - - + +
244C ASP* 1.3 62.6 + - - +
246C ILE* 3.5 12.5 + - + +
247C SER* 3.5 19.8 + - - -
323C VAL* 3.9 18.2 - - + +
331C LYS* 2.6 36.6 + - - -
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Residues in contact with ASP 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C LEU* 3.6 19.8 - - + +
241C HIS* 2.8 10.5 + - - +
243C GLU* 1.3 76.9 - - - +
245C MET* 1.3 62.8 + - - +
247C SER* 3.3 5.9 + - - -
248C LEU* 3.2 5.2 + - - +
319C TRP* 2.9 31.1 + - + -
320C SER 4.2 1.2 - - - +
321C PRO* 3.5 14.4 - - + +
322C LYS* 2.7 38.0 + - - +
323C VAL* 2.8 37.1 + - - +
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Residues in contact with MET 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 5.2 1.6 - - + -
13C LEU* 3.8 30.3 - - + +
16C ASN* 3.7 30.5 - - + +
17C LEU* 3.5 25.6 - - - -
192C HIS* 5.0 0.9 - - + -
195C MET* 3.7 31.0 - - + -
240C LEU* 4.4 8.7 - - + +
241C HIS 3.2 9.6 + - - +
242C ALA* 3.1 23.6 + - + +
244C ASP* 1.3 76.1 - - - +
246C ILE* 1.3 67.4 + - + +
248C LEU* 3.2 6.5 + - + +
249C TYR* 3.0 37.7 + - + -
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Residues in contact with ILE 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ASN* 3.6 33.0 - - + +
17C LEU* 3.7 10.5 - - + -
19C SER* 4.9 2.5 - - - +
20C PHE* 3.7 40.2 - - + -
242C ALA 3.0 17.6 + - - +
243C GLU* 3.9 12.6 - - + +
245C MET* 1.3 91.5 - - + +
247C SER* 1.3 64.4 + - - +
249C TYR* 3.2 0.5 + - - -
250C PHE* 3.1 31.4 + - + +
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLU 3.5 9.1 + - - -
244C ASP* 3.3 9.5 + - - -
245C MET 3.3 0.2 - - - -
246C ILE* 1.3 79.6 - - - +
248C LEU* 1.3 62.0 + - - +
250C PHE* 5.1 2.5 - - - -
251C THR* 2.8 34.2 + - - +
319C TRP* 3.1 22.3 + - - -
320C SER 5.4 0.3 + - - -
322C LYS* 5.8 6.9 - - - +
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C PHE* 3.7 37.5 - - + -
192C HIS* 4.4 5.4 - - + -
240C LEU* 5.3 0.4 - - + -
244C ASP 3.2 4.4 + - - +
245C MET* 3.2 11.3 + - - +
247C SER* 1.3 81.7 + - - +
249C TYR* 1.3 61.8 + - + +
251C THR* 2.9 6.9 - - - +
252C ALA* 2.8 33.4 + - - +
266C ILE* 3.6 32.8 - - + -
313C ILE* 4.0 21.1 - - + -
317C ILE* 4.3 6.1 - - + -
319C TRP* 3.5 36.3 - - + +
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Residues in contact with TYR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.9 3.7 - - + +
17C LEU* 3.5 28.9 - - + -
78C PHE* 3.8 30.3 - + + -
80C LEU* 3.8 18.6 - - + +
121C ILE* 3.6 32.5 - - + +
123C SER* 3.4 19.2 - - - -
190C PHE* 3.6 17.6 - + - -
192C HIS* 2.7 37.3 + + - -
245C MET* 3.0 37.0 + - + -
248C LEU* 1.3 79.6 - - + +
250C PHE* 1.3 58.4 + - - +
253C LEU* 2.8 29.8 + - - +
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Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.1 13.9 - - + -
17C LEU* 3.4 45.5 - - + -
20C PHE* 3.5 45.3 - + + -
21C ALA* 3.9 7.4 - - + -
26C ILE* 4.0 23.1 - - + -
78C PHE* 3.8 17.3 - + - -
246C ILE* 3.1 21.2 + - + +
247C SER* 4.4 2.5 - - - +
249C TYR* 1.3 77.6 - - - +
251C THR* 1.3 57.7 + - - +
253C LEU* 3.3 12.0 + - + +
254C ALA* 2.9 28.1 + - - +
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C SER* 2.8 28.5 + - - +
248C LEU* 2.9 14.1 - - - +
250C PHE* 1.3 73.4 - - - +
252C ALA* 1.3 79.0 + - - +
254C ALA* 3.2 4.8 + - - -
255C ASN* 2.9 38.1 + - - +
317C ILE* 3.3 29.4 + - + +
319C TRP* 4.3 9.4 - - + +
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 4.0 6.1 - - + -
188C VAL* 5.5 0.5 - - - +
190C PHE* 3.7 26.2 - - + -
248C LEU 2.8 18.8 + - - +
249C TYR 3.8 2.7 - - - +
251C THR* 1.3 78.4 - - - +
253C LEU* 1.3 66.5 + - - +
255C ASN* 3.0 12.1 + - - -
256C VAL* 3.1 11.1 + - - +
259C ILE* 3.7 22.5 - - + +
317C ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.5 6.1 - - + -
76C SER* 3.6 36.8 - - - +
78C PHE* 4.2 25.8 - - + -
119C ASN* 3.7 23.7 + - + +
121C ILE* 4.0 11.6 - - + +
249C TYR 2.8 19.3 + - - +
250C PHE* 3.6 15.9 - - + +
251C THR 3.2 0.2 - - - -
252C ALA* 1.3 78.6 - - - +
254C ALA* 1.3 63.1 + - - +
255C ASN 3.2 0.7 + - - -
256C VAL* 3.2 25.7 + - + +
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Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PHE 2.9 17.0 + - - +
251C THR* 3.8 6.5 - - - +
252C ALA 3.1 0.4 - - - -
253C LEU* 1.3 79.8 - - - +
255C ASN* 1.3 61.1 + - - +
256C VAL* 3.4 2.7 + - - +
257C SER* 5.3 0.9 + - - -
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Residues in contact with ASN 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C THR* 2.9 33.9 + - - +
252C ALA 3.0 6.2 + - - +
254C ALA* 1.3 83.5 - - - +
256C VAL* 1.3 64.3 + - - +
257C SER* 3.2 5.8 - - - -
258C LYS* 3.0 34.2 + - + +
259C ILE* 3.3 10.1 + - + +
316C ALA 5.1 0.2 - - - +
317C ILE* 3.8 30.0 + - + +
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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