Contacts of the helix formed by residues 310 - 318 (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 ILE 310 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C GLU* 5.4 0.4 - - - -
265C ASN 3.6 20.6 - - - +
266C ILE* 4.3 1.3 - - - -
267C GLY 3.9 24.5 - - - +
269C THR* 3.5 28.3 - - + -
308C ALA* 3.6 6.6 + - + +
309C ASP* 1.3 72.5 + - - +
311C LYS* 1.3 65.8 + - - +
312C LYS 3.1 4.3 + - - -
313C ILE* 3.2 13.6 + - + -
314C THR* 3.0 37.1 + - - +
319C TRP* 3.9 13.5 - - + +
320C SER* 4.4 2.9 - - - -
321C PRO* 3.8 19.7 - - + -
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Residues in contact with LYS 311 (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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151C ASN* 6.3 1.1 - - - +
154C ASP* 6.0 1.8 - - + +
309C ASP* 3.2 30.3 + - - +
310C ILE* 1.3 77.0 - - - +
312C LYS* 1.4 53.6 + - - +
314C THR* 3.2 5.1 + - - -
315C ASN* 2.7 54.1 + - - +
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Residues in contact with LYS 312 (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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155C GLU* 3.5 39.3 + - + +
262C ASN* 2.8 31.0 + - - +
263C ALA 2.9 30.6 + - - +
264C PHE* 3.6 17.7 - - + -
309C ASP 4.8 1.0 + - - -
310C ILE 3.1 1.2 + - - -
311C LYS* 1.4 78.9 - - - +
313C ILE* 1.3 65.0 + - - +
315C ASN* 3.8 7.0 - - - +
316C ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 313 (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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155C GLU* 5.0 0.2 + - - -
190C PHE* 4.4 5.8 - - + -
248C LEU* 4.0 24.0 - - + -
259C ILE* 5.0 3.1 - - + -
264C PHE* 3.6 40.2 - - + +
265C ASN 4.2 2.0 - - - +
266C ILE* 3.7 19.7 - - + -
310C ILE* 3.3 27.3 - - + +
312C LYS* 1.3 79.3 - - - +
314C THR* 1.3 62.3 + - - +
316C ALA* 3.0 0.9 + - - +
317C ILE* 2.8 57.8 + - + +
319C TRP* 4.0 13.9 - - + -
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Residues in contact with THR 314 (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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310C ILE* 3.0 32.3 + - - +
311C LYS* 3.7 6.5 - - - -
313C ILE* 1.3 76.8 - - - +
315C ASN* 1.3 65.2 + - - +
318C ASP* 2.6 45.3 + - - +
319C TRP 2.9 26.9 + - - +
320C SER* 4.8 6.0 - - - -
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Residues in contact with ASN 315 (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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258C LYS* 4.8 3.8 + - - -
311C LYS* 2.7 42.2 + - - +
312C LYS* 3.8 6.0 - - - +
314C THR* 1.3 81.2 - - - +
316C ALA* 1.3 62.5 + - - +
318C ASP 4.6 0.5 + - - -
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Residues in contact with ALA 316 (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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255C ASN* 5.1 0.2 - - - +
258C LYS* 3.0 37.5 + - + +
259C ILE* 3.7 26.7 - - + -
264C PHE* 4.1 10.5 - - + -
312C LYS 3.0 18.6 + - - +
313C ILE* 3.0 3.8 + - + +
315C ASN* 1.3 77.7 - - - +
317C ILE* 1.3 65.1 + - + +
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Residues in contact with ILE 317 (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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248C LEU* 4.3 1.6 - - + -
251C THR* 3.3 39.5 + - + +
252C ALA* 3.8 15.5 - - + -
255C ASN* 3.8 35.0 + - + +
258C LYS* 5.3 0.2 - - + -
259C ILE* 4.0 13.2 - - + -
313C ILE* 2.8 37.3 + - + +
316C ALA* 1.3 88.2 - - + +
318C ASP* 1.3 70.2 + - - +
319C TRP* 3.4 13.4 + - + -
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Residues in contact with ASP 318 (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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314C THR* 2.6 36.4 + - - +
315C ASN 4.5 0.8 + - - -
317C ILE* 1.3 75.6 - - - +
319C TRP* 1.3 60.4 + - - +
320C SER* 4.0 3.5 + - - -
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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