Contacts of the helix formed by residues 314 - 320 (chain B) in PDB entry 2ORY
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 VAL 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B TYR* 2.8 60.1 + - + +
313B VAL* 1.3 72.6 - - + +
315B GLY* 1.3 62.8 - - - +
317B PRO* 3.1 5.4 - - - +
318B GLU* 3.1 20.1 + - - +
323B MET* 4.0 14.1 - - + -
328B LEU* 4.0 14.1 - - + -
340B LEU* 3.9 10.3 - - + -
342B HIS* 3.6 30.3 - - + -
345B HIS* 3.9 12.1 - - + +
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASN* 4.1 9.2 - - - -
310B TYR* 2.9 12.5 + - - -
311B GLN* 3.7 18.3 + - - -
313B VAL 3.4 1.2 - - - -
314B VAL* 1.3 75.9 - - - +
316B TYR* 1.3 58.8 + - - +
318B GLU* 4.1 12.3 - - - -
319B LEU* 2.8 40.4 + - - +
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Residues in contact with TYR 316 (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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10B LEU* 3.8 7.9 - - + -
14B TYR* 3.7 9.9 - - - +
173B HIS* 3.9 6.1 - + - -
206B PHE* 4.3 5.8 - + + -
207B ALA* 3.2 20.7 - - + +
231B ILE* 3.6 24.2 - - + -
232B ALA* 3.6 3.0 - - - -
233B ASN* 2.9 37.8 + - + -
236B ASP* 2.6 27.8 + - - +
239B PRO* 4.2 0.7 - - - +
293B LEU* 4.5 3.8 - - + -
311B GLN 3.8 8.3 - - - -
312B HIS 3.2 28.3 - - - -
314B VAL 3.3 0.2 - - - -
315B GLY* 1.3 71.9 - - - +
317B PRO* 1.3 74.2 - - + +
319B LEU* 3.8 1.5 - - - -
320B MET* 3.0 54.8 + - + +
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Residues in contact with PRO 317 (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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10B LEU* 3.8 11.0 - - + -
14B TYR* 3.6 10.5 - - + +
313B VAL 3.3 16.2 - - - +
314B VAL 3.1 20.4 - - - +
316B TYR* 1.3 89.2 - - + +
318B GLU* 1.3 58.3 + - - +
321B GLY 3.4 1.0 + - - -
322B MET* 2.7 50.4 + - + +
323B MET* 3.1 10.3 + - - +
326B ILE* 4.1 14.4 - - + +
328B LEU* 4.0 24.2 - - + -
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Residues in contact with GLU 318 (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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296B ASN* 4.4 16.6 + - - +
310B TYR* 2.5 41.0 + - - -
311B GLN* 5.0 2.4 - - - +
314B VAL* 3.1 18.0 + - - +
315B GLY* 3.5 8.1 - - - +
316B TYR 3.0 0.4 - - - -
317B PRO* 1.3 81.5 - - - +
319B LEU* 1.3 77.4 + - + +
320B MET 3.1 1.8 + - - -
321B GLY* 3.4 8.7 + - - -
323B MET* 3.5 26.7 - - + +
345B HIS* 5.2 0.2 - - - +
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Residues in contact with LEU 319 (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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233B ASN* 3.5 37.7 - - + +
293B LEU* 4.0 37.3 - - + +
294B GLU 3.5 18.8 - - - +
295B GLY* 3.7 12.3 - - - -
296B ASN* 4.2 13.7 - - - +
311B GLN* 5.3 0.4 - - - +
315B GLY 2.8 24.0 + - - +
318B GLU* 1.3 87.8 - - + +
320B MET* 1.3 61.6 + - - +
321B GLY 3.5 0.7 - - - -
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Residues in contact with MET 320 (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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6B GLU* 5.2 7.9 - - - +
7B GLN* 3.2 28.9 + - + -
10B LEU* 3.2 46.2 - - + -
206B PHE* 3.8 20.0 - - + -
231B ILE* 4.2 10.3 - - + -
293B LEU* 3.7 23.8 - - + -
316B TYR* 3.0 44.2 + - + +
318B GLU 3.1 0.2 - - - -
319B LEU* 1.3 76.9 - - - +
321B GLY* 1.3 65.3 + - - +
322B MET* 3.3 6.1 + - + +
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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