Contacts of the helix formed by residues 303 - 314 (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 GLU 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS* 5.1 8.1 + - - -
63A MET* 4.5 12.0 - - - +
64A PRO* 3.5 26.5 - - + +
261B VAL* 3.8 1.1 - - - -
264B LEU* 5.9 5.0 - - + +
301B LEU* 3.5 1.0 - - - +
302B ILE* 1.3 91.5 - - + +
304B TYR* 1.3 60.4 - - - +
305B LEU* 4.6 2.5 - - + +
306B VAL* 3.0 28.4 + - + +
307B GLN* 2.8 30.7 + - - +
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Residues in contact with TYR 304 (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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102B PHE* 4.7 9.0 - + - -
237B ILE* 3.8 28.7 - - + +
250B LEU* 2.7 38.6 + - - +
251B LYS 4.6 1.3 - - - -
253B ILE* 4.0 4.3 - - + -
254B TYR* 3.6 27.9 - + + -
261B VAL* 3.5 19.9 - - - +
262B LYS 3.6 21.3 + - - +
263B PRO* 3.5 42.6 - - + -
264B LEU* 4.8 6.2 - - + +
267B GLN* 4.6 4.0 - - + -
271B ILE* 3.9 6.9 - - + +
302B ILE 3.7 0.4 + - - -
303B GLU* 1.3 70.4 - - - +
305B LEU* 1.3 77.2 + - + +
307B GLN* 3.5 2.6 + - - +
308B ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 305 (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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63A MET* 5.2 4.0 - - + -
64A PRO* 4.1 14.1 - - + +
65A PHE* 3.7 11.0 - - + +
66A THR* 3.5 33.4 - - + -
95B VAL 5.0 0.7 - - - +
97B ILE* 5.4 3.8 - - + +
98B SER* 3.9 24.0 - - - +
102B PHE* 5.0 5.4 - - + -
237B ILE* 5.5 0.4 - - + -
264B LEU* 6.1 2.5 - - + -
267B GLN* 3.8 38.1 - - + +
303B GLU* 3.3 2.7 - - + +
304B TYR* 1.3 89.3 - - + +
306B VAL* 1.3 61.4 + - + +
308B ALA* 3.8 8.3 - - + +
309B ALA* 3.1 27.2 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 3.7 29.8 - - + -
65A PHE* 3.9 15.9 - - + -
301B LEU* 3.7 25.1 - - + -
303B GLU* 3.0 31.7 + - + +
305B LEU* 1.3 74.2 - - + +
307B GLN* 1.3 67.3 + - - +
309B ALA* 3.2 3.5 + - - +
310B TYR* 3.0 21.8 + - - +
339B LEU* 3.6 27.1 - - + +
340B LEU* 4.1 2.0 - - + +
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Residues in contact with GLN 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.6 29.5 - - + -
261B VAL* 4.2 8.7 - - + +
297B ILE* 3.7 14.3 - - - +
298B ASN* 2.9 36.4 + - - +
301B LEU* 2.9 33.5 - - - +
303B GLU 2.8 15.8 + - - +
304B TYR 3.7 4.3 - - - +
306B VAL* 1.3 78.4 - - - +
308B ALA* 1.3 56.3 + - - +
310B TYR* 3.3 4.8 + - - +
311B GLN* 2.8 67.2 + - - +
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Residues in contact with ALA 308 (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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97B ILE* 3.9 9.9 - - + +
236B ASP* 4.7 1.4 - - - +
237B ILE* 3.7 30.7 - - + +
254B TYR* 3.3 18.1 + - + +
304B TYR* 3.0 19.4 + - + +
305B LEU* 3.8 11.4 - - + +
306B VAL 3.2 0.2 - - - -
307B GLN* 1.3 74.5 - - - +
309B ALA* 1.3 60.3 + - - +
311B GLN* 3.2 2.1 + - - +
312B HIS* 2.8 32.2 + - - +
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Residues in contact with ALA 309 (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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65A PHE* 3.7 20.9 - - + -
95B VAL* 3.7 30.5 - - + +
97B ILE* 4.2 7.1 - - - +
305B LEU 3.1 18.6 + - - +
306B VAL 3.7 4.5 - - - +
308B ALA* 1.3 75.4 - - - +
310B TYR* 1.3 57.6 + - - +
312B HIS* 4.4 1.1 - - - -
313B VAL* 2.9 35.9 + - - +
340B LEU* 3.8 8.5 - - + +
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Residues in contact with TYR 310 (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 5.3 0.7 - - - -
298B ASN* 3.5 26.5 + - + -
301B LEU* 3.4 30.5 - - + -
306B VAL 3.0 7.7 + - - +
307B GLN 3.4 7.0 - - - +
309B ALA* 1.3 77.9 - - - +
311B GLN* 1.3 77.0 + - - +
314B VAL* 2.8 59.4 + - + +
315B GLY 2.9 9.6 + - - -
318B GLU* 2.5 39.0 + - - -
340B LEU* 3.7 18.1 - - + +
345B HIS* 3.5 29.4 - + + +
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Residues in contact with GLN 311 (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* 2.9 38.8 + - - +
235B LEU* 3.4 40.0 - - + +
236B ASP* 3.9 4.4 - - - +
254B TYR* 3.6 7.0 - - + +
295B GLY* 4.8 0.2 - - - -
296B ASN 3.0 27.8 + - - +
297B ILE* 3.8 2.8 - - - +
298B ASN 3.8 1.8 - - - +
307B GLN* 2.8 47.2 + - - +
308B ALA 3.2 3.3 + - - +
310B TYR* 1.3 88.4 - - - +
312B HIS* 1.3 59.8 + - - +
315B GLY* 3.7 12.4 - - - +
316B TYR* 3.8 7.4 - - - -
318B GLU* 5.0 2.6 - - - +
319B LEU* 5.3 0.5 - - - +
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Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 3.5 32.8 - - + -
97B ILE* 3.8 7.9 - - + -
100B TRP* 3.9 0.6 - - - -
173B HIS* 2.8 32.5 + + - -
174B SER* 2.7 30.4 + - - -
207B ALA* 3.4 31.6 - - + -
236B ASP* 2.9 30.8 + - - +
238B VAL* 3.3 23.9 - - + +
308B ALA 2.8 17.3 + - - +
309B ALA* 3.8 3.4 - - - +
311B GLN* 1.3 79.4 - - - +
313B VAL* 1.3 56.2 + - + +
316B TYR* 3.2 11.1 - - - -
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Residues in contact with VAL 313 (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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14B TYR* 2.6 31.9 + - + -
94B PRO* 4.1 20.4 - - + -
95B VAL* 4.0 24.0 - - + +
173B HIS* 4.5 2.0 - - + -
309B ALA 2.9 16.2 + - - +
312B HIS* 1.3 85.0 - - + +
314B VAL* 1.3 71.1 + - + +
315B GLY 3.4 1.1 + - - -
316B TYR 4.0 0.2 + - - -
317B PRO* 3.3 7.1 - - - +
328B LEU* 4.3 5.4 - - + -
332B PHE* 3.7 35.9 - - + -
340B LEU* 4.7 8.7 - - + -
342B HIS* 5.8 0.4 - - + -
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Residues in contact with VAL 314 (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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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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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