Contacts of the helix formed by residues 303 - 314 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A VAL* 3.6 1.8 - - - -
264A LEU* 5.9 0.9 - - - +
301A LEU* 3.3 1.2 - - - +
302A ILE* 1.3 89.0 - - + +
304A TYR* 1.3 67.9 + - - +
305A LEU* 4.6 2.2 - - + +
306A VAL* 2.9 29.2 + - + +
307A GLN* 2.8 22.2 + - - +
28B LYS* 5.9 0.7 + - - -
63B MET* 4.5 9.5 - - - +
64B PRO* 3.6 24.8 - - + +
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Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 4.8 14.6 - + - -
237A ILE* 3.6 32.8 - - + +
250A LEU* 2.7 40.1 + - - +
251A LYS 4.6 0.9 - - - -
253A ILE* 3.8 3.6 - - + -
254A TYR* 3.7 26.9 - + - -
261A VAL* 3.2 20.8 - - - +
262A LYS 3.6 17.2 + - - +
263A PRO* 3.5 42.4 - - + -
264A LEU* 4.9 3.1 - - + +
267A GLN* 4.8 4.5 - - + -
271A ILE* 5.1 2.4 - - + +
302A ILE 3.8 0.4 + - - -
303A GLU* 1.3 70.0 - - - +
305A LEU* 1.3 72.2 + - + +
307A GLN* 3.2 2.3 + - - +
308A ALA* 2.8 31.3 + - + +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL 4.9 1.0 - - - +
97A ILE* 5.8 2.4 - - + +
98A SER* 3.8 27.1 - - - +
102A PHE* 5.6 1.8 - - + -
237A ILE* 6.0 1.6 - - + -
264A LEU* 5.7 3.6 - - + -
267A GLN* 4.1 33.0 - - + +
303A GLU* 3.3 2.5 - - + +
304A TYR* 1.3 88.3 - - + +
306A VAL* 1.3 59.8 + - + +
308A ALA* 3.7 7.2 - - + +
309A ALA* 3.0 27.9 + - - +
63B MET* 4.8 6.5 - - + -
64B PRO* 3.7 26.9 - - + +
65B PHE* 3.9 11.1 - - + +
66B THR* 3.9 23.1 - - + -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 4.1 27.4 - - + -
303A GLU* 2.9 33.0 + - + +
305A LEU* 1.3 74.5 - - - +
307A GLN* 1.3 68.0 + - - +
309A ALA 3.2 1.2 + - - -
310A TYR* 3.0 20.1 + - - +
338A GLY 5.7 1.6 - - - -
339A LEU* 3.5 25.7 - - + +
64B PRO* 3.7 26.9 - - + -
65B PHE* 3.9 13.7 - - + -
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Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.7 34.5 - - + -
261A VAL* 4.2 7.0 - - + +
297A ILE* 3.7 16.4 - - - +
298A ASN* 2.9 35.8 + - - +
301A LEU* 2.8 38.0 + - - +
303A GLU 2.8 11.7 + - - +
304A TYR 3.5 7.4 - - - +
306A VAL* 1.3 76.2 - - - +
308A ALA* 1.3 56.5 + - - +
310A TYR* 3.3 2.4 + - - +
311A GLN* 3.0 60.8 + - - +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.5 9.1 - - + +
236A ASP* 4.6 1.7 - - - +
237A ILE* 3.7 26.6 - - + +
254A TYR* 3.2 22.1 + - + +
304A TYR* 2.8 19.4 + - + +
305A LEU* 3.7 11.0 - - + +
307A GLN* 1.3 76.0 - - - +
309A ALA* 1.3 63.3 + - - +
311A GLN* 3.6 1.4 + - - +
312A HIS* 3.1 25.5 + - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 3.6 28.9 - - + +
97A ILE* 4.3 4.7 - - - +
305A LEU 3.0 18.5 + - - +
306A VAL 3.2 4.0 + - - +
308A ALA* 1.3 75.7 - - - +
310A TYR* 1.3 65.2 + - - +
312A HIS* 4.5 1.1 - - - -
313A VAL* 3.0 29.8 + - - +
339A LEU* 4.0 12.9 - - + +
65B PHE* 4.0 19.5 - - + -
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ASN 5.1 3.1 - - - -
298A ASN* 3.7 30.7 + - + -
301A LEU* 3.4 31.0 - - + -
306A VAL 3.0 6.0 + - - +
307A GLN* 3.6 6.5 - - - +
308A ALA 3.2 0.2 - - - -
309A ALA* 1.3 77.8 - - - +
311A GLN* 1.3 79.2 - - - +
314A VAL* 2.7 65.9 + - + +
315A GLY* 2.9 11.4 + - - -
318A GLU* 2.7 37.0 + - - -
323A MET* 5.2 0.7 - - - +
339A LEU* 3.9 21.1 - - + +
340A LEU* 5.3 2.9 - - - -
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASN* 2.9 39.4 + - - +
235A LEU* 3.6 40.3 - - - +
236A ASP* 4.1 3.4 - - - -
254A TYR* 4.0 7.0 - - + +
295A GLY* 4.6 0.3 - - - -
296A ASN 3.1 30.5 + - - +
297A ILE* 3.9 1.6 - - - +
298A ASN 3.9 0.6 - - - +
307A GLN* 3.0 43.1 + - - +
308A ALA 4.0 3.6 - - - +
309A ALA 3.4 0.2 - - - -
310A TYR* 1.3 89.7 - - - +
312A HIS* 1.3 60.5 + - - +
315A GLY* 3.4 14.5 - - - +
316A TYR* 3.6 6.8 - - - -
319A LEU* 5.4 0.2 - - - +
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PRO* 3.4 32.5 - - + -
97A ILE* 3.7 6.5 - - + -
100A TRP* 3.9 0.8 - - - -
173A HIS* 2.8 29.0 + + - -
174A SER* 2.9 30.1 + - - -
207A ALA* 3.5 29.6 - - + +
236A ASP* 2.8 32.3 + - - +
238A VAL* 3.4 25.3 - - + +
308A ALA 3.1 18.7 + - - +
309A ALA 4.0 2.9 - - - +
311A GLN* 1.3 78.7 - - - +
313A VAL* 1.3 58.9 + - + +
316A TYR* 3.2 10.3 - - - -
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 2.6 27.9 + - + -
94A PRO* 4.0 25.4 - - + -
95A VAL* 4.0 19.1 - - + +
173A HIS* 4.5 1.6 - - + -
309A ALA 3.0 15.6 + - - +
312A HIS* 1.3 89.2 - - + +
314A VAL* 1.3 71.0 + - + +
315A GLY 3.4 0.2 - - - -
317A PRO* 3.3 6.9 - - - +
328A LEU* 4.5 3.9 - - + +
332A PHE* 3.7 39.0 - - + -
336A ILE* 5.4 5.4 - - + -
339A LEU* 5.2 2.7 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A TYR* 2.7 63.3 + - + +
313A VAL* 1.3 76.4 - - + +
315A GLY* 1.3 63.3 + - - +
317A PRO* 3.1 19.0 - - - +
318A GLU* 3.2 9.5 + - + +
323A MET* 3.9 24.2 - - + -
328A LEU* 4.2 16.6 - - + -
336A ILE* 4.9 7.6 - - + -
339A LEU* 4.6 17.7 - - + -
340A LEU* 5.5 5.8 - - + +
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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