Contacts of the helix formed by residues 264 - 279 (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 LEU 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LYS 3.7 4.6 + - - +
263A PRO* 1.3 78.4 - - - +
265A LEU* 1.3 66.7 + - - +
266A TYR* 3.2 4.9 - - + +
267A GLN* 3.1 26.7 + - - +
268A ARG* 3.0 16.3 + - - +
303A GLU* 5.9 0.4 - - - +
304A TYR* 4.9 2.7 - - + +
305A LEU* 5.7 3.6 - - + -
61B TYR* 4.7 5.2 - - - +
63B MET* 3.7 42.4 - - + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PRO 3.8 0.2 + - - -
264A LEU* 1.3 70.5 - - - +
266A TYR* 1.3 66.1 + - - +
268A ARG* 3.1 26.2 + - + +
269A ALA 2.9 19.6 + - - -
131B TYR* 3.6 30.1 + - + +
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 5.1 1.0 + - - -
264A LEU* 3.2 4.1 - - + +
265A LEU* 1.3 79.0 - - - +
267A GLN* 1.3 83.0 + - - +
269A ALA* 3.3 4.3 + - - +
270A LEU* 3.1 38.1 + - + +
66B THR* 5.7 1.1 - - - -
68B PHE* 3.8 30.5 + + + +
69B ASN* 3.4 33.9 - - - +
104B ASP* 4.0 7.6 + - - -
106B MET* 3.3 31.3 - - + +
128B SER* 4.4 11.7 + - - -
131B TYR* 3.7 45.1 - + + -
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 2.9 27.9 + - - +
102A PHE* 4.2 13.2 - - + -
263A PRO* 4.1 14.6 - - + -
264A LEU* 3.1 33.7 + - - +
266A TYR* 1.3 98.8 - - - +
268A ARG* 1.3 59.4 + - - +
270A LEU* 3.2 7.5 + - - +
271A ILE* 2.8 35.0 + - + +
304A TYR* 4.8 5.4 - - + -
305A LEU* 4.1 34.9 - - + +
63B MET* 5.9 0.4 - - - +
66B THR* 5.0 2.6 + - - -
69B ASN* 4.8 6.5 + - - +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LYS* 4.0 30.5 + - + +
255A ILE* 5.8 1.8 - - - +
262A LYS* 4.4 18.4 - - - +
263A PRO* 3.5 39.2 + - + +
264A LEU 3.0 12.6 + - - +
265A LEU* 3.1 33.0 + - + +
267A GLN* 1.3 75.6 - - - +
269A ALA* 1.3 62.6 + - - +
271A ILE* 3.4 9.0 + - - +
272A ARG* 3.1 41.9 + - - +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU 2.9 12.0 + - - +
266A TYR 3.5 9.0 - - - +
268A ARG* 1.3 74.7 - - - +
270A LEU* 1.3 59.5 + - - +
272A ARG* 3.4 21.8 + - - +
273A ALA* 2.9 28.8 + - - +
106B MET* 3.8 17.4 - - + +
127B GLU* 4.1 7.0 - - - +
131B TYR* 3.8 24.5 - - + +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.6 24.0 - - - +
102A PHE* 4.0 26.0 - - + +
103A ASN* 3.7 35.7 - - - +
266A TYR* 3.1 36.0 + - + +
267A GLN* 3.2 9.2 + - - +
269A ALA* 1.3 74.4 - - - +
271A ILE* 1.3 59.7 + - - +
273A ALA* 3.1 2.8 + - - +
274A MET* 2.8 34.8 + - - +
105B PHE* 4.2 7.2 - - + -
106B MET* 3.2 29.4 - - + -
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Residues in contact with ILE 271 (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* 3.4 28.0 - - + -
247A LEU* 4.0 19.5 - - + +
248A LYS* 5.7 0.2 - - - -
250A LEU* 3.4 38.4 - - + -
251A LYS* 5.3 10.5 - - + +
263A PRO* 6.0 3.8 - - + -
267A GLN* 2.8 24.5 + - + +
268A ARG* 3.6 8.7 - - - +
270A LEU* 1.3 75.9 - - - +
272A ARG* 1.3 63.7 + - + +
274A MET* 3.1 10.2 + - - +
275A ILE* 3.0 33.0 + - + +
304A TYR* 5.1 2.7 - - + +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU 5.3 0.2 + - - -
268A ARG* 3.1 35.7 + - - +
269A ALA* 3.8 23.2 - - - +
271A ILE* 1.3 80.4 - - + +
273A ALA* 1.3 57.9 + - - +
275A ILE* 3.3 11.5 + - + +
276A ALA* 2.9 30.2 + - - +
111B LYS* 6.3 0.4 - - - +
127B GLU* 4.3 10.3 + - - -
131B TYR* 4.7 5.5 + - - -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA 2.9 17.8 + - - +
270A LEU 3.1 5.4 + - - +
272A ARG* 1.3 77.2 - - - +
274A MET* 1.3 55.7 + - - +
276A ALA* 3.2 7.0 + - - +
277A GLU* 2.8 35.7 + - + +
105B PHE* 3.8 17.5 - - + -
106B MET* 3.8 16.2 - - + -
108B SER* 3.9 12.3 - - - +
109B ALA* 5.2 7.6 - - + -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.7 1.6 - - + -
102A PHE* 3.4 66.2 - - + +
241A ALA* 4.1 9.0 - - + -
242A TRP* 3.8 24.2 - - + +
247A LEU* 3.6 31.4 - - + -
250A LEU* 4.7 1.1 - - + -
270A LEU 2.8 22.3 + - - +
271A ILE* 3.4 16.2 - - - +
273A ALA* 1.3 72.6 - - - +
275A ILE* 1.3 56.8 + - - +
277A GLU* 3.9 0.8 - - - +
278A THR* 2.7 37.9 + - - +
105B PHE* 3.9 9.6 - - + -
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 4.9 10.1 - - - +
247A LEU* 3.7 26.2 - - + -
248A LYS* 3.6 49.1 - - + +
271A ILE* 3.0 33.1 + - + +
272A ARG* 3.6 13.2 - - + +
274A MET* 1.3 74.1 - - - +
276A ALA* 1.3 67.2 + - - +
278A THR* 3.7 1.3 + - - -
279A LYS* 3.0 30.5 + - + +
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Residues in contact with ALA 276 (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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272A ARG 2.9 17.5 + - - +
273A ALA* 3.5 7.9 - - - +
275A ILE* 1.3 80.6 - - - +
277A GLU* 1.3 68.8 + - - +
278A THR 3.5 0.3 + - - -
279A LYS* 3.6 19.4 + - - +
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Residues in contact with GLU 277 (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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107A VAL* 5.9 1.8 - - + -
108A SER* 3.9 19.8 - - - -
273A ALA* 2.8 19.1 + - - +
274A MET* 4.2 2.0 - - - +
276A ALA* 1.3 80.0 - - - +
278A THR* 1.3 63.2 + - + +
279A LYS 3.5 0.4 - - - -
281A LYS* 3.4 23.1 + - - -
105B PHE* 3.2 35.7 - - + -
108B SER* 4.4 17.7 + - - +
277B GLU* 2.5 29.2 - - - +
281B LYS* 5.5 3.5 + - - -
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Residues in contact with THR 278 (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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107A VAL* 3.8 20.2 - - + +
242A TRP* 3.8 27.3 + - + +
244A THR* 3.9 10.5 - - - +
247A LEU* 3.6 17.3 - - - +
274A MET* 2.7 22.1 + - - +
275A ILE* 3.7 2.3 + - - -
277A GLU* 1.3 80.9 - - + +
279A LYS* 1.3 66.5 + - - +
280A GLY 3.3 0.5 + - - -
281A LYS* 3.1 23.5 + - - +
282A LYS 4.4 0.7 + - - -
283A TYR* 3.9 25.0 + - + +
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Residues in contact with LYS 279 (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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244A THR* 4.3 9.4 - - + -
275A ILE* 3.0 22.0 + - + +
276A ALA* 3.6 15.9 - - - +
277A GLU 3.5 1.2 - - - +
278A THR* 1.3 77.0 - - - +
280A GLY* 1.3 63.1 + - - +
281A LYS* 3.2 11.4 + - - +
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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
------------------------------------------------------------
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