Contacts of the helix formed by residues 264 - 279 (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 LEU 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.6 4.7 - - - +
63A MET* 3.7 47.1 - - + -
262B LYS* 4.5 8.1 - - - +
263B PRO* 1.3 76.4 - - - +
265B LEU* 1.3 79.9 + - + +
266B TYR 3.4 1.8 - - - +
267B GLN* 3.2 25.7 + - + +
268B ARG* 3.0 23.0 + - - +
303B GLU* 5.9 5.6 - - + +
304B TYR* 4.8 4.9 - - + +
305B LEU* 6.1 2.9 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 5.1 12.3 - - + +
131A TYR* 4.6 16.4 - - + -
135A THR* 5.6 7.4 - - + -
138A LYS* 2.9 35.4 - - - +
264B LEU* 1.3 89.7 - - + +
266B TYR* 1.3 65.6 + - + +
268B ARG* 3.5 28.4 + - - +
269B ALA* 3.2 21.5 + - - +
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.6 32.9 + + + +
69A ASN* 3.4 48.5 + - + +
106A MET* 3.9 20.0 - - + -
128A SER 4.6 2.3 + - - -
131A TYR* 3.2 23.5 + + + -
132A GLY* 3.2 31.9 + - - -
135A THR* 3.2 26.5 + - + +
264B LEU* 3.4 1.4 - - - +
265B LEU* 1.3 79.5 - - + +
267B GLN* 1.3 75.2 + - - +
269B ALA* 3.2 3.8 + - - +
270B LEU* 2.8 33.9 + - + +
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Residues in contact with GLN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.7 3.6 + - - -
63A MET* 5.4 2.4 - - - +
66A THR* 4.6 6.2 + - - +
69A ASN* 4.5 3.5 + - - -
98B SER* 2.8 26.0 + - - +
102B PHE* 4.3 11.4 - - + -
263B PRO* 4.2 12.3 - - + -
264B LEU* 3.2 35.0 + - + +
266B TYR* 1.3 87.6 - - - +
268B ARG* 1.3 57.1 + - - +
270B LEU* 3.8 12.3 - - - +
271B ILE* 2.9 37.0 + - + +
304B TYR* 4.6 5.8 - - + -
305B LEU* 3.8 38.6 - - + +
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LYS* 5.2 15.0 - - + +
262B LYS* 3.6 31.1 - - - +
263B PRO* 3.0 34.8 + - + +
264B LEU* 3.0 12.1 + - - +
265B LEU* 3.6 42.0 + - - +
267B GLN* 1.3 74.2 - - - +
269B ALA* 1.3 65.9 + - - +
271B ILE* 3.4 7.3 + - - +
272B ARG* 3.0 23.6 + - - +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 3.8 20.5 - - + +
127A GLU* 5.7 2.2 - - - +
131A TYR* 3.8 32.3 - - + +
265B LEU 3.2 11.1 + - - +
266B TYR* 3.2 9.1 + - - +
268B ARG* 1.3 75.9 - - - +
270B LEU* 1.3 67.9 + - - +
272B ARG* 3.1 11.7 + - - +
273B ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 4.0 18.8 - - - +
105A PHE* 5.1 10.8 - - + +
106A MET* 4.4 20.0 - - + -
98B SER* 3.6 24.2 - - - +
102B PHE* 4.1 22.9 - - + +
103B ASN* 3.3 33.0 - - - +
266B TYR* 2.8 20.8 + - + +
267B GLN* 3.8 11.4 - - - +
269B ALA* 1.3 76.9 - - - +
271B ILE* 1.3 56.3 + - - +
273B ALA* 3.2 5.7 + - - +
274B MET* 2.9 33.3 + - - +
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 3.7 25.8 - - + -
247B LEU* 4.0 21.3 - - + +
250B LEU* 3.8 31.2 - - + -
251B LYS* 4.5 13.5 - - + +
263B PRO* 5.0 2.7 - - + -
267B GLN 2.9 27.8 + - - +
268B ARG* 3.7 7.4 - - - +
269B ALA 3.2 0.2 - - - -
270B LEU* 1.3 75.3 - - - +
272B ARG* 1.3 63.7 + - - +
274B MET* 3.4 12.7 + - + +
275B ILE* 3.2 30.3 + - + +
304B TYR* 3.9 16.6 - - + +
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 5.2 3.0 - - - +
111A LYS* 4.5 7.1 - - - +
127A GLU* 2.9 32.5 + - - -
131A TYR* 5.2 6.2 + - - -
268B ARG 3.0 14.2 + - - +
269B ALA* 3.1 12.1 + - - +
271B ILE* 1.3 78.7 - - - +
273B ALA* 1.3 56.5 - - - +
275B ILE* 3.3 11.9 + - + +
276B ALA* 3.0 26.7 + - + +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.9 32.8 - - + +
106A MET* 5.0 7.6 - - + +
108A SER* 5.6 0.4 - - - +
109A ALA* 6.5 0.7 - - + -
127A GLU* 5.8 3.4 - - - +
269B ALA 3.0 12.4 + - - +
270B LEU* 3.7 8.7 - - - +
272B ARG* 1.3 74.3 - - - +
274B MET* 1.3 55.8 + - - +
276B ALA* 3.1 6.6 + - - +
277B GLU* 2.8 45.2 + - + +
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.3 11.7 - - + -
101B LEU* 4.6 1.3 - - + +
102B PHE* 3.6 56.8 - - + +
241B ALA* 4.2 8.7 - - + -
242B TRP* 3.3 44.6 - - + -
247B LEU* 3.8 24.9 - - + -
250B LEU* 5.0 1.6 - - + -
270B LEU 2.9 19.6 + - - +
271B ILE* 3.6 16.2 - - - +
273B ALA* 1.3 75.6 - - - +
275B ILE* 1.3 63.3 + - - +
277B GLU 3.9 0.2 - - - -
278B THR* 2.9 32.1 + - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B THR* 4.5 11.8 + - + -
247B LEU* 3.7 44.4 - - + +
248B LYS* 3.9 38.4 - - + -
271B ILE* 3.2 21.9 + - + +
272B ARG* 3.4 12.1 - - + +
274B MET* 1.3 77.2 - - - +
276B ALA* 1.3 64.4 + - - +
278B THR* 3.9 0.9 + - - -
279B LYS* 3.1 28.0 + - + +
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Residues in contact with ALA 276 (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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272B ARG 3.0 14.0 + - - +
273B ALA* 3.1 9.8 + - - +
275B ILE* 1.3 79.9 - - - +
277B GLU* 1.3 73.4 + - - +
278B THR 3.2 1.0 + - - -
279B LYS* 3.2 17.4 + - - +
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Residues in contact with GLU 277 (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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105A PHE* 3.4 33.7 - - + -
108A SER* 3.1 26.2 + - - +
109A ALA* 6.1 0.2 - - - +
277A GLU* 2.5 32.8 - - - +
105B PHE* 4.9 3.5 - - + -
108B SER* 4.6 12.8 - - - -
273B ALA* 2.8 26.5 + - + +
274B MET 4.1 0.7 - - - +
276B ALA* 1.3 80.9 - - - +
278B THR* 1.3 63.1 + - + +
279B LYS 4.9 0.4 - - - +
281B LYS* 3.9 21.1 + - - -
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Residues in contact with THR 278 (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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105A PHE* 5.4 0.2 - - + -
107B VAL* 3.8 32.5 - - + +
242B TRP* 3.7 25.2 + - + +
244B THR* 3.8 8.2 + - - -
247B LEU* 3.7 9.0 - - - +
274B MET 2.9 20.5 + - - +
275B ILE 4.0 1.4 + - - -
277B GLU* 1.3 83.6 - - + +
279B LYS* 1.3 65.5 + - - +
280B GLY 3.3 0.5 + - - -
281B LYS* 3.1 23.3 + - - +
282B LYS 4.1 2.1 + - - -
283B TYR* 4.0 25.4 + - + -
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Residues in contact with LYS 279 (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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244B THR* 3.8 23.8 - - + +
248B LYS* 5.4 8.6 - - - +
275B ILE* 3.1 22.0 + - + +
276B ALA* 3.2 13.2 + - - +
277B GLU 4.9 0.3 - - - +
278B THR* 1.3 77.8 - - - +
280B GLY* 1.3 63.2 + - - +
281B LYS* 3.2 9.2 + - - +
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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
------------------------------------------------------------
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