Contacts of the helix formed by residues 247 - 263 (chain A) in PDB entry 2OO3
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 THR 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 5.1 2.3 - - - -
245A PRO 3.3 1.2 + - - -
246A TYR* 1.3 117.0 + - + +
248A PHE* 1.3 64.1 + - - +
249A PRO* 3.5 6.0 - - - +
250A SER* 3.3 14.3 + - - +
251A GLU* 3.1 36.7 + - - +
279A CYS 5.7 2.6 + - - -
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Residues in contact with PHE 248 (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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21A THR* 3.8 11.9 - - + -
24A ARG* 4.2 20.6 - - + -
25A LEU* 4.0 20.6 - - + -
220A VAL* 4.0 18.6 - - + -
222A ILE* 4.6 4.3 - - + -
241A ILE* 3.4 31.9 - - + -
244A PRO* 4.3 5.2 - - + -
245A PRO* 3.1 31.2 + - + +
246A TYR 3.2 2.4 + - - -
247A THR* 1.3 75.6 + - - +
249A PRO* 1.4 68.2 - - + +
251A GLU* 3.3 9.8 + - + +
252A ILE* 2.8 72.8 + - + +
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 4.6 17.3 - - + -
244A PRO* 5.1 1.6 - - + -
245A PRO 3.7 7.9 - - - +
247A THR* 3.7 4.9 - - - +
248A PHE* 1.4 97.6 - - + +
250A SER* 1.3 59.6 + - - +
252A ILE* 3.2 23.1 - - + +
253A LYS* 3.3 11.3 + - - +
272A ILE* 3.9 12.1 - - + +
274A SER* 5.8 2.9 - - - -
278A LEU* 4.1 24.7 - - + -
279A CYS* 4.6 12.3 - - - +
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A THR* 3.3 19.2 + - - +
248A PHE 3.3 0.4 - - - -
249A PRO* 1.3 76.7 - - - +
251A GLU* 1.3 67.2 + - - +
253A LYS* 3.5 11.3 + - - +
254A LEU* 3.4 16.5 + - - +
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Residues in contact with GLU 251 (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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24A ARG* 2.9 38.2 + - - +
78A LEU* 3.3 43.5 - - + +
247A THR* 3.1 32.9 + - - +
248A PHE* 3.7 11.2 - - + +
250A SER* 1.3 76.1 + - - +
252A ILE* 1.3 64.2 + - + +
254A LEU 3.1 11.6 + - - -
255A VAL* 3.1 11.0 + - - +
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Residues in contact with ILE 252 (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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17A ILE* 4.4 4.5 - - + -
20A ILE* 5.3 0.2 - - + -
21A THR* 3.7 27.1 - - - +
24A ARG* 4.9 5.4 - - + -
222A ILE* 3.7 41.7 - - + -
248A PHE* 2.8 42.7 + - + +
249A PRO* 3.2 18.4 - - + +
251A GLU* 1.3 73.6 - - + +
253A LYS* 1.3 58.5 + - - +
255A VAL* 3.2 18.7 + - + +
256A LEU* 2.9 39.2 + - + +
272A ILE* 4.0 8.5 - - + -
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Residues in contact with LYS 253 (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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249A PRO 3.3 5.8 + - - +
250A SER* 3.6 13.7 - - - +
251A GLU 3.2 0.2 - - - -
252A ILE* 1.3 78.9 - - - +
254A LEU* 1.3 60.8 + - - +
256A LEU* 3.4 3.3 + - - +
257A GLU* 2.7 63.6 + - - +
270A TYR* 3.4 22.6 + - - +
272A ILE* 3.4 25.1 - - + -
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Residues in contact with LEU 254 (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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76A PRO* 4.0 25.8 - - + -
78A LEU* 3.8 23.1 - - + -
79A PHE* 6.0 0.2 - - + -
250A SER 3.4 7.3 + - - +
251A GLU 3.1 9.7 + - - +
253A LYS* 1.3 75.2 - - - +
255A VAL* 1.3 66.8 + - - +
257A GLU* 3.7 15.6 - - + +
258A THR* 3.0 38.8 + - - +
303A SO4 4.6 8.5 - - - +
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Residues in contact with VAL 255 (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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17A ILE* 4.0 12.8 - - + -
20A ILE* 3.8 32.8 - - + -
24A ARG* 4.7 4.3 - - - -
78A LEU* 4.1 23.1 - - + -
79A PHE* 4.0 17.4 - - + -
251A GLU 3.1 13.6 + - - +
252A ILE* 3.2 17.7 + - + +
254A LEU* 1.3 76.1 - - - +
256A LEU* 1.3 57.5 + - - +
258A THR* 3.1 5.2 + - - -
259A LEU* 2.9 46.2 + - + +
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Residues in contact with LEU 256 (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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17A ILE* 3.5 34.5 - - + -
222A ILE* 4.1 19.7 - - + -
223A GLU 4.2 13.2 - - - +
224A LEU* 4.3 15.4 - - + +
252A ILE* 2.9 24.6 + - + +
253A LYS 4.0 1.1 - - - +
255A VAL* 1.3 74.2 - - - +
257A GLU* 1.3 65.2 + - - +
259A LEU* 3.3 5.8 + - + +
260A THR* 3.1 27.9 + - - +
270A TYR* 3.6 35.2 - - + -
271A MET 4.1 3.4 - - - +
272A ILE* 3.8 19.1 - - + -
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Residues in contact with GLU 257 (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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253A LYS* 2.7 57.1 + - - +
254A LEU* 3.7 16.5 - - + +
256A LEU* 1.3 74.5 - - - +
258A THR* 1.3 63.4 + - - +
260A THR* 2.8 23.3 + - - -
261A THR* 3.5 11.4 - - - +
270A TYR* 3.6 23.2 + - + +
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Residues in contact with THR 258 (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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75A LEU* 4.1 1.3 - - + -
76A PRO* 3.4 34.0 - - + +
79A PHE* 3.8 20.8 - - + -
254A LEU* 3.0 21.0 + - - +
255A VAL 3.1 7.8 + - - -
257A GLU* 1.3 75.5 - - - +
259A LEU* 1.3 62.2 + - - +
261A THR* 2.6 31.8 + - - +
262A TYR* 3.3 26.4 - - + +
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Residues in contact with LEU 259 (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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16A VAL* 3.8 22.7 - - + -
17A ILE* 4.0 33.4 - - + -
20A ILE* 4.3 1.1 - - + -
68A VAL* 4.0 12.8 - - + -
79A PHE* 3.8 22.4 - - + -
224A LEU* 4.3 8.5 - - + -
255A VAL* 2.9 39.9 + - + +
256A LEU* 3.8 6.5 - - + +
258A THR* 1.3 72.9 - - - +
260A THR* 1.3 58.4 + - - +
262A TYR* 2.9 7.6 + - + +
263A PHE* 2.8 52.2 + - + -
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Residues in contact with THR 260 (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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224A LEU* 3.9 19.1 - - + -
256A LEU 3.1 14.2 + - - +
257A GLU* 2.8 21.8 + - - -
259A LEU* 1.3 75.7 - - - +
261A THR* 1.3 61.6 + - - +
263A PHE 3.5 2.1 - - - +
265A PRO* 3.5 15.2 - - - +
266A GLY 4.6 0.9 + - - -
268A SER* 3.0 34.4 + - - +
269A SER* 4.0 21.1 - - - +
270A TYR* 4.1 10.8 - - + -
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Residues in contact with THR 261 (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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257A GLU 3.5 15.5 - - - +
258A THR* 2.6 21.8 + - - +
260A THR* 1.3 79.7 - - - +
262A TYR* 1.3 72.4 + - - +
265A PRO* 3.5 22.5 - - - +
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Residues in contact with TYR 262 (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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67A PRO* 3.7 34.5 - - + +
68A VAL* 4.3 14.6 - - + -
71A ASP* 2.5 45.6 + - + -
74A ASN* 4.6 5.4 + - - +
75A LEU* 3.4 32.4 - - + +
258A THR* 3.3 30.6 - - + +
259A LEU* 2.9 7.6 + - + +
261A THR* 1.3 91.6 + - - +
263A PHE* 1.3 78.0 + - + +
264A ASN 3.7 2.1 + - - -
265A PRO* 3.9 8.1 - - - +
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Residues in contact with PHE 263 (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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13A PHE* 3.9 21.1 - - + -
16A VAL* 4.1 21.1 - - + -
63A GLU 3.4 22.9 - - - -
64A GLY* 3.2 29.8 - - - -
67A PRO* 5.1 2.5 - - + -
68A VAL* 4.1 7.6 - - + -
224A LEU* 3.9 25.6 - - + -
226A LEU* 3.6 18.6 - - + -
259A LEU* 2.8 44.7 + - + +
260A THR* 3.5 1.1 - - - +
262A TYR* 1.3 83.1 - - + +
264A ASN* 1.3 62.6 + - - +
265A PRO 3.3 0.6 - - - -
268A SER* 2.6 35.3 + - - +
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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