Contacts of the helix formed by residues 256 - 273 (chain A) in PDB entry 1I60
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 3.8 0.7 - - - -
254A LYS 5.8 0.2 - - - +
255A LEU* 1.3 78.8 - - - +
257A ALA* 1.3 67.2 + - - +
258A GLU* 3.7 6.1 + - - +
259A GLU* 2.9 44.3 + - - +
260A ALA* 3.1 19.6 + - - +
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Residues in contact with ALA 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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10A THR* 4.1 5.3 - - + +
13A ASN* 3.5 30.5 + - - +
14A SER* 3.7 17.3 - - - +
18A LEU* 3.7 22.0 - - + -
22A LEU* 3.7 10.1 - - + -
256A THR* 1.3 73.8 - - - +
258A GLU* 1.3 57.9 + - - +
260A ALA* 3.3 2.1 + - - +
261A ILE* 2.9 33.4 + - + +
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Residues in contact with GLU 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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22A LEU* 3.5 28.3 - - + +
25A LYS* 3.0 27.4 + - - +
26A HIS* 2.7 29.6 + - + +
256A THR* 3.2 6.5 + - - +
257A ALA* 1.3 77.3 - - - +
259A GLU* 1.3 60.7 + - + +
261A ILE* 3.7 3.2 - - - +
262A GLN* 2.8 45.8 + - - +
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Residues in contact with GLU 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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255A LEU* 3.6 22.9 - - + +
256A THR* 2.9 47.0 + - - +
258A GLU* 1.3 76.6 - - + +
260A ALA* 1.3 55.5 + - - +
262A GLN* 3.4 6.9 + - - +
263A THR* 2.7 40.1 + - - +
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Residues in contact with ALA 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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9A THR* 4.7 7.0 - - + +
10A THR* 3.8 19.7 - - + -
13A ASN* 4.2 7.6 - - - +
219A TRP* 3.6 13.7 - - + -
252A TYR* 4.5 3.6 - - + +
255A LEU* 4.2 18.5 - - + +
256A THR 3.1 12.9 + - - +
257A ALA 3.6 7.6 - - - +
259A GLU* 1.3 77.7 - - - +
261A ILE* 1.3 57.6 + - - +
263A THR 3.4 0.3 + - - -
264A ALA* 2.9 31.9 + - - +
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Residues in contact with ILE 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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5A PHE* 3.8 24.7 - - + -
10A THR* 4.2 2.2 - - + -
19A ASP* 4.0 21.8 - - - +
22A LEU* 3.5 41.3 - - + +
23A CYS* 4.0 16.8 - - - -
26A HIS* 4.4 6.7 - - + -
28A TYR* 2.7 49.4 + - + +
257A ALA* 2.9 21.9 + - + +
258A GLU* 3.3 5.4 + - - +
260A ALA* 1.3 76.5 - - - +
262A GLN* 1.3 60.5 + - - +
265A LYS* 3.2 7.6 + - - +
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Residues in contact with GLN 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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26A HIS* 3.1 45.7 + - + +
258A GLU* 2.8 35.2 + - - +
259A GLU* 3.9 6.4 + - - +
261A ILE* 1.3 74.8 - - - +
263A THR* 1.3 60.4 + - - +
265A LYS* 3.4 6.7 + - - +
266A LYS* 3.0 29.3 + - - +
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Residues in contact with THR 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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219A TRP* 3.4 40.6 - - + +
222A GLN* 5.4 0.7 - - - +
255A LEU* 5.0 4.4 - - + +
259A GLU* 2.7 24.2 + - - +
260A ALA* 3.9 2.7 - - - -
262A GLN* 1.3 74.6 - - - +
264A ALA* 1.3 63.4 + - - +
266A LYS* 4.5 4.0 - - - +
267A THR* 2.8 37.9 + - + +
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Residues in contact with ALA 264 (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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5A PHE* 4.5 1.8 - - + -
9A THR* 4.3 8.1 - - + -
28A TYR* 3.7 13.7 - - - +
219A TRP* 3.6 22.8 - - + -
245A VAL* 3.8 20.1 - - + +
260A ALA 2.9 18.6 + - - +
261A ILE* 3.8 1.6 - - - +
263A THR* 1.3 78.1 - - - +
265A LYS* 1.3 57.7 + - - +
267A THR* 3.4 2.3 + - - -
268A THR* 2.7 34.8 + - - -
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Residues in contact with LYS 265 (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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3A LEU* 3.4 27.6 - - + -
26A HIS* 2.8 36.9 + - + +
27A GLY* 4.5 6.5 + - - -
28A TYR* 3.2 19.7 + - + +
261A ILE 3.2 9.5 + - - +
262A GLN* 3.6 6.7 - - - +
263A THR 3.2 0.2 - - - -
264A ALA* 1.3 78.0 - - - +
266A LYS* 1.3 61.2 + - - +
268A THR* 3.7 2.6 - - - -
269A VAL* 2.9 40.8 + - + +
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Residues in contact with LYS 266 (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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262A GLN 3.0 17.4 + - - +
263A THR* 4.1 4.7 - - - +
265A LYS* 1.3 78.1 - - - +
267A THR* 1.3 60.0 + - + +
269A VAL* 4.8 3.1 - - - -
270A ASP* 2.9 67.5 + - - +
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Residues in contact with THR 267 (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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219A TRP* 3.8 18.5 - - + +
220A PRO* 3.4 34.8 - - - +
222A GLN* 4.0 13.2 - - + +
263A THR* 2.8 32.4 + - + +
264A ALA* 3.4 5.7 + - - -
266A LYS* 1.3 78.8 - - + +
268A THR* 1.3 63.1 + - - +
270A ASP* 4.1 3.6 - - - +
271A VAL* 3.2 30.8 + - - +
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Residues in contact with THR 268 (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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3A LEU* 3.8 25.6 - - + -
201A ILE* 3.7 21.4 - - + +
220A PRO* 3.7 10.0 - - - +
243A VAL* 4.2 8.5 - - + -
245A VAL* 3.4 21.7 - - + +
264A ALA 2.7 23.2 + - - -
265A LYS 3.7 2.2 - - - -
266A LYS 3.2 0.2 - - - -
267A THR* 1.3 76.8 + - - +
269A VAL* 1.3 63.3 + - - +
271A VAL* 3.1 2.6 + - - +
272A VAL* 2.9 43.9 + - + +
278A MSE 5.2 0.4 - - - +
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Residues in contact with VAL 269 (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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3A LEU* 4.2 22.7 - - + -
265A LYS* 2.9 34.2 + - + +
266A LYS* 4.1 3.1 - - - +
268A THR* 1.3 72.1 - - - +
270A ASP* 1.3 67.6 + - - +
273A SER* 2.7 41.0 + - - +
278A MSE 4.0 31.2 - - + +
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Residues in contact with ASP 270 (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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266A LYS* 2.9 59.2 + - - +
267A THR* 4.1 4.6 - - - +
269A VAL* 1.3 84.9 - - - +
271A VAL* 1.3 62.1 + - + +
273A SER* 3.8 5.7 + - - -
274A LYS* 3.4 31.3 + - - +
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Residues in contact with VAL 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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201A ILE* 4.0 16.2 - - + -
220A PRO 3.7 23.6 - - - +
221A GLY* 4.0 9.4 - - - -
227A LEU* 4.1 13.9 - - + -
228A ASP* 6.0 1.6 - - - +
231A LEU* 3.7 25.5 - - + +
267A THR 3.2 18.7 + - - +
268A THR 3.1 3.8 + - - +
270A ASP* 1.3 77.9 - - + +
272A VAL* 1.3 66.1 + - - +
274A LYS* 3.4 23.4 + - - +
275A TYR* 4.2 1.8 - - + -
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Residues in contact with VAL 272 (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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1A MSE 3.6 29.6 - - - -
201A ILE* 3.7 26.2 - - + -
231A LEU* 4.2 15.9 - - + -
243A VAL* 4.2 9.6 - - + -
268A THR* 2.9 33.1 + - + +
271A VAL* 1.3 67.8 - - - +
273A SER* 1.3 55.6 + - - +
274A LYS 3.0 5.2 - - - -
275A TYR* 3.0 21.3 + - - +
276A PHE* 3.0 22.7 + - + -
278A MSE 3.8 18.6 - - + +
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Residues in contact with SER 273 (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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269A VAL* 2.7 36.8 + - - +
270A ASP* 3.8 7.8 + - - -
272A VAL* 1.3 72.1 - - - +
274A LYS* 1.3 61.4 + - - +
275A TYR 3.1 2.7 + - - -
276A PHE 3.1 21.8 + - - +
277A SER* 5.3 0.6 - - - -
278A MSE 3.9 15.1 - - - +
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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