Contacts of the helix formed by residues 258 - 273 (chain A) in PDB entry 1Q0W
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 ASP 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A TYR 4.2 3.7 + - - +
256A PRO 5.5 1.2 - - - -
257A GLU* 1.3 76.4 + - - +
259A GLU* 1.3 76.5 + - - +
261A GLU* 3.0 24.0 - - - +
262A LEU* 2.9 31.7 + - - +
73B LEU* 3.6 31.1 - - - +
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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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257A GLU* 3.0 1.9 - - - -
258A ASP* 1.3 85.5 + - - +
260A GLU* 1.3 58.6 + - - +
262A LEU* 3.3 8.6 + - - +
263A ILE* 3.0 34.8 + - + +
42B ARG* 5.7 1.7 + - - -
70B VAL* 3.3 18.8 - - - +
71B LEU 2.6 32.5 - - - +
72B ARG* 3.1 15.9 + - + +
73B LEU* 3.5 36.2 + - + +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 3.1 31.0 + - + +
259A GLU* 1.3 78.2 - - - +
261A GLU* 1.3 67.0 + - - +
263A ILE* 3.1 32.1 + - - +
264A ARG* 3.1 16.0 + - + +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR* 5.2 11.6 + - - +
257A GLU 3.1 5.8 + - - +
258A ASP* 3.0 37.3 - - - +
260A GLU* 1.3 80.9 - - - +
262A LEU* 1.3 57.8 + - + +
264A ARG* 3.0 16.8 - - + +
265A LYS* 2.7 56.3 + - + +
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Residues in contact with LEU 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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258A ASP 2.9 21.9 + - - +
259A GLU* 3.4 9.4 - - - +
261A GLU* 1.3 78.0 - - + +
263A ILE* 1.3 62.4 + - - +
265A LYS* 3.2 30.6 + - + +
266A ALA* 3.0 20.1 + - + +
8B LEU* 3.4 50.7 - - + -
70B VAL* 3.8 26.9 - - + -
71B LEU 5.8 0.2 - - - +
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Residues in contact with ILE 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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259A GLU* 3.0 19.2 + - + +
260A GLU* 3.1 27.5 + - - +
262A LEU* 1.3 77.4 - - - +
264A ARG* 1.3 63.8 + - + +
266A ALA 3.3 0.3 + - - -
267A ILE* 3.0 29.3 + - + +
42B ARG* 3.4 31.0 - - - +
44B ILE* 3.1 22.9 - - + +
49B GLN* 3.8 21.5 - - + +
70B VAL* 3.4 25.1 - - + -
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 3.1 12.1 + - + +
261A GLU* 3.0 26.8 - - - +
263A ILE* 1.3 78.9 - - + +
265A LYS* 1.3 89.1 + - - +
267A ILE* 2.8 21.3 + - + +
268A GLU* 2.8 58.1 + - + +
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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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261A GLU* 2.7 51.8 + - + +
262A LEU* 3.2 30.2 + - + +
264A ARG* 1.3 83.2 - - - +
266A ALA* 1.3 63.3 + - - +
268A GLU* 3.4 10.6 + - - +
269A LEU* 3.1 33.5 + - + +
8B LEU* 6.3 0.4 - - + -
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Residues in contact with ALA 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 LEU* 3.0 15.2 + - + +
263A ILE 3.6 8.1 - - - +
265A LYS* 1.3 73.4 - - - +
267A ILE* 1.3 67.4 + - - +
269A LEU* 3.2 7.1 + - + +
270A SER* 2.9 14.0 + - - -
8B LEU* 5.1 7.6 - - + +
44B ILE* 4.2 9.2 - - + -
68B HIS* 2.8 49.9 + - + +
70B VAL* 4.3 6.7 - - + -
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Residues in contact with ILE 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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263A ILE* 3.0 25.3 + - + +
264A ARG* 2.8 29.5 + - + +
266A ALA* 1.3 77.4 - - - +
268A GLU* 1.3 60.2 + - + +
270A SER* 3.5 2.5 + - - -
271A LEU* 3.0 39.5 + - + +
44B ILE* 3.6 24.0 - - + +
47B GLY* 3.4 29.1 - - - +
49B GLN* 3.1 25.4 - - - +
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Residues in contact with GLU 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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264A ARG* 2.8 53.3 + - + +
265A LYS* 3.8 10.4 - - - +
267A ILE* 1.3 72.5 - - + +
269A LEU* 1.3 67.8 + - + +
271A LEU* 3.2 13.4 + - + +
272A LYS* 3.0 31.7 + - + +
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Residues in contact with LEU 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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265A LYS* 3.1 21.7 + - + +
266A ALA* 3.6 8.5 - - + +
268A GLU* 1.3 79.9 - - + +
270A SER* 1.3 62.3 + - - +
272A LYS* 3.4 16.6 + - + +
273A GLU* 3.5 19.6 + - - +
6B LYS* 6.0 3.6 - - - +
8B LEU* 6.1 4.9 - - + -
68B HIS* 3.6 16.4 - - + +
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Residues in contact with SER 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 ALA 2.9 11.4 + - - -
267A ILE* 3.8 5.4 - - - -
269A LEU* 1.3 73.1 - - - +
271A LEU* 1.3 66.6 + - - +
273A GLU* 3.1 10.6 + - - +
274A SER* 3.0 23.5 + - - -
44B ILE 4.9 0.7 - - - -
45B PHE* 3.4 22.4 - - - -
46B ALA* 3.4 24.1 + - - -
66B THR 5.2 0.5 + - - -
68B HIS* 3.2 28.4 + - - -
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Residues in contact with LEU 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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267A ILE* 3.0 41.7 + - + +
268A GLU* 3.2 11.9 + - + +
270A SER* 1.3 75.5 - - - +
272A LYS* 1.3 65.6 + - + +
274A SER* 3.4 22.7 + - - +
275A ARG* 3.4 4.3 + - - +
46B ALA* 3.5 11.4 - - - +
47B GLY* 3.3 26.2 - - - +
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Residues in contact with LYS 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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268A GLU* 3.0 24.3 + - + +
269A LEU* 3.5 12.6 - - + +
270A SER 3.2 0.2 - - - -
271A LEU* 1.3 79.2 - - + +
273A GLU* 1.3 64.0 + - + +
275A ARG* 3.3 25.6 + - - +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 3.6 15.6 - - - +
270A SER* 3.1 10.8 + - - +
272A LYS* 1.3 72.8 - - + +
274A SER* 1.3 59.7 + - - +
275A ARG* 2.9 32.7 + - - +
276A ASN* 3.8 6.1 - - - +
278A ALA* 3.9 2.8 - - - +
6B LYS* 6.0 2.3 - - - +
66B THR* 4.9 13.2 - - - +
68B HIS* 4.7 12.3 + - - -
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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