Contacts of the helix formed by residues 260 - 271 (chain A) in PDB entry 2HU2
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A HIS* 3.1 37.4 + - - +
236A ILE 2.9 20.1 + - - +
237A ASN* 3.9 8.9 - - - +
238A ASP* 4.3 10.8 - - - +
258A LEU 4.3 0.6 - - - -
259A VAL* 1.3 70.9 - - - +
261A GLU* 1.3 58.2 + - - +
262A LYS* 3.0 34.0 + - - +
263A ALA* 3.2 19.4 + - + +
264A LEU* 2.9 27.4 + - - +
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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
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256A GLY 5.0 0.6 - - - +
259A VAL* 4.1 10.3 - - + +
260A ASP* 1.3 70.3 + - - +
262A LYS* 1.3 59.3 + - - +
264A LEU* 3.9 7.9 - - + +
265A ALA* 2.9 30.3 + - - +
278A LEU* 5.7 1.5 - - + +
281A HIS* 3.4 14.5 - - - +
282A GLU* 2.7 55.2 + - + +
283A SER* 4.3 2.2 + - - -
286A PHE* 5.5 3.0 - - - -
291A GLY* 5.3 0.2 - - - -
292A PRO* 3.6 33.3 - - + +
293A LEU* 3.7 31.8 + - + +
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Residues in contact with LYS 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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234A HIS* 5.5 3.0 - - - -
238A ASP* 5.7 2.1 + - - +
260A ASP* 3.0 25.4 + - - +
261A GLU* 1.3 77.6 - - - +
263A ALA* 1.3 61.3 + - - +
265A ALA* 3.8 3.3 - - - +
266A GLN* 3.2 23.7 + - - +
282A GLU* 5.0 0.2 + - - -
292A PRO* 3.7 26.4 - - + +
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Residues in contact with ALA 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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237A ASN 3.9 19.5 - - - +
238A ASP* 3.5 25.2 + - - +
241A VAL* 4.2 12.3 - - + +
260A ASP* 3.2 25.8 + - + +
262A LYS* 1.3 76.4 - - - +
264A LEU* 1.3 65.9 + - - +
266A GLN* 3.6 5.6 + - - +
267A ALA* 3.0 24.3 + - - +
272A ARG* 5.0 0.9 + - - -
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Residues in contact with LEU 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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236A ILE* 6.2 0.4 - - + -
241A VAL* 5.0 4.0 - - + +
250A LEU* 3.9 17.9 - - + -
259A VAL* 3.9 21.8 - - + -
260A ASP 2.9 16.8 + - - +
261A GLU* 3.9 7.0 - - + +
262A LYS 3.4 0.2 - - - -
263A ALA* 1.3 73.4 - - - +
265A ALA* 1.3 64.6 + - - +
267A ALA* 3.2 5.2 + - - +
268A LEU* 2.9 46.2 + - + +
273A ILE* 3.8 26.2 - - + -
276A ALA* 4.2 12.1 - - + -
278A LEU* 4.0 29.8 - - + -
293A LEU* 4.2 10.5 - - + -
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Residues in contact with ALA 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 2.9 19.0 + - - +
262A LYS* 3.8 5.8 - - - +
264A LEU* 1.3 76.0 - - - +
266A GLN* 1.3 63.7 + - - +
268A LEU* 3.1 5.7 + - - +
269A LYS* 3.0 24.8 + - - +
292A PRO* 3.4 24.5 - - + +
293A LEU* 4.4 3.7 - - - +
296A ALA* 4.2 21.9 - - + +
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Residues in contact with GLN 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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238A ASP* 5.9 1.6 - - - +
262A LYS 3.2 14.2 + - - +
263A ALA* 3.8 6.7 - - - +
265A ALA* 1.3 77.7 - - - +
267A ALA* 1.3 61.6 + - - +
269A LYS* 3.5 11.5 + - - +
270A GLU* 2.8 53.4 + - - +
272A ARG* 3.5 10.5 - - - +
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Residues in contact with ALA 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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241A VAL* 3.8 13.5 - - + -
263A ALA 3.0 18.8 + - - +
264A LEU 3.2 4.7 + - - +
266A GLN* 1.3 76.0 - - - +
268A LEU* 1.3 57.8 + - - +
271A GLY 3.1 6.6 + - - -
272A ARG* 3.0 54.5 + - - +
273A ILE* 3.2 24.9 + - + +
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Residues in contact with LEU 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 LEU* 2.9 44.0 + - + +
265A ALA 3.1 3.8 + - - +
267A ALA* 1.3 75.4 - - - +
269A LYS* 1.3 64.4 + - - +
271A GLY* 3.6 9.7 + - - -
273A ILE* 3.7 33.5 - - + +
274A ARG 4.6 1.1 - - - -
275A GLY* 3.9 6.3 - - - -
276A ALA* 3.9 3.8 - - + +
293A LEU* 4.3 2.0 - - + -
296A ALA* 4.1 16.4 - - + -
297A PRO* 3.6 25.2 - - - +
298A ASN* 3.5 28.1 - - + +
299A LEU* 3.8 22.4 - - + -
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Residues in contact with LYS 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 ALA 3.0 15.2 + - - +
266A GLN* 3.9 13.0 - - - +
268A LEU* 1.3 78.9 - - - +
270A GLU* 1.3 62.9 + - + +
271A GLY* 3.5 0.7 + - - -
295A ASP 5.1 7.8 + - - -
296A ALA* 5.6 2.0 - - + +
297A PRO* 3.9 26.9 - - + +
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Residues in contact with GLU 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 GLN* 2.8 46.4 + - - +
267A ALA 4.3 0.2 - - - +
269A LYS* 1.3 81.7 - - + +
271A GLY* 1.3 58.8 + - - +
272A ARG* 2.9 40.6 + - + +
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Residues in contact with GLY 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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246A GLN* 5.0 5.4 - - - +
247A GLY* 4.0 13.5 + - - -
267A ALA 3.1 5.7 + - - -
268A LEU 3.6 7.8 + - - -
269A LYS 3.3 3.7 - - - -
270A GLU* 1.3 78.1 - - - +
272A ARG* 1.3 64.7 + - - +
273A ILE 3.3 8.8 + - - -
274A ARG* 4.3 3.6 + - - +
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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