Contacts of the helix formed by residues 265 - 276 (chain A) in PDB entry 1MHP
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 ARG 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ALA* 4.1 14.6 - - + +
228A LEU* 3.3 46.2 - - - +
231A ASP* 3.4 30.3 + - - +
262A ASP* 3.5 11.5 + - + +
264A TYR* 1.3 77.6 - - + +
266A LEU* 1.3 59.1 + - - +
267A LYS 3.1 2.0 - - - -
268A GLN* 3.4 31.6 + - - +
269A VAL* 3.0 36.7 + - - +
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Residues in contact with LEU 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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226A THR* 4.6 0.7 - - + -
227A ALA* 4.0 20.6 - - - +
230A ILE* 4.0 18.2 - - + -
260A SER* 4.0 13.9 - - - +
262A ASP 3.6 8.7 + - - +
263A ASN* 3.1 17.0 + - - +
265A ARG* 1.3 75.2 - - - +
267A LYS* 1.3 66.3 + - - +
269A VAL* 4.5 3.4 - - + -
270A ILE* 3.1 34.5 + - + +
302A GLU* 3.7 32.3 - - + +
305A SER* 4.9 4.3 - - - +
306A ILE* 3.9 33.2 - - + -
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Residues in contact with LYS 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 ASN 4.2 1.2 + - - +
264A TYR 3.9 11.6 + - - +
266A LEU* 1.3 81.1 - - - +
268A GLN* 1.3 65.6 + - + +
270A ILE* 3.9 3.9 - - - +
271A GLN* 3.1 27.6 + - + +
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Residues in contact with GLN 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 TYR 5.2 0.7 - - - +
265A ARG* 3.4 34.9 + - - +
267A LYS* 1.3 83.4 - - + +
269A VAL* 1.3 65.3 + - + +
271A GLN* 2.9 10.7 - - - +
272A ASP* 2.9 31.6 + - - +
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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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227A ALA* 3.8 16.2 - - + +
230A ILE* 3.8 20.6 - - + -
231A ASP* 3.5 47.1 - - + +
234A ARG* 4.9 0.7 - - - +
265A ARG* 3.0 34.2 + - + +
266A LEU* 3.9 7.6 - - + +
268A GLN* 1.3 77.0 - - + +
270A ILE* 1.3 64.4 + - - +
271A GLN 3.0 0.3 + - - -
272A ASP* 3.1 11.6 + - - +
273A CYS* 3.0 23.0 + - - -
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Residues in contact with ILE 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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230A ILE* 4.2 13.0 - - + -
266A LEU* 3.1 23.2 + - + +
267A LYS* 3.9 4.5 - - - +
269A VAL* 1.3 75.5 - - - +
271A GLN* 1.3 62.8 + - - +
273A CYS* 3.2 7.6 + - - +
274A GLU* 3.0 22.6 + - + +
280A ARG* 3.7 28.5 - - - +
305A SER* 3.7 16.8 - - - +
306A ILE* 3.3 53.2 - - + +
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Residues in contact with GLN 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 LYS* 3.1 19.2 + - + +
268A GLN* 2.9 19.0 + - - +
270A ILE* 1.3 74.4 - - - +
272A ASP* 1.3 63.6 + - - +
274A GLU* 2.8 30.6 + - - +
275A ASP* 2.9 31.1 - - - +
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Residues in contact with ASP 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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231A ASP* 4.4 4.9 - - - +
234A ARG* 3.8 32.5 + - - +
268A GLN* 2.9 24.6 + - - +
269A VAL* 3.6 7.0 - - - +
271A GLN* 1.3 77.4 - - - +
273A CYS* 1.3 59.5 + - - +
275A ASP* 3.4 12.7 + - - +
276A GLU* 3.0 34.2 + - - +
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Residues in contact with CYS 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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230A ILE* 3.8 27.6 - - - -
234A ARG* 3.9 25.6 - - - +
252A MET* 4.1 6.1 - - - -
269A VAL* 3.0 17.3 + - - -
270A ILE* 3.3 11.0 - - - +
271A GLN 3.0 0.4 - - - -
272A ASP* 1.3 78.6 - - - +
274A GLU* 1.3 59.9 + - - +
276A GLU 3.2 2.4 + - - -
277A ASN 3.2 4.2 + - - -
278A ILE* 3.0 38.8 + - + +
280A ARG* 3.8 22.7 - - - +
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Residues in contact with GLU 274 (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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270A ILE* 3.0 12.2 + - + +
271A GLN* 2.8 22.0 + - - +
273A CYS* 1.3 73.6 - - - +
275A ASP* 1.3 62.2 + - - +
276A GLU 3.0 4.7 - - - -
277A ASN* 3.1 20.0 + - - +
278A ILE 5.0 0.9 - - - +
280A ARG* 3.2 32.8 + - - +
308A SER* 4.2 8.7 + - - -
309A GLU* 4.8 7.3 + - - +
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Residues in contact with ASP 275 (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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271A GLN* 2.9 33.7 + - - +
272A ASP* 3.7 15.9 - - - +
273A CYS 3.3 0.2 - - - -
274A GLU* 1.3 77.7 - - - +
276A GLU* 1.3 63.4 + - + +
277A ASN* 3.4 7.1 + - - -
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Residues in contact with GLU 276 (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 ARG* 3.2 44.9 + - - +
250A LYS* 4.0 29.4 + - - +
272A ASP* 3.0 16.3 - - - +
273A CYS 3.2 4.8 + - - +
274A GLU 3.0 1.0 - - - -
275A ASP* 1.3 84.3 - - + +
277A ASN* 1.3 75.0 + - - +
278A ILE* 3.4 12.8 + - + +
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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