Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 3M6L
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 GLY 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLN* 2.8 22.1 + - - -
259A PRO* 3.3 2.6 - - - -
260A LEU* 1.3 77.7 - - - +
262A GLU* 1.3 66.0 + - - -
263A GLU 3.3 2.4 + - - -
264A VAL* 3.4 3.5 + - - -
265A ILE* 3.1 22.5 + - - +
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Residues in contact with GLU 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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22A GLN* 4.1 22.1 + - + +
261A GLY* 1.3 70.6 - - - -
263A GLU* 1.3 67.9 + - + +
265A ILE* 3.3 6.4 + - - +
266A LYS* 3.0 39.0 + - - +
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Residues in contact with GLU 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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261A GLY 3.3 0.8 - - - -
262A GLU* 1.3 80.4 - - + +
264A VAL* 1.3 66.5 + - + +
266A LYS* 3.3 29.7 + - - +
267A LYS* 3.0 49.2 + - - +
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Residues in contact with VAL 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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246A ALA* 3.5 34.3 - - + +
248A GLU* 3.7 35.2 - - + +
249A LEU* 4.1 9.4 - - + -
260A LEU* 3.4 40.6 - - + +
261A GLY 3.4 1.7 + - - +
262A GLU 3.4 0.2 - - - -
263A GLU* 1.3 77.6 - - + +
265A ILE* 1.3 58.4 + - - +
267A LYS* 3.4 7.6 + - - +
268A ALA* 2.9 27.4 + - + +
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Residues in contact with ILE 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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15A PHE* 5.0 3.4 - - + -
18A ALA* 3.8 32.5 - - + +
19A ASP* 3.9 6.5 - - - +
22A GLN* 3.7 33.7 - - + +
260A LEU* 4.0 22.9 - - + +
261A GLY 3.1 13.1 + - - +
262A GLU* 3.8 5.6 - - - +
264A VAL* 1.3 77.7 - - - +
266A LYS* 1.3 62.8 + - + +
268A ALA* 3.2 6.6 + - - +
269A LYS* 3.0 54.7 + - + +
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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 GLU* 3.0 25.5 + - + +
263A GLU* 3.3 33.4 + - - +
265A ILE* 1.3 75.9 - - + +
267A LYS* 1.3 62.7 - - + +
269A LYS* 3.3 3.6 + - - +
270A GLU* 3.0 31.8 + - - +
276A PRO* 3.7 31.1 - - + +
277A ASN* 3.2 26.9 + - - +
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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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247A GLY* 6.4 2.5 - - - -
248A GLU* 6.3 2.7 - - + -
263A GLU* 3.0 38.5 + - - +
264A VAL* 3.8 6.3 - - - +
266A LYS* 1.3 75.2 - - + +
268A ALA* 1.3 62.7 + - - +
270A GLU* 3.4 15.3 + - - +
271A GLN* 3.0 32.9 + - + +
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Residues in contact with ALA 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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15A PHE* 3.5 24.6 - - + -
33A LEU* 6.2 0.9 - - + -
245A GLY 3.3 28.7 - - - +
246A ALA* 4.3 8.1 - - + -
247A GLY 5.7 1.3 - - - +
260A LEU* 6.2 1.8 - - + -
264A VAL* 2.9 17.7 + - + +
265A ILE* 3.2 7.8 + - - +
267A LYS* 1.3 76.5 - - - +
269A LYS* 1.3 62.7 + - - +
271A GLN* 3.4 7.1 + - - +
272A ALA* 3.1 17.5 + - - +
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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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15A PHE* 3.8 32.1 - - + -
19A ASP* 3.0 35.4 + - - -
265A ILE* 3.0 32.1 + - + +
266A LYS 3.6 3.6 - - - +
268A ALA* 1.3 73.2 - - - +
270A GLU* 1.3 64.7 + - - +
272A ALA 3.0 8.0 + - - -
274A PHE* 2.9 49.7 + - + +
275A ASP 3.9 14.6 - - - +
276A PRO* 4.0 15.3 + - + +
278A ILE 2.9 24.5 + - - -
279A SER* 4.0 2.2 - - - +
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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 LYS* 3.0 17.4 + - - +
267A LYS* 3.4 24.5 + - - +
269A LYS* 1.3 74.9 - - - +
271A GLN* 1.3 65.6 + - + +
273A GLY* 3.2 12.6 + - - -
274A PHE 3.8 5.7 + - - -
276A PRO* 3.9 24.3 - - + +
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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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245A GLY 5.7 2.2 - - - +
267A LYS* 3.0 26.8 + - + +
268A ALA* 3.8 7.0 - - - +
269A LYS 3.3 0.2 - - - -
270A GLU* 1.3 78.6 - - - +
272A ALA* 1.4 57.9 + - - +
273A GLY 3.8 0.3 + - - -
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Residues in contact with ALA 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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7A GLN* 4.9 7.6 - - - +
11A ASN* 3.6 24.5 + - - +
15A PHE* 3.5 32.5 - - + -
268A ALA 3.1 9.3 + - - +
269A LYS 3.0 4.4 + - - +
271A GLN* 1.4 77.9 - - - +
273A GLY* 1.3 59.5 + - - +
274A PHE* 3.6 10.4 + - + -
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Residues in contact with GLY 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 LYS 3.0 2.6 + - - -
270A GLU 3.2 11.5 + - - -
271A GLN 3.5 0.8 + - - -
272A ALA* 1.3 77.5 - - - +
274A PHE* 1.3 63.4 + - - +
275A ASP 4.1 0.5 + - - -
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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