Contacts of the helix formed by residues 260 - 272 (chain L) in PDB entry 3D1N
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 260 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258L LEU 4.9 3.4 - - - +
259L PRO* 1.3 76.6 - - - +
261L GLY* 1.3 65.0 + - - +
262L GLN* 3.4 11.0 + - - +
263L GLU* 2.9 51.9 + - - +
264L ILE* 3.0 11.7 + - - +
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Residues in contact with GLY 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L PRO 4.0 0.4 + - - -
260L THR* 1.3 74.4 - - - +
262L GLN* 1.3 58.8 + - - +
264L ILE* 3.2 9.4 + - - +
265L THR* 3.0 14.9 + - - +
275L ARG* 2.7 32.4 + - - -
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Residues in contact with GLN 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C A 6.3 4.0 - - - +
260L THR* 3.1 9.5 + - - +
261L GLY* 1.3 76.4 - - - +
263L GLU* 1.3 68.8 + - - +
265L THR* 3.1 14.7 + - - +
266L GLU* 3.0 22.7 + - + +
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Residues in contact with GLU 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256L ASN* 2.8 26.6 + - - +
258L LEU 4.4 0.5 - - - +
259L PRO* 3.2 6.7 - - + +
260L THR* 2.9 44.5 + - - +
262L GLN* 1.3 87.0 - - + +
264L ILE* 1.3 56.8 + - - +
266L GLU* 3.3 8.1 + - - +
267L MSE 2.9 39.9 + - + +
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Residues in contact with ILE 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L PRO* 3.7 32.3 - - + +
260L THR 3.0 15.0 + - - +
261L GLY* 3.5 14.8 - - - +
262L GLN 3.1 0.2 - - - -
263L GLU* 1.3 75.6 - - - +
265L THR* 1.3 65.5 + - - +
267L MSE 3.5 6.5 + - - +
268L ALA* 3.0 22.5 + - - +
275L ARG* 3.8 20.4 - - + +
278L VAL* 4.2 11.6 - - + +
279L ARG* 3.7 43.5 - - + +
282L PHE* 5.2 8.3 - - + -
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Residues in contact with THR 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C A 5.5 4.5 - - - +
2C G 3.9 20.0 + - - +
178L PRO* 5.8 1.0 - - - +
237L ARG* 4.9 1.0 + - - -
261L GLY 3.0 16.4 + - - +
262L GLN* 3.1 12.7 + - - +
264L ILE* 1.3 75.5 - - - +
266L GLU* 1.3 66.9 + - - +
268L ALA* 3.3 3.1 + - - +
269L LYS* 2.9 26.3 + - - +
275L ARG* 2.8 39.3 - - - +
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Residues in contact with GLU 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L GLN* 3.0 12.9 + - + +
263L GLU* 3.5 12.1 - - - +
264L ILE 3.3 0.2 - - - -
265L THR* 1.3 85.1 + - - +
267L MSE 1.3 63.1 + - + +
269L LYS* 3.4 6.4 + - - +
270L GLU* 3.3 22.8 + - - +
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Residues in contact with MSE 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249L LEU* 6.2 0.2 - - + -
252L TYR* 3.5 53.6 - - + +
256L ASN* 3.8 33.0 - - + +
259L PRO* 4.6 6.5 - - - -
263L GLU* 2.9 27.9 + - + +
264L ILE* 3.8 7.2 - - - +
266L GLU* 1.3 76.8 - - + +
268L ALA* 1.3 62.3 + - - +
270L GLU* 3.3 12.7 - - - +
271L LEU* 3.1 26.5 + - + +
278L VAL* 4.7 7.9 - - + -
282L PHE* 3.9 29.2 - - + -
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Residues in contact with ALA 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237L ARG* 3.4 8.1 + - - +
264L ILE 3.0 19.0 + - - +
265L THR 3.8 3.4 - - - +
267L MSE 1.3 76.6 - - - +
269L LYS* 1.3 51.6 + - - +
271L LEU* 3.2 2.8 + - - -
272L ASN 2.8 30.0 + - - -
273L TYR 3.0 25.0 + - - +
275L ARG* 3.9 16.4 - - + -
278L VAL* 3.7 24.8 - - + +
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Residues in contact with LYS 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C G 4.8 1.6 - - - -
3C C 3.3 35.5 + - - +
173L THR* 5.7 6.7 - - - +
178L PRO* 4.2 28.0 - - + +
237L ARG* 3.1 23.2 + - - +
265L THR 2.9 17.6 + - - +
266L GLU* 3.6 7.4 - - - +
267L MSE 3.3 0.2 - - - -
268L ALA* 1.3 75.5 - - - +
270L GLU* 1.3 59.8 + - - +
272L ASN* 3.0 20.4 + - - +
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Residues in contact with GLU 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L ALA* 5.5 0.2 - - - +
252L TYR* 2.8 31.4 + - - +
266L GLU 3.3 10.2 + - - +
267L MSE 3.3 9.0 - - - +
269L LYS* 1.3 81.6 - - + +
271L LEU* 1.3 89.7 + - - +
272L ASN* 3.2 1.3 + - - +
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Residues in contact with LEU 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238L ARG* 5.7 0.3 - - - -
245L ALA* 4.9 8.3 - - + +
248L ALA* 3.6 26.0 - - + -
249L LEU* 3.7 35.2 - - + -
252L TYR* 4.3 9.2 - - + -
267L MSE 3.1 17.1 + - + +
268L ALA 3.7 4.0 - - - +
270L GLU* 1.3 98.3 - - - +
272L ASN* 1.3 69.5 + - - +
273L TYR* 3.3 29.5 - - + +
278L VAL* 4.6 10.3 - - + -
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Residues in contact with ASN 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L ARG* 3.4 45.6 - - - +
236L LYS 3.2 21.1 + - - -
237L ARG* 3.7 18.5 + - - +
238L ARG* 2.8 36.6 + - - +
268L ALA 2.8 9.3 + - - -
269L LYS 3.0 12.6 + - - +
270L GLU 3.2 2.0 - - - +
271L LEU* 1.3 81.9 - - - +
273L TYR* 1.3 56.4 + - - +
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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