Contacts of the helix formed by residues 271 - 285 (chain W) in PDB entry 6AH0
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 PHE 271 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270W MET* 1.3 77.1 - - - +
272W LEU* 1.3 65.9 + - - +
273W LEU 3.2 2.7 - - - -
274W VAL* 3.0 14.8 + - - +
275W GLN* 3.0 6.1 + - - -
333W ALA 4.6 6.7 + - - -
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Residues in contact with LEU 272 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271W PHE* 1.3 71.2 - - - +
273W LEU* 1.3 61.2 + - - +
275W GLN* 4.0 2.2 - - - +
276W ARG* 3.0 21.3 + - - -
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Residues in contact with LEU 273 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271W PHE 3.1 1.4 + - - -
272W LEU* 1.3 74.7 - - - +
274W VAL* 1.3 57.1 + - - +
276W ARG* 3.9 0.7 - - - -
277W PHE* 3.0 24.1 + - - -
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Residues in contact with VAL 274 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270W MET 5.2 2.2 - - - -
271W PHE 3.0 8.7 + - - +
273W LEU* 1.3 73.5 - - - +
275W GLN* 1.3 66.3 + - - +
277W PHE* 3.3 1.1 + - - +
278W GLY* 3.0 22.9 + - - -
333W ALA 5.8 6.7 + - - -
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Residues in contact with GLN 275 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260W LYS* 6.1 4.7 - - - +
270W MET 4.5 5.3 + - - -
271W PHE 3.0 12.6 + - - -
272W LEU* 4.0 3.6 - - - +
274W VAL* 1.3 75.5 - - - +
276W ARG* 1.3 55.8 + - - +
278W GLY* 3.5 1.0 + - - -
279W GLU* 3.0 23.4 + - - -
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Residues in contact with ARG 276 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272W LEU 3.0 16.2 + - - -
273W LEU 4.0 0.7 - - - -
275W GLN* 1.3 76.6 - - - +
277W PHE* 1.3 61.4 + - - +
279W GLU* 3.0 4.1 + - - +
280W LEU* 3.0 19.4 + - - -
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Residues in contact with PHE 277 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273W LEU 3.0 17.3 + - - -
274W VAL* 3.3 2.4 + - - +
276W ARG* 1.3 73.2 - - - +
278W GLY* 1.3 60.7 + - - +
280W LEU* 3.3 3.1 + - - +
281W MET* 3.0 20.6 + - - -
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Residues in contact with GLY 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253W PHE* 5.5 14.8 - - - -
274W VAL 3.0 16.4 + - - -
275W GLN* 3.7 2.5 - - - -
277W PHE* 1.3 75.4 - - - +
279W GLU* 1.3 56.7 + - - +
281W MET* 3.3 2.4 + - - -
282W ARG* 3.0 25.1 + - - -
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Residues in contact with GLU 279 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275W GLN 3.0 11.2 + - - -
276W ARG* 3.0 8.3 + - - +
278W GLY* 1.3 72.0 - - - +
280W LEU* 1.3 59.7 + - - +
282W ARG* 3.8 1.6 - - - +
283W LYS* 3.0 26.2 + - - -
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Residues in contact with LEU 280 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276W ARG 3.0 12.9 + - - -
277W PHE* 3.3 4.4 + - - +
279W GLU* 1.3 75.7 - - - +
281W MET* 1.3 56.9 + - - +
283W LYS* 3.3 2.9 + - - +
284W LEU* 3.0 25.3 + - - -
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Residues in contact with MET 281 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244W SER* 5.8 8.7 - - - +
254W LEU* 6.1 1.3 - - - -
277W PHE 3.0 14.0 + - - -
278W GLY* 3.3 3.1 + - - -
280W LEU* 1.3 71.0 - - - +
282W ARG* 1.3 68.1 + - - +
284W LEU* 3.4 2.8 + - - +
285W TRP* 3.2 16.5 + - - -
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Residues in contact with ARG 282 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195W PRO* 5.3 18.1 - - - +
254W LEU* 5.3 13.9 - - - +
278W GLY 3.0 14.9 + - - -
279W GLU* 3.8 3.8 - - - +
281W MET* 1.3 73.3 - - - +
283W LYS* 1.3 60.9 + - - +
285W TRP* 3.1 12.8 + - - -
286W ASN* 3.2 11.3 + - - -
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Residues in contact with LYS 283 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195W PRO* 5.8 1.9 - - - -
279W GLU 3.0 14.2 + - - -
280W LEU 3.6 3.4 - - - -
281W MET 3.3 0.2 - - - -
282W ARG* 1.3 74.6 - - - +
284W LEU* 1.3 56.7 + - - +
286W ASN* 3.0 21.7 + - - +
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Residues in contact with LEU 284 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222W PRO 3.0 21.5 - - - +
223W GLY* 3.2 13.7 - - - -
225W VAL* 5.3 1.2 + - - -
280W LEU 3.0 14.8 + - - -
281W MET* 3.9 3.1 - - - +
283W LYS* 1.3 73.5 - - - +
285W TRP* 1.3 55.4 - - - +
286W ASN 3.8 0.2 + - - -
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Residues in contact with TRP 285 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222W PRO* 4.6 7.1 - - - +
223W GLY* 4.3 11.3 + - - +
281W MET 3.2 8.7 + - - -
282W ARG 3.1 9.8 + - - -
284W LEU* 1.3 74.7 - - - +
286W ASN* 1.3 62.7 + - - +
287W PRO* 3.3 4.3 - - - +
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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