Contacts of the helix formed by residues 244 - 255 (chain A) in PDB entry 1AZ1
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.2 33.2 + - - +
233A ILE* 4.3 13.0 - - - +
234A LYS* 3.4 46.0 - - + -
237A ALA* 3.9 10.1 - - + -
243A THR* 1.3 74.1 - - - +
245A ALA* 1.3 59.2 + - - +
247A VAL* 3.3 4.5 + - - +
248A LEU* 2.9 36.2 + - - +
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Residues in contact with ALA 245 (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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212A LEU* 3.9 16.3 - - + +
228A LEU* 4.0 10.7 - - + +
243A THR* 3.8 6.7 - - - +
244A THR* 1.3 81.5 + - - +
246A GLN* 1.3 56.3 + - - +
248A LEU* 3.2 1.9 + - - +
249A ILE* 2.9 36.1 + - - +
271A GLU* 3.9 1.3 - - - +
272A ASN* 4.1 5.2 - - - +
316A NAP 3.4 40.2 - - + +
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Residues in contact with GLN 246 (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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242A LYS* 3.4 32.0 - - + +
243A THR* 2.9 39.9 + - - +
245A ALA* 1.3 75.8 - - - +
247A VAL* 1.3 56.8 + - - +
249A ILE* 3.4 1.5 + - - -
250A ARG* 3.1 30.1 + - - +
271A GLU* 3.0 43.6 + - + +
272A ASN* 5.0 1.8 - - - +
274A LYS* 3.6 18.8 + - - +
275A VAL* 3.7 21.6 - - + +
278A PHE* 3.7 3.7 - - + -
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Residues in contact with VAL 247 (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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233A ILE* 4.3 17.3 - - + -
236A ILE* 4.2 13.7 - - + +
237A ALA* 3.5 31.9 - - + +
240A HIS* 5.0 1.1 - - + -
242A LYS* 4.5 8.7 - - + -
243A THR 3.2 9.0 + - - +
244A THR* 3.7 8.1 - - - +
246A GLN* 1.3 73.3 - - - +
248A LEU* 1.3 60.5 + - + +
250A ARG* 3.4 2.5 + - - +
251A PHE* 3.0 29.6 + - - +
278A PHE* 4.5 8.3 - - + -
280A LEU* 4.0 30.3 - - + +
288A LEU* 4.4 10.5 - - + -
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Residues in contact with LEU 248 (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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188A PRO* 3.8 34.9 - - + +
211A PRO* 3.8 24.4 - - - +
212A LEU* 3.8 10.5 - - + -
227A LEU* 3.9 29.2 - - + +
228A LEU* 3.9 23.3 - - + -
233A ILE* 4.1 22.0 - - + -
244A THR* 2.9 21.7 + - - +
245A ALA 3.2 5.4 + - - +
247A VAL* 1.3 77.2 - - + +
249A ILE* 1.3 57.7 + - - +
251A PHE* 4.1 4.8 - - + +
252A PRO* 3.0 22.2 - - - +
288A LEU* 5.5 1.1 - - + -
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Residues in contact with ILE 249 (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 LEU* 4.3 6.3 - - + -
211A PRO* 5.0 1.1 - - + -
212A LEU* 4.1 12.3 - - + -
245A ALA 2.9 22.3 + - - +
246A GLN* 4.0 4.0 - - - +
247A VAL 3.2 0.2 - - - -
248A LEU* 1.3 76.7 - - - +
250A ARG* 1.3 61.7 + - - +
252A PRO* 3.1 22.6 - - - +
253A MET* 3.5 22.7 - - + +
259A VAL* 3.6 22.8 - - + +
261A PRO* 4.0 19.1 - - + -
272A ASN* 3.5 47.6 - - + +
275A VAL* 4.1 13.7 - - + -
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Residues in contact with ARG 250 (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 3.1 17.2 + - - +
247A VAL 3.8 3.4 - - - +
249A ILE* 1.3 77.9 - - - +
251A PHE* 1.3 66.2 + - - +
253A MET* 3.1 23.4 + - - +
254A GLN* 2.9 59.5 + - - +
275A VAL* 2.9 29.4 + - + +
276A PHE* 3.9 15.8 + - - +
278A PHE* 3.1 41.2 + - + -
279A GLU* 3.9 11.9 - - - +
280A LEU* 4.1 9.9 - - + +
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Residues in contact with PHE 251 (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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186A CYS* 5.9 0.4 - - - -
187A HIS* 4.2 7.4 - - - -
188A PRO* 3.5 42.4 - - + -
191A THR* 4.5 1.3 - - + -
247A VAL* 3.0 18.0 + - + +
248A LEU* 4.1 4.5 - - + +
250A ARG* 1.3 76.6 - - - +
252A PRO* 1.4 74.3 - - + +
254A GLN 3.3 6.8 + - - -
255A ARG* 3.4 30.2 + - - +
280A LEU* 3.8 12.3 - - + +
285A MET* 3.5 28.0 - - + +
288A LEU* 3.7 38.4 - - + -
289A LEU* 3.5 33.4 - - + -
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Residues in contact with PRO 252 (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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186A CYS* 5.7 3.1 - - - +
187A HIS* 6.6 0.2 - - - -
208A ALA* 4.2 11.7 - - + -
211A PRO* 5.0 2.5 - - + -
248A LEU 3.0 27.1 - - - +
249A ILE 3.1 16.4 - - - +
251A PHE* 1.4 91.6 - - + +
253A MET* 1.3 59.7 + - - +
255A ARG* 3.0 16.5 + - + -
257A LEU* 3.0 47.4 + - + +
259A VAL* 3.7 22.2 - - + -
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Residues in contact with MET 253 (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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14A ILE* 3.9 20.8 - - + +
15A LEU* 3.9 23.6 - - + -
249A ILE* 3.5 17.0 - - + +
250A ARG* 3.1 33.7 + - - +
252A PRO* 1.3 77.7 - - - +
254A GLN* 1.3 57.1 + - - +
256A ASN* 3.0 21.0 + - - +
257A LEU 3.7 8.5 - - - +
259A VAL* 3.8 24.2 - - + -
275A VAL* 3.5 32.3 - - + -
276A PHE* 4.2 14.4 - - + -
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Residues in contact with GLN 254 (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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250A ARG* 2.9 51.2 + - - +
251A PHE 3.3 0.2 + - - -
252A PRO 3.2 0.2 - - - -
253A MET* 1.3 75.1 - - - +
255A ARG* 1.3 60.3 + - - +
256A ASN* 3.3 6.7 + - - -
279A GLU* 3.6 11.8 + - + +
280A LEU* 2.8 50.7 + - - +
285A MET* 3.8 29.7 - - + +
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Residues in contact with ARG 255 (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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186A CYS* 3.6 17.8 - - - -
191A THR* 2.9 32.9 + - - +
193A GLU* 4.0 17.8 + - - +
196A ILE* 3.6 22.0 - - + +
200A GLN* 3.1 16.5 + - - +
251A PHE* 3.4 37.1 - - - +
252A PRO* 3.0 14.7 + - - +
254A GLN* 1.3 77.2 - - - +
256A ASN* 1.3 71.3 + - - +
257A LEU* 3.2 11.3 + - + +
285A MET* 3.6 14.1 - - + -
289A LEU* 3.7 27.7 - - + +
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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