Contacts of the helix formed by residues 59 - 66 (chain C) in PDB entry 1AX4
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 ASP 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 3.7 19.5 - - - +
14A VAL 3.0 14.1 + - - +
15A GLU* 4.0 15.4 - - - +
16A LYS 4.9 2.3 + - - -
66B ILE* 3.4 27.2 - - - +
67B THR* 3.8 12.6 - - - +
76B ARG* 5.3 2.1 + - - -
12C LYS* 2.9 26.6 + - + +
58C SER* 1.3 75.8 - - - +
60C HIS* 1.3 81.6 + - - -
62C TRP 3.2 1.4 + - - +
63C ALA* 2.9 26.7 + - - +
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 6.1 4.5 - - + -
67B THR* 3.9 24.6 - - + +
76B ARG* 5.5 5.8 + - - -
58C SER* 3.3 6.4 + - - +
59C ASP* 1.3 107.8 + - - +
61C GLN* 1.3 56.2 + - - +
63C ALA* 3.7 2.8 - - - +
64C ALA* 3.0 28.4 + - - +
314C GLN* 3.8 29.6 + - - +
318C GLU* 5.2 0.9 - - - -
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Residues in contact with GLN 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C MET* 3.1 20.2 - - + +
58C SER* 2.8 38.3 + - - +
60C HIS* 1.3 72.8 - - - +
62C TRP* 1.3 66.9 + - - +
64C ALA* 3.3 7.0 + - - +
65C MET* 3.0 27.2 + - - +
268C PRO 3.7 0.8 + - - -
269C LEU* 3.4 20.8 + - - +
270C LEU* 3.5 13.5 - - - +
311C ALA* 4.1 6.6 - - + +
314C GLN* 3.5 26.2 - - + -
315C GLY* 3.3 24.2 - - - -
318C GLU* 3.5 5.9 - - - +
420C ARG* 2.9 16.7 + - - -
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Residues in contact with TRP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 4.5 19.8 + - + +
13A MET* 3.4 31.1 - - + +
66B ILE* 3.9 17.0 - - + -
13C MET* 5.9 2.9 - - - -
57C MET* 3.6 33.0 - - + +
58C SER 3.1 20.2 + - - +
59C ASP 3.2 5.8 + - - +
61C GLN* 1.3 76.5 - - - +
63C ALA* 1.3 62.7 + - - +
65C MET* 3.2 34.5 + - + +
66C ILE* 3.1 33.5 + - + +
271C ASN* 5.6 0.2 - - - -
62D TRP* 5.5 6.1 - + - -
65D MET* 4.4 10.3 - - + -
66D ILE* 3.2 47.8 - - + -
307D ARG* 4.7 12.3 - - - -
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA* 3.7 30.9 - - + +
66B ILE* 4.0 5.1 - - + +
67B THR* 3.7 20.6 - - + -
59C ASP 2.9 16.4 + - - +
60C HIS* 3.7 5.4 - - - +
62C TRP* 1.3 78.3 - - - +
64C ALA* 1.3 61.8 + - - +
66C ILE* 3.1 14.8 + - - +
67C THR* 3.3 13.8 + - - -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C HIS 3.0 17.2 + - - +
61C GLN* 3.6 8.7 - - - +
63C ALA* 1.3 76.7 - - - +
65C MET* 1.3 60.7 + - - +
67C THR* 3.5 8.5 + - - -
68C GLY 3.1 17.0 + - - -
77C ASN* 5.3 0.2 + - - -
310C ALA* 3.2 38.4 - - + +
314C GLN* 4.7 6.5 - - + -
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 5.1 0.7 + - - -
57C MET* 3.7 18.6 - - + -
61C GLN 3.0 19.2 + - - +
62C TRP* 3.2 46.0 + - + +
64C ALA* 1.3 75.0 - - - +
66C ILE* 1.3 67.0 + - + +
68C GLY 3.0 10.0 + - - +
307C ARG* 3.4 51.7 - - + +
308C ASP* 4.1 8.1 - - - +
311C ALA* 3.8 8.7 - - + -
62D TRP* 4.5 7.4 - - + -
65D MET* 5.5 2.2 - - + -
307D ARG* 3.8 33.4 - - - +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 6.4 1.8 - - + -
12B LYS* 2.9 26.0 + - - -
13B MET* 6.2 0.2 - - + -
59B ASP* 3.5 30.8 - - + +
62B TRP* 3.9 20.4 - - + +
63B ALA* 4.0 3.4 - - - +
66B ILE* 4.6 15.0 - - + -
62C TRP* 3.3 22.9 - - + +
63C ALA* 3.1 11.2 + - - +
65C MET* 1.3 76.7 - - + +
67C THR* 1.3 58.7 + - - +
68C GLY 3.3 0.2 - - - -
13D MET* 4.4 11.2 - - + -
62D TRP* 3.3 39.3 - - + -
66D ILE* 6.4 0.4 - - + -
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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