Contacts of the helix formed by residues 59 - 66 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 2.9 27.7 + - + +
58B SER* 1.3 75.6 - - - +
60B HIS* 1.3 81.2 + - - -
62B TRP 3.3 1.0 + - - -
63B ALA* 2.9 29.5 + - - +
66C ILE* 3.5 23.9 - - - +
67C THR* 3.7 13.3 - - + +
76C ARG* 5.1 2.1 + - - -
13D MET* 3.7 20.1 - - - +
14D VAL 3.1 14.5 + - - +
15D GLU* 4.0 15.6 - - - +
16D LYS 4.9 1.4 + - - -
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B SER* 3.3 5.8 + - - +
59B ASP* 1.3 106.8 + - - +
61B GLN* 1.3 57.6 + - - +
63B ALA* 3.6 2.5 - - - +
64B ALA* 3.0 28.4 + - - +
314B GLN* 3.7 30.6 + - - +
318B GLU* 4.0 0.9 - - - +
67C THR* 3.9 23.0 - - + +
76C ARG* 5.5 6.4 + - - -
16D LYS* 6.1 4.5 - - + -
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B MET* 3.0 22.0 - - + +
58B SER* 2.9 40.7 + - - +
60B HIS* 1.3 73.9 - - - +
62B TRP* 1.3 65.4 + - - +
64B ALA* 3.2 6.7 + - - +
65B MET* 3.1 25.6 + - - +
268B PRO 3.8 0.6 + - - -
269B LEU* 3.4 19.0 + - - +
270B LEU* 3.5 13.3 - - - +
311B ALA* 3.6 7.4 + - + +
314B GLN* 3.5 23.8 - - + -
315B GLY* 3.4 24.4 - - - -
318B GLU* 3.6 5.6 - - - +
420B ARG* 2.9 17.3 + - - -
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 5.5 6.5 - + - -
65A MET* 4.5 9.4 - - + -
66A ILE* 3.4 43.5 - - + -
307A ARG* 4.6 12.1 - - - -
13B MET* 5.9 3.1 - - - -
57B MET* 3.7 31.5 - - + +
58B SER 3.1 20.9 + - - +
59B ASP 3.8 5.8 - - - +
61B GLN* 1.3 79.0 - - - +
63B ALA* 1.3 59.5 + - - +
65B MET* 3.2 35.1 + - + +
66B ILE* 3.2 33.5 + - + +
271B ASN* 5.7 0.4 - - - -
66C ILE* 3.9 18.2 - - + -
12D LYS* 4.4 26.5 + - + +
13D MET* 3.3 29.8 - - + +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASP 2.9 17.6 + - - +
60B HIS* 3.6 5.8 - - - +
62B TRP* 1.3 74.1 - - - +
64B ALA* 1.4 63.6 + - - +
66B ILE* 3.1 16.2 + - - +
67B THR* 3.3 13.4 + - - -
63C ALA* 3.7 31.0 - - + +
66C ILE* 4.0 4.4 - - + +
67C THR* 3.7 20.2 - - + -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS 3.0 18.2 + - - +
61B GLN* 3.2 8.0 + - - +
63B ALA* 1.4 78.1 - - - +
65B MET* 1.3 60.4 + - - +
67B THR* 3.5 8.3 + - - -
68B GLY* 3.2 16.5 + - - -
310B ALA* 3.3 38.6 - - + +
314B GLN* 4.7 6.3 - - + -
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 4.5 7.5 - - + -
65A MET* 5.5 2.5 - - + -
307A ARG* 3.8 33.2 - - - +
57B MET* 3.7 18.4 - - + -
61B GLN 3.1 15.8 + - - +
62B TRP* 3.3 48.2 - - + +
63B ALA 3.2 0.2 - - - -
64B ALA* 1.3 77.3 - - - +
66B ILE* 1.3 64.7 + - + +
68B GLY* 3.1 10.2 + - - +
307B ARG* 3.3 49.3 - - + +
308B ASP* 4.1 8.1 - - - +
311B ALA* 3.9 8.7 - - + -
12C LYS* 5.5 0.5 - - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 4.5 10.3 - - + -
62A TRP* 3.3 38.5 - - + -
62B TRP* 3.3 21.8 - - + +
63B ALA* 3.1 11.1 + - - +
65B MET* 1.3 77.0 - - + +
67B THR* 1.4 56.1 + - - +
12C LYS* 3.0 26.3 + - - -
59C ASP* 3.4 31.2 - - + +
62C TRP* 3.9 19.3 - - + -
63C ALA* 4.0 4.5 - - + +
66C ILE* 4.6 17.3 - - + -
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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