Contacts of the helix formed by residues 59 - 66 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.4 27.5 - - - +
67A THR* 3.7 11.7 - - + +
76A ARG* 5.3 2.3 + - - -
13B MET* 3.7 21.3 - - - +
14B VAL 3.2 13.7 + - - +
15B GLU* 4.0 13.6 - - - +
16B LYS 5.0 1.9 + - - -
12D LYS* 2.9 28.1 + - + +
58D SER* 1.3 74.8 - - - +
60D HIS* 1.3 81.4 + - - -
62D TRP 3.2 0.9 + - - +
63D ALA* 2.9 26.9 + - - +
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Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR* 4.0 23.6 - - + +
76A ARG* 5.8 3.4 + - - -
16B LYS* 6.3 3.8 - - + -
58D SER* 3.2 8.6 + - - +
59D ASP* 1.3 107.6 + - - +
61D GLN* 1.3 56.0 + - - +
63D ALA* 3.4 3.2 + - - +
64D ALA* 3.0 28.6 + - - +
314D GLN* 3.8 27.4 + - - +
318D GLU* 4.1 1.3 - - - +
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Residues in contact with GLN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D MET* 3.1 25.3 - - - -
58D SER* 2.9 38.9 + - - +
60D HIS* 1.3 74.6 - - - +
62D TRP* 1.4 64.2 + - - +
64D ALA* 3.3 5.0 + - - +
65D MET* 3.1 26.0 + - - +
268D PRO 3.7 0.8 + - - -
269D LEU* 3.3 20.8 + - - +
270D LEU* 3.5 14.5 - - - +
311D ALA* 3.7 6.1 + - + +
314D GLN* 3.5 28.0 - - + -
315D GLY* 3.3 23.8 - - - -
318D GLU* 3.5 6.9 - - - +
420D ARG* 3.1 10.4 + - - -
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Residues in contact with TRP 62 (chain D).
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* 4.0 12.1 - - + -
12B LYS* 4.4 24.8 + - + +
13B MET* 3.2 36.8 - - + +
62C TRP* 5.5 6.3 - + - -
65C MET* 4.5 9.2 - - + -
66C ILE* 3.3 44.0 - - + -
307C ARG* 4.7 12.1 - - - -
13D MET* 5.9 2.9 - - - -
57D MET* 3.7 33.8 - - + +
58D SER 3.1 22.5 + - - -
59D ASP 3.2 6.9 + - - +
61D GLN* 1.4 77.8 - - - +
63D ALA* 1.3 61.7 + - - +
65D MET* 3.1 42.9 + - + +
66D ILE* 3.2 26.7 + - + +
271D ASN* 5.6 0.7 - - - -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 3.8 30.7 - - + +
66A ILE* 4.2 4.4 - - + +
67A THR* 3.8 19.1 - - + -
59D ASP 2.9 16.4 + - - +
60D HIS* 3.6 6.3 - - - +
61D GLN 3.2 0.2 - - - -
62D TRP* 1.3 77.4 - - - +
64D ALA* 1.3 62.0 + - - +
66D ILE* 3.2 16.5 + - - +
67D THR* 3.3 13.1 + - - -
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D HIS 3.0 14.1 + - - +
61D GLN* 3.5 11.0 - - - +
63D ALA* 1.3 74.8 - - - +
65D MET* 1.3 61.0 + - - +
67D THR* 3.4 10.1 + - - -
68D GLY 3.1 16.5 + - - -
310D ALA* 3.3 37.4 - - + +
311D ALA* 4.6 0.2 - - - -
314D GLN* 4.7 6.1 - - + -
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Residues in contact with MET 65 (chain D).
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* 5.5 0.7 - - - -
62C TRP* 4.4 8.5 - - + -
65C MET* 5.5 2.7 - - + -
307C ARG* 3.8 38.6 - - - +
57D MET* 3.8 13.5 - - + -
61D GLN 3.1 20.7 + - - +
62D TRP* 3.1 46.4 + - + +
64D ALA* 1.3 76.9 - - - +
66D ILE* 1.3 64.0 + - + +
68D GLY 3.1 10.2 + - - +
307D ARG* 3.3 49.5 - - + +
308D ASP* 4.1 8.1 - - - +
311D ALA* 3.8 8.5 - - + -
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Residues in contact with ILE 66 (chain D).
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* 3.1 24.9 + - - -
59A ASP* 3.5 29.7 - - + +
62A TRP* 3.9 19.3 - - + -
63A ALA* 4.2 4.0 - - + +
66A ILE* 4.7 15.5 - - + -
13C MET* 4.3 11.8 - - + +
62C TRP* 3.2 39.9 - - + -
62D TRP* 3.3 21.8 - - + +
63D ALA* 3.2 10.4 + - - +
65D MET* 1.3 76.6 - - + +
67D THR* 1.3 56.6 + - - +
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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