Contacts of the helix formed by residues 59 - 66 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 2.9 25.7 + - + +
58A SER* 1.3 74.7 - - - +
60A HIS* 1.3 84.9 + - - +
62A TRP 3.3 1.2 + - - -
63A ALA* 2.8 30.3 + - - +
13C MET* 3.7 19.9 - - - +
14C VAL 3.1 14.9 + - - +
15C GLU* 3.9 16.7 - - - +
16C LYS 4.9 1.6 + - - -
66D ILE* 3.5 24.3 - - - +
67D THR* 3.8 12.4 - - + +
76D ARG* 5.3 2.1 + - - -
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Residues in contact with HIS 60 (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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58A SER* 3.3 6.2 - - - +
59A ASP* 1.3 108.8 + - - +
61A GLN* 1.3 60.2 + - - +
63A ALA* 3.5 3.2 + - - +
64A ALA* 3.0 23.7 + - - +
314A GLN* 3.7 30.9 + - - +
318A GLU* 4.0 1.1 - - - +
16C LYS* 6.2 4.0 - - + -
67D THR* 4.0 23.6 - - + +
76D ARG* 5.8 3.2 + - - -
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.0 25.9 - - + +
58A SER* 2.8 40.0 + - - +
60A HIS* 1.3 71.4 - - - +
62A TRP* 1.3 66.4 + - - +
64A ALA* 3.2 7.7 + - - +
65A MET* 3.0 26.0 + - - +
268A PRO 3.7 0.2 + - - -
269A LEU* 3.3 20.6 + - - +
270A LEU* 3.5 12.9 - - - +
311A ALA* 3.6 6.7 + - + +
314A GLN* 3.5 26.0 - - + -
315A GLY* 3.3 25.5 - - - -
318A GLU* 3.5 7.3 - - - +
420A ARG* 3.1 10.0 + - - -
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Residues in contact with TRP 62 (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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13A MET* 5.7 3.6 - - + -
57A MET* 3.6 32.3 - - + +
58A SER 3.1 23.2 + - - -
59A ASP 3.3 5.8 + - - +
61A GLN* 1.3 74.8 - - - +
63A ALA* 1.3 64.3 + - - +
65A MET* 3.1 42.9 + - + +
66A ILE* 3.2 25.3 + - + +
271A ASN* 5.5 0.7 - - - -
62B TRP* 5.5 6.1 - + - -
65B MET* 4.5 9.4 - - + -
66B ILE* 3.3 43.7 - - + -
307B ARG* 4.6 12.6 - - - -
12C LYS* 4.4 26.1 + - + +
13C MET* 3.3 38.2 - - + +
66D ILE* 3.9 11.4 - - + -
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Residues in contact with ALA 63 (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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59A ASP 2.8 16.7 + - - +
60A HIS* 3.7 5.4 - - - +
61A GLN 3.3 0.2 - - - -
62A TRP* 1.3 76.3 - - - +
64A ALA* 1.3 61.2 + - - +
66A ILE* 3.1 15.8 + - - +
67A THR* 3.4 12.8 + - - -
63D ALA* 3.8 39.1 - - + +
66D ILE* 4.2 4.6 - - + +
67D THR* 3.9 12.3 - - + -
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Residues in contact with ALA 64 (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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60A HIS 3.0 18.8 + - - +
61A GLN* 3.4 8.1 - - - +
63A ALA* 1.3 76.0 - - - +
65A MET* 1.3 62.1 + - - +
67A THR* 3.4 8.5 + - - -
68A GLY 3.1 16.6 + - - -
310A ALA* 3.4 35.8 - - + +
311A ALA* 4.6 0.2 - - - -
314A GLN* 4.8 6.1 - - + -
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Residues in contact with MET 65 (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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57A MET* 4.0 11.0 - - + -
61A GLN 3.0 19.8 + - - +
62A TRP* 3.1 50.6 + - + +
64A ALA* 1.3 77.1 - - - +
66A ILE* 1.3 64.6 + - + +
68A GLY* 3.0 10.9 + - - +
307A ARG* 3.3 50.7 - - + +
308A ASP* 4.0 9.0 - - - +
311A ALA* 3.8 8.1 - - + -
62B TRP* 4.5 8.6 - - + -
65B MET* 5.5 2.9 - - + -
307B ARG* 3.8 35.9 - - - +
12D LYS* 5.2 0.9 + - - -
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Residues in contact with ILE 66 (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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62A TRP* 3.4 22.0 - - + +
63A ALA* 3.1 10.4 + - - +
65A MET* 1.3 77.5 - - + +
67A THR* 1.3 56.2 + - - +
13B MET* 4.4 10.5 - - + -
62B TRP* 3.4 35.6 - - + -
12D LYS* 2.9 25.3 + - - -
13D MET* 6.2 0.2 - - + -
59D ASP* 3.4 32.0 - - + +
62D TRP* 4.0 20.9 - - + -
63D ALA* 4.2 4.7 - - + +
66D ILE* 4.7 15.3 - - + -
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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