Contacts of the helix formed by residues 72 - 81 (chain A) in PDB entry 1AXC
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 LEU 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.7 16.7 - - + +
19A LEU* 4.2 14.6 - - + -
20A LYS* 3.9 8.7 - - - +
23A ILE* 3.4 51.4 - - + +
24A ASN 2.6 15.8 + - - +
26A ALA* 4.0 15.0 - - + -
28A TRP* 3.3 41.5 - - + +
37A LEU* 4.7 1.1 - - + -
70A VAL* 3.5 8.0 + - + +
71A ASN* 1.3 71.0 - - - +
73A THR* 1.3 54.3 + - - +
75A MET* 3.9 3.4 - - - +
76A SER* 2.9 30.3 + - - -
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Residues in contact with THR 73 (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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20A LYS* 4.0 12.8 + - + +
24A ASN* 3.6 23.0 + - - +
71A ASN* 2.7 21.1 + - - -
72A LEU* 1.3 73.7 - - - +
74A SER* 1.3 58.8 + - - +
76A SER* 3.5 6.7 + - - -
77A LYS* 3.3 37.0 + - + +
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Residues in contact with SER 74 (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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71A ASN* 2.9 29.6 + - - +
73A THR* 1.3 71.8 - - - +
75A MET* 1.3 65.8 + - - +
76A SER 3.1 1.6 - - - -
77A LYS* 3.2 8.3 + - - +
78A ILE* 3.1 24.6 + - - +
116A MET* 4.3 12.1 - - - -
117A LYS 5.7 1.6 - - - -
175C LEU* 4.0 32.7 - - - +
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Residues in contact with MET 75 (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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12A LEU* 5.3 4.9 - - + -
16A LEU* 3.3 27.5 - - + +
28A TRP* 3.8 35.4 - - + -
70A VAL* 3.7 20.9 - - + -
71A ASN 3.1 12.0 + - - +
72A LEU* 4.0 4.5 - - - +
74A SER* 1.3 78.1 - - - +
76A SER* 1.3 58.2 + - - +
78A ILE* 3.7 2.9 - - - +
79A LEU* 2.9 33.4 + - + +
90A LEU* 5.0 10.8 - - + -
99A LEU* 4.2 20.9 - - + -
101A LEU* 4.5 16.8 - - + -
116A MET* 3.5 23.9 - - + -
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Residues in contact with SER 76 (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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16A LEU* 3.5 13.6 - - - +
17A GLU* 2.8 28.0 + - - +
20A LYS* 3.0 30.1 + - - +
72A LEU 2.9 19.5 + - - -
73A THR* 3.5 6.3 - - - -
74A SER 3.1 0.2 - - - -
75A MET* 1.3 74.9 - - - +
77A LYS* 1.3 60.8 + - - +
79A LEU* 3.3 2.2 + - - +
80A LYS* 2.9 35.2 + - - +
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Residues in contact with LYS 77 (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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73A THR* 3.3 26.0 + - - +
74A SER* 3.2 8.8 + - - +
76A SER* 1.3 77.0 - - - +
78A ILE* 1.3 62.8 + - - +
80A LYS* 3.2 23.0 + - - +
81A CYS* 3.3 13.7 - - - -
153C HIS* 4.0 32.2 + - + +
154C ILE* 5.2 0.9 - - + -
175C LEU* 3.8 24.8 - - + +
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Residues in contact with ILE 78 (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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74A SER 3.1 10.1 + - - +
75A MET* 3.7 7.2 - - - +
77A LYS* 1.3 80.3 - - - +
79A LEU* 1.3 61.7 + - - +
81A CYS* 3.0 26.3 + - - +
101A LEU* 3.7 26.5 - - + -
103A PHE* 3.3 14.5 - - + -
114A TYR* 3.9 29.8 - - + -
115A GLU 4.8 0.7 - - - -
116A MET* 3.5 36.6 - - + +
154C ILE* 4.2 8.7 - - + -
175C LEU* 3.7 26.9 - - + -
177C ASN 5.5 0.7 - - - +
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Residues in contact with LEU 79 (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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12A LEU* 3.7 33.2 - - + +
13A LYS* 3.4 23.4 + - + +
16A LEU* 3.2 31.6 - - + -
75A MET* 2.9 23.8 + - + +
76A SER* 4.1 2.7 - - - +
78A ILE* 1.3 71.6 - - - +
80A LYS* 1.3 57.3 + - - +
81A CYS 3.0 4.9 - - - -
82A ALA* 2.9 23.9 + - - +
88A ILE* 3.5 33.2 - - + -
101A LEU* 4.2 12.8 - - + -
103A PHE* 3.8 15.5 - - + -
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Residues in contact with LYS 80 (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 LYS* 4.5 6.4 + - - +
17A GLU* 3.7 30.7 - - + +
20A LYS* 4.5 6.5 - - - +
76A SER* 2.9 26.0 + - - +
77A LYS* 3.3 14.6 - - - +
78A ILE 3.1 0.4 - - - -
79A LEU* 1.3 76.6 - - - +
81A CYS* 1.3 56.9 + - - +
82A ALA 3.2 2.0 - - - +
146C ARG* 3.0 18.7 + - - -
149C ARG* 4.0 8.9 + - - +
150C ASP* 4.6 0.9 - - - -
153C HIS* 4.4 21.7 - - + +
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Residues in contact with CYS 81 (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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77A LYS 3.3 18.6 - - - -
78A ILE* 3.0 15.0 + - - +
79A LEU 3.0 0.8 - - - -
80A LYS* 1.3 76.8 - - - +
82A ALA* 1.3 58.8 + - - +
83A GLY 4.1 0.3 + - - -
86A ASP* 4.7 1.7 - - - +
103A PHE* 4.0 7.3 - - + -
110A LYS* 5.4 4.5 + - - -
112A SER* 5.1 3.3 + - - -
114A TYR* 3.5 30.6 + - + +
146C ARG* 3.4 7.3 + - - -
150C ASP* 3.6 47.0 - - - +
153C HIS* 4.3 4.3 - - - -
154C ILE* 4.3 8.3 - - - -
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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