Contacts of the helix formed by residues 74 - 86 (chain C) in PDB entry 2AXZ
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 GLU 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C ASN* 1.3 85.4 + - - +
75C THR* 1.3 70.8 + - - +
76C GLY 3.1 2.0 + - - +
77C LYS* 3.3 14.6 + - - +
78C GLU* 3.0 29.0 - - + +
102C LYS* 5.0 7.0 + - - -
109C TYR* 2.6 31.7 + - + +
52D GLU* 2.8 27.8 - - - +
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Residues in contact with THR 75 (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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73C ASN* 3.7 13.9 + - - +
74C GLU* 1.3 74.9 - - + +
76C GLY* 1.3 68.1 + - - +
78C GLU* 3.2 13.0 + - - +
79C LYS* 2.8 42.0 + - - +
108C GLN* 2.9 41.5 + - + +
109C TYR* 3.9 32.1 - - + +
112C ILE* 4.1 6.7 - - - +
52D GLU* 5.2 1.8 - - + +
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Residues in contact with GLY 76 (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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73C ASN* 3.7 12.1 + - - -
74C GLU 3.1 2.1 - - - +
75C THR* 1.3 82.5 + - - +
77C LYS* 1.3 61.3 + - - +
79C LYS* 3.2 19.5 + - - +
80C LEU* 3.2 26.9 + - - +
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Residues in contact with LYS 77 (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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73C ASN 5.6 1.0 - - - +
74C GLU* 3.3 12.0 + - - +
76C GLY* 1.3 75.7 - - - +
78C GLU* 1.3 70.1 + - - +
80C LEU* 3.3 11.7 + - + +
81C LEU* 2.9 35.6 + - + +
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Residues in contact with GLU 78 (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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74C GLU* 3.0 28.1 - - + +
75C THR* 3.4 14.6 - - - +
77C LYS* 1.3 94.9 - - - +
79C LYS* 1.3 60.9 + - - +
81C LEU* 3.3 15.4 - - - +
82C ILE* 3.2 25.8 + - - +
95C ASN* 5.2 3.7 - - - +
98C ARG* 5.1 6.9 + - - -
99C ILE* 4.1 19.3 - - + +
109C TYR* 5.0 4.7 - - + -
112C ILE* 3.7 25.6 - - + -
116C TYR* 3.4 5.3 + - - +
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Residues in contact with LYS 79 (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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75C THR* 2.8 49.5 + - - +
76C GLY* 3.3 13.5 - - - +
77C LYS 3.2 0.2 - - - -
78C GLU* 1.3 74.1 - - - +
80C LEU* 1.3 65.6 + - + +
82C ILE* 3.2 29.2 + - + +
83C SER* 3.8 5.7 + - - -
108C GLN* 5.0 8.7 - - - +
111C SER* 6.0 0.4 - - - -
112C ILE* 4.1 18.2 - - + +
154C GLU* 4.3 20.4 - - - +
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Residues in contact with LEU 80 (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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76C GLY 3.2 15.1 + - - +
77C LYS* 3.3 12.1 + - + +
79C LYS* 1.3 76.3 - - + +
81C LEU* 1.3 62.2 + - - +
83C SER* 3.2 24.3 + - - +
84C LYS* 3.5 9.9 + - - +
224D LYS* 4.1 28.9 - - - +
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Residues in contact with LEU 81 (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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77C LYS* 2.9 23.5 + - + +
78C GLU* 3.3 17.7 - - - +
79C LYS 3.1 0.2 - - - -
80C LEU* 1.3 76.6 - - - +
82C ILE* 1.3 56.2 + - - +
84C LYS* 2.8 42.5 + - + +
85C ILE* 3.0 50.7 + - + -
95C ASN* 3.2 24.2 - - - +
116C TYR* 3.0 23.1 - - - +
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Residues in contact with ILE 82 (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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78C GLU 3.2 14.4 + - - +
79C LYS* 3.2 24.2 + - + +
81C LEU* 1.3 76.9 - - - +
83C SER* 1.3 62.7 + - - +
85C ILE* 3.5 6.5 + - - +
86C PHE* 3.2 31.5 + - + +
111C SER 4.9 1.1 - - - +
112C ILE* 3.8 33.7 - - + +
115C GLY* 4.2 19.1 - - - +
116C TYR* 3.8 17.7 - - + -
119C ILE* 4.1 15.7 - - + -
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Residues in contact with SER 83 (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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79C LYS 3.8 5.7 + - - -
80C LEU* 3.2 16.7 + - - +
81C LEU 3.1 0.4 - - - -
82C ILE* 1.3 79.2 - - - +
84C LYS* 1.3 63.3 + - - +
86C PHE* 3.3 18.3 - - - +
87C THR* 3.4 10.7 + - - -
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Residues in contact with LYS 84 (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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80C LEU 4.0 7.6 - - - +
81C LEU* 2.8 26.7 + - + +
83C SER* 1.3 74.1 - - - +
85C ILE* 1.3 61.2 + - - +
86C PHE 3.0 1.1 - - - -
87C THR* 2.7 28.8 + - - -
88C ASN* 2.9 22.2 + - - +
91C LEU* 3.6 24.0 - - - +
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Residues in contact with ILE 85 (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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81C LEU* 3.0 41.0 + - + +
82C ILE 3.9 0.7 - - - +
84C LYS* 1.3 76.4 - - - +
86C PHE* 1.3 62.1 + - - +
88C ASN 3.0 8.0 - - - +
89C PRO* 3.0 25.7 - - + +
91C LEU* 3.3 37.9 - - + +
92C PHE* 3.6 46.4 - - + +
95C ASN* 5.0 0.9 - - + -
116C TYR* 4.1 9.6 - - + -
119C ILE* 3.9 14.4 - - + -
123C TYR* 4.0 2.3 - - - -
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Residues in contact with PHE 86 (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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82C ILE* 3.2 20.3 + - + +
83C SER* 3.3 16.2 - - - +
84C LYS 3.0 0.6 - - - -
85C ILE* 1.3 76.9 - - - +
87C THR* 1.3 56.2 + - - +
115C GLY 4.2 5.2 - - - -
118C SER* 4.2 21.5 - - - -
119C ILE* 3.2 42.4 - - + -
122C HIS* 4.1 24.7 - + + -
123C TYR* 2.4 30.6 + + - -
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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