Contacts of the helix formed by residues 73 - 86 (chain B) 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 ASN 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A SER* 5.1 4.2 + - - -
52A GLU* 6.1 3.4 - - - +
1B MSE 6.0 1.2 - - - +
2B PHE* 4.4 9.9 - - - -
69B THR* 2.8 42.9 - - - +
70B LYS 4.2 0.8 - - - +
71B SER 3.0 3.8 - - - +
72B VAL* 1.3 90.7 - - - +
74B GLU* 1.3 59.6 + - - +
75B THR* 4.6 6.5 - - - +
76B GLY* 2.7 31.1 + - - +
77B LYS* 2.9 12.2 + - - +
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Residues in contact with GLU 74 (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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52A GLU* 3.3 28.9 + - - +
72B VAL 4.1 1.0 + - - -
73B ASN* 1.3 72.4 - - - +
75B THR* 1.3 65.9 + - - +
77B LYS* 3.2 29.0 + - - +
78B GLU* 3.3 19.0 + - + +
102B LYS* 4.6 6.8 + - - -
109B TYR* 2.8 40.9 + - - +
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Residues in contact with THR 75 (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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52A GLU* 5.7 7.2 - - + +
73B ASN* 4.6 6.9 - - - +
74B GLU* 1.3 83.5 - - - +
76B GLY* 1.3 64.2 + - - +
78B GLU* 3.2 6.0 + - - +
79B LYS* 3.1 27.9 + - - +
106B SER* 4.8 1.3 - - - +
108B GLN* 3.9 33.6 + - + +
109B TYR* 3.6 36.3 - - + -
112B ILE* 3.5 14.9 - - + +
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Residues in contact with GLY 76 (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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70B LYS* 2.7 41.4 - - - +
71B SER 4.0 0.2 - - - -
73B ASN* 2.7 20.1 + - - +
75B THR* 1.3 76.0 + - - +
77B LYS* 1.3 58.6 + - - -
79B LYS* 3.2 12.6 + - - +
80B LEU* 3.2 15.2 + - - +
7F VAL 5.9 0.4 - - - -
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Residues in contact with LYS 77 (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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70B LYS 3.7 2.6 + - - -
71B SER* 2.8 34.5 - - - +
72B VAL 5.4 1.3 - - - +
73B ASN 2.9 7.1 + - - +
74B GLU* 3.6 26.7 - - - +
76B GLY* 1.3 75.4 - - - +
78B GLU* 1.3 61.8 + - + +
80B LEU* 3.3 7.0 + - - +
81B LEU* 2.9 30.6 + - - +
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Residues in contact with GLU 78 (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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74B GLU* 3.3 19.0 - - - +
75B THR* 3.2 4.2 + - - +
77B LYS* 1.3 80.6 - - - +
79B LYS* 1.3 60.3 + - - +
81B LEU* 3.3 8.9 - - - +
82B ILE* 3.1 25.2 + - - +
98B ARG* 2.5 48.3 + - - -
99B ILE* 3.6 13.5 - - + +
109B TYR* 4.5 11.0 + - + +
112B ILE* 3.3 31.4 - - + +
116B TYR* 4.0 8.3 + - - -
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Residues in contact with LYS 79 (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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70B LYS* 5.5 4.3 - - + -
75B THR 3.1 16.9 + - - +
76B GLY* 3.5 10.5 - - - +
77B LYS 3.2 0.2 - - - -
78B GLU* 1.3 75.4 - - - +
80B LEU* 1.3 60.1 + - + +
82B ILE* 3.2 18.9 + - - +
108B GLN* 2.6 38.4 + - - +
111B SER* 5.1 0.9 - - - -
112B ILE* 3.8 20.4 - - + -
151B ILE* 4.9 0.2 - - - -
154B GLU* 3.1 28.0 + - - -
299B TYR* 2.7 29.4 + - + -
6F PHE* 4.1 25.8 - - + -
7F VAL 2.6 30.9 + - - +
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Residues in contact with LEU 80 (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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224A LYS* 4.0 26.9 - - - +
70B LYS* 2.9 39.3 - - + +
71B SER* 3.7 20.4 - - - +
76B GLY 3.2 2.2 + - - +
77B LYS* 3.8 8.1 - - - +
79B LYS* 1.3 79.2 - - - +
81B LEU* 1.3 63.2 + - - +
83B SER* 3.2 19.7 + - - -
84B LYS* 3.5 5.0 + - - +
299B TYR* 3.9 27.4 - - + -
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Residues in contact with LEU 81 (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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77B LYS 2.9 18.0 + - - +
78B GLU* 3.3 14.1 - - - +
79B LYS 3.1 0.2 - - - -
80B LEU* 1.3 75.1 - - - +
82B ILE* 1.3 56.8 + - - +
84B LYS* 2.8 49.8 + - + +
85B ILE* 3.0 45.0 + - + -
91B LEU* 5.9 1.1 - - + -
95B ASN* 4.1 14.1 - - - +
98B ARG* 5.3 2.5 - - - +
116B TYR* 3.7 10.1 - - - +
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Residues in contact with ILE 82 (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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78B GLU 3.1 13.8 + - - +
79B LYS* 3.2 19.3 + - - +
81B LEU* 1.3 78.8 - - - +
83B SER* 1.3 61.7 + - - +
85B ILE* 3.5 1.4 + - - -
86B PHE* 3.2 23.6 + - + -
112B ILE* 3.9 27.4 - - + +
115B GLY* 4.1 14.1 - - - +
116B TYR* 4.3 15.3 - - + -
119B ILE* 3.7 22.3 - - + +
297B MSE 4.2 18.4 - - + -
299B TYR* 4.1 1.8 - - - +
6F PHE* 3.5 30.1 - - + -
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Residues in contact with SER 83 (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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80B LEU* 3.2 12.5 + - - -
81B LEU 3.1 0.4 - - - -
82B ILE* 1.3 78.2 - - - +
84B LYS* 1.3 63.5 + - - +
86B PHE* 3.4 18.2 - - - +
87B THR* 3.6 12.8 + - - +
297B MSE 4.6 12.2 - - - -
299B TYR* 3.5 28.0 + - - -
305B ILE* 5.2 1.9 - - - +
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Residues in contact with LYS 84 (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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80B LEU 3.5 2.6 + - - +
81B LEU* 2.8 40.1 + - + +
83B SER* 1.3 75.2 - - - +
85B ILE* 1.3 56.7 + - - +
86B PHE 3.0 1.6 - - - -
87B THR* 2.5 36.2 + - - +
88B ASN* 2.9 18.1 + - - +
91B LEU* 3.7 26.9 - - + -
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Residues in contact with ILE 85 (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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81B LEU* 3.0 32.8 + - + +
82B ILE 4.0 1.3 - - - +
84B LYS* 1.3 75.4 - - + +
86B PHE* 1.3 61.5 + - - +
88B ASN* 3.5 10.3 - - - +
89B PRO* 3.0 22.0 - - + +
91B LEU* 3.5 13.5 - - + +
92B PHE* 3.9 23.3 - - + +
95B ASN* 3.4 20.4 - - - +
116B TYR* 3.2 32.8 - - + -
119B ILE* 3.5 31.6 - - + +
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Residues in contact with PHE 86 (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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82B ILE* 3.2 22.2 + - + -
83B SER 3.4 12.1 - - - +
84B LYS 3.0 0.6 - - - -
85B ILE* 1.3 76.9 - - - +
87B THR* 1.3 57.8 + - - +
115B GLY 4.5 1.1 - - - -
118B SER* 4.1 6.3 - - - -
119B ILE* 3.8 42.1 - - + +
122B HIS* 4.2 14.8 - + + -
123B TYR* 2.8 32.8 + + - -
295B VAL* 3.8 26.0 - - + -
297B MSE 3.6 28.0 - - + -
305B ILE* 3.4 40.9 - - + +
4F LEU* 3.8 12.1 - - + -
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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