Contacts of the helix formed by residues 74 - 86 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A VAL* 2.5 15.8 + - + +
73A ASN* 1.3 76.2 - - - +
75A THR* 1.3 63.8 + - + +
76A GLY 3.1 1.6 + - - -
77A LYS* 3.2 17.3 + - - +
78A GLU* 3.0 36.2 + - - +
102A LYS* 5.0 3.3 + - - +
109A TYR* 2.9 32.2 + - + +
52B GLU* 3.9 15.3 - - - +
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Residues in contact with THR 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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73A ASN* 2.9 26.7 + - - +
74A GLU* 1.3 77.5 - - + +
76A GLY* 1.3 64.6 + - - +
78A GLU* 3.2 11.1 + - - +
79A LYS* 3.1 26.2 + - - +
106A SER* 4.8 0.9 - - - +
108A GLN* 3.8 33.7 + - + +
109A TYR* 3.5 38.6 - - + -
112A ILE* 3.6 9.8 - - + +
52B GLU* 5.7 7.2 - - + +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 5.4 0.7 - - - -
70A LYS* 3.7 30.1 - - - +
72A VAL 3.8 2.4 + - - -
73A ASN* 3.1 21.3 - - - +
74A GLU 3.1 1.0 - - - -
75A THR* 1.3 77.4 - - - +
77A LYS* 1.3 60.6 - - - +
79A LYS* 3.2 9.0 + - - +
80A LEU* 3.2 25.1 + - - +
7E VAL 5.8 0.7 - - - -
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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
----------------------------------------------------------
70A LYS 4.1 6.6 + - - +
72A VAL* 3.2 45.7 + - - +
74A GLU* 3.2 11.0 + - - +
76A GLY* 1.3 74.6 - - - +
78A GLU* 1.3 58.8 + - + +
80A LEU* 3.3 9.1 + - + +
81A LEU* 2.9 36.2 + - + +
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Residues in contact with GLU 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 GLU* 3.0 33.9 - - - +
75A THR* 3.2 6.9 + - - +
77A LYS* 1.3 79.6 - - - +
79A LYS* 1.3 60.9 + - - +
81A LEU* 3.3 13.0 - - - +
82A ILE* 3.2 24.8 + - - +
98A ARG* 2.5 43.2 + - - -
99A ILE* 3.7 14.6 - - + +
109A TYR* 4.3 4.6 + - + -
112A ILE* 3.3 31.0 - - + +
116A TYR* 4.4 3.5 + - - -
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Residues in contact with LYS 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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70A LYS* 4.6 5.4 - - - -
75A THR 3.1 15.5 + - - +
76A GLY* 3.6 8.5 - - - +
77A LYS 3.2 0.4 - - - -
78A GLU* 1.3 74.5 - - - +
80A LEU* 1.3 59.1 + - - +
82A ILE* 3.2 17.3 + - - +
108A GLN* 2.7 36.7 + - - +
111A SER* 4.7 1.6 - - - -
112A ILE* 3.8 21.8 - - + -
151A ILE* 3.9 0.2 - - - +
154A GLU* 2.9 29.2 + - - -
299A TYR* 2.6 29.0 + - + -
6E PHE* 3.9 29.6 - - + -
7E VAL* 2.7 30.1 + - - +
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Residues in contact with LEU 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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70A LYS* 3.3 57.0 - - + +
76A GLY 3.2 9.7 + - - +
77A LYS* 3.8 11.2 - - + +
79A LYS* 1.3 76.2 - - - +
81A LEU* 1.3 62.5 + - - +
83A SER* 3.2 19.2 + - - -
84A LYS* 3.5 4.9 + - - +
299A TYR* 4.0 15.5 - - + -
224B LYS* 4.1 30.5 - - - +
225B ASN* 6.1 0.4 - - - +
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Residues in contact with LEU 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* 2.9 21.9 + - + +
78A GLU* 3.3 15.7 - - - +
80A LEU* 1.3 75.7 - - - +
82A ILE* 1.3 57.9 + - - +
84A LYS* 2.8 39.2 + - + -
85A ILE* 3.0 34.5 + - + +
91A LEU* 5.4 4.3 - - + -
95A ASN* 3.6 13.2 - - - +
98A ARG* 3.6 27.4 - - - +
116A TYR* 4.2 4.5 - - - +
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Residues in contact with ILE 82 (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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78A GLU 3.3 11.7 - - - +
79A LYS* 3.2 15.7 - - - +
81A LEU* 1.3 78.6 - - - +
83A SER* 1.3 61.1 + - - +
85A ILE* 3.5 4.1 + - - +
86A PHE* 3.2 32.4 + - + -
112A ILE* 3.8 29.2 - - + +
115A GLY* 4.1 7.4 - - - +
116A TYR* 4.3 15.7 + - + -
119A ILE* 3.6 14.7 - - + +
297A MSE 3.9 22.2 - - + -
299A TYR* 4.0 1.1 - - - +
6E PHE* 3.4 34.1 - - + -
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Residues in contact with SER 83 (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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80A LEU* 3.2 12.2 + - - -
81A LEU 3.1 0.2 - - - -
82A ILE* 1.3 80.3 - - - +
84A LYS* 1.3 64.8 + - - +
86A PHE* 3.4 18.1 - - - +
87A THR* 3.4 10.7 + - - -
297A MSE 4.5 11.2 - - - -
299A TYR* 3.4 28.5 + - - -
305A ILE* 4.4 6.2 - - - +
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Residues in contact with LYS 84 (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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80A LEU 3.5 2.8 + - - +
81A LEU* 2.8 28.5 + - + +
83A SER* 1.3 76.9 - - - +
85A ILE* 1.3 55.9 + - - +
87A THR* 2.7 30.3 + - - -
88A ASN* 2.9 30.2 + - - +
91A LEU* 4.8 15.5 - - + -
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Residues in contact with ILE 85 (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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81A LEU* 3.0 22.6 + - + +
82A ILE* 4.0 1.6 - - - +
84A LYS* 1.3 74.8 - - - +
86A PHE* 1.3 60.8 + - - +
88A ASN* 3.5 9.9 - - - +
89A PRO* 3.0 22.6 - - + +
91A LEU* 3.7 17.3 - - + +
92A PHE* 3.8 26.5 - - + +
95A ASN* 3.3 21.3 - - - +
116A TYR* 3.3 35.7 - - + +
119A ILE* 3.6 29.6 - - + +
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 3.2 24.3 + - + -
83A SER 3.4 11.7 - - - +
84A LYS 3.0 0.4 - - - -
85A ILE* 1.3 77.4 - - - +
87A THR* 1.3 57.4 + - - +
115A GLY 4.3 1.6 - - - -
118A SER* 4.1 4.9 - - - -
119A ILE* 3.5 40.8 - - + +
122A HIS* 4.3 12.6 - - + -
123A TYR* 2.7 37.7 + + - -
295A VAL* 3.9 33.0 - - + -
297A MSE 3.6 31.6 - - + -
305A ILE* 3.5 33.0 - - + +
306A GLU* 5.2 0.3 - - - +
4E LEU* 3.9 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