Contacts of the helix formed by residues 75 - 85 (chain A) in PDB entry 4ENM
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 4.0 18.1 - - + +
67A SER 4.6 1.8 - - - -
68A LYS* 3.3 41.4 - - - +
69A ARG* 3.7 37.2 + - + +
72A SER 4.3 0.8 + - - -
73A ALA* 5.0 11.2 - - + +
74A GLY* 1.3 76.0 - - - +
76A GLN* 1.3 79.9 + - + +
78A GLN* 3.2 12.5 + - - +
79A LYS* 3.2 13.5 + - - +
95A GLY 5.0 7.1 - - - +
96A GLU* 6.1 0.5 - - - -
97A TYR* 4.7 12.6 + - + -
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Residues in contact with GLN 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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73A ALA* 4.5 12.0 + - - +
75A GLU* 1.3 87.2 + - - +
77A ARG* 1.3 62.7 + - - +
78A GLN 2.9 5.5 + - - -
79A LYS* 3.1 15.6 + - + +
80A ASP* 3.1 22.2 + - - +
97A TYR* 2.5 40.4 + - - -
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Residues in contact with ARG 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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50A PRO* 3.1 34.3 + - - +
56A TRP* 3.7 23.3 - - + -
74A GLY* 3.1 21.1 + - - +
76A GLN* 1.3 79.8 - - - +
78A GLN* 1.3 57.5 + - - +
80A ASP* 4.1 6.9 - - - +
81A ARG* 3.0 50.2 + - + +
7B BZG 3.3 32.9 - - - -
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Residues in contact with GLN 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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25A TYR* 5.3 0.9 + - - -
56A TRP* 3.9 12.3 + - + -
57A HIS* 3.2 30.8 + - - +
59A VAL 2.8 30.0 + - - +
60A ILE* 3.9 5.7 - - - +
66A ILE* 3.3 29.3 - - + +
67A SER* 5.0 0.5 + - - -
69A ARG* 3.0 25.6 + - - +
74A GLY 3.2 9.0 + - - +
75A GLU 3.2 10.2 + - - +
76A GLN 2.9 1.0 - - - -
77A ARG* 1.3 77.4 - - - +
79A LYS* 1.3 67.5 + - - +
81A ARG* 3.4 6.0 + - - +
82A LEU* 3.2 20.8 + - + +
7B BZG 3.7 8.9 + - - -
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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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66A ILE* 3.8 11.9 - - + +
75A GLU 3.2 3.8 + - - +
76A GLN* 3.1 16.4 + - + +
78A GLN* 1.3 74.5 - - - +
80A ASP* 1.3 70.5 + - + +
82A LEU* 2.9 13.5 + - - +
83A GLU* 2.9 43.3 + - + +
89A ILE* 4.1 23.1 - - + -
91A GLN* 4.9 15.1 - - - +
97A TYR* 3.6 40.8 - - + -
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Residues in contact with ASP 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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76A GLN 3.1 12.6 + - - +
77A ARG* 4.1 7.6 - - - +
79A LYS* 1.3 83.4 - - + +
81A ARG* 1.3 60.0 + - + +
82A LEU 2.9 1.4 + - - -
83A GLU* 3.0 21.0 + - - +
84A GLU* 2.6 35.9 + - - +
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Residues in contact with ARG 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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50A PRO 5.3 1.0 + - - -
52A THR 4.8 7.1 + - - -
54A VAL 4.6 3.2 + - - -
56A TRP* 3.4 44.8 - - + +
57A HIS* 3.7 42.8 + - + +
77A ARG* 3.0 44.4 + - + +
78A GLN 3.4 6.2 + - - +
79A LYS 3.3 0.6 - - - -
80A ASP* 1.3 79.5 - - + +
82A LEU* 1.3 58.2 + - - +
84A GLU* 3.0 19.7 + - - +
85A GLU* 3.2 24.8 + - - +
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Residues in contact with LEU 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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20A GLY 6.2 0.2 - - - -
21A LYS 4.9 2.2 - - - +
22A VAL* 3.8 28.0 - - + -
57A HIS* 3.8 28.5 - - + +
58A ARG* 4.8 2.2 - - + -
60A ILE* 4.8 7.9 - - + -
66A ILE* 3.9 24.7 - - + -
78A GLN* 3.2 18.0 + - + +
79A LYS 2.9 7.2 + - - +
81A ARG* 1.3 75.0 - - - +
83A GLU* 1.3 57.7 + - - +
84A GLU 3.0 1.8 - - - -
85A GLU* 2.7 34.2 + - + +
86A GLY 3.0 7.1 + - - -
87A VAL* 3.6 24.1 + - + +
89A ILE* 4.0 16.2 - - + -
99A LEU* 5.2 3.6 - - + -
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Residues in contact with GLU 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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79A LYS* 2.9 52.1 + - + +
80A ASP* 3.0 14.1 + - - +
82A LEU* 1.3 75.9 - - - +
84A GLU* 1.3 59.3 + - + +
86A GLY* 2.8 19.2 + - - -
87A VAL 4.0 22.6 + - - +
88A GLU* 5.2 3.8 - - - +
89A ILE* 4.5 14.6 + - + +
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Residues in contact with GLU 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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19A TYR* 3.1 13.8 + - - +
80A ASP* 2.6 37.3 + - - +
81A ARG* 3.0 25.0 + - - +
82A LEU 3.0 0.4 - - - -
83A GLU* 1.3 74.8 - - + +
85A GLU* 1.3 60.2 + - + +
86A GLY* 3.0 6.0 + - - -
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Residues in contact with GLU 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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19A TYR* 3.3 38.4 - - + -
20A GLY* 2.7 44.5 + - - -
21A LYS 4.8 0.3 - - - +
57A HIS* 2.6 19.0 + - - -
58A ARG* 2.5 37.6 + - - -
81A ARG 3.2 17.2 - - - +
82A LEU* 2.7 16.3 + - + +
84A GLU* 1.3 74.5 - - + +
86A GLY* 1.3 63.1 + - - +
87A VAL* 4.8 2.7 - - + -
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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