Contacts of the helix formed by residues 80 - 92 (chain E) in PDB entry 4NAW
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 THR 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E THR 4.0 9.0 - - - +
79E ARG* 1.3 82.2 - - - +
81E ILE* 1.3 65.6 + - - +
82E GLN* 3.4 6.8 + - - +
83E GLY* 3.1 19.3 + - - +
84E LEU* 3.0 19.6 + - - +
112E PRO 3.4 12.0 + - - -
113E ASP* 4.0 18.8 - - + +
114E GLN 3.2 7.6 - - - +
115E GLU* 4.7 5.8 - - + -
116E VAL* 4.5 2.6 - - - +
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Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E THR* 1.3 71.4 - - - +
82E GLN* 1.3 58.3 + - - +
84E LEU* 3.1 12.7 + - + +
85E ILE* 2.8 45.2 + - + +
102E ILE* 4.1 26.5 - - + -
110E PRO* 3.8 24.2 - - + +
111E SER 3.6 19.3 - - - +
112E PRO* 3.3 9.8 + - + +
114E GLN* 2.9 19.7 + - + +
116E VAL* 4.3 12.1 - - + -
119E LEU* 3.7 23.8 - - + -
131E LEU* 4.5 4.5 - - + -
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Residues in contact with GLN 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E THR* 3.7 4.7 - - - +
81E ILE* 1.3 77.2 - - - +
83E GLY* 1.3 57.8 + - - +
85E ILE* 3.1 24.3 + - - +
86E ASP* 2.8 65.0 + - - +
89E LYS* 5.5 0.6 - - - +
99E GLN* 4.1 12.9 + - - +
112E PRO* 2.9 40.8 + - + +
113F LEU* 6.3 1.6 - - + -
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Residues in contact with GLY 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ARG* 3.4 28.0 + - - -
80E THR* 3.1 17.7 + - - -
82E GLN* 1.3 77.2 - - - +
84E LEU* 1.3 60.7 + - - +
86E ASP* 3.6 10.1 + - - +
87E PHE 3.3 16.1 + - - -
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Residues in contact with LEU 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ILE* 4.6 12.1 - - + -
59E LEU* 4.4 17.0 - - + -
73E TRP* 6.3 2.9 - - + -
75E VAL* 5.1 5.6 - - + -
79E ARG* 4.1 16.7 - - + +
80E THR 3.0 11.7 + - - +
81E ILE* 3.1 19.5 + - + +
83E GLY* 1.3 75.0 - - - +
85E ILE* 1.3 63.9 + - - +
87E PHE* 3.3 11.2 + - + +
88E ILE* 3.2 40.2 + - + +
102E ILE* 4.6 8.7 - - + -
116E VAL* 4.6 8.5 - - + -
131E LEU* 3.2 34.8 - - + -
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Residues in contact with ILE 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E ILE* 2.8 34.9 + - + +
82E GLN* 3.1 30.9 + - - +
84E LEU* 1.3 73.7 - - - +
86E ASP* 1.3 65.7 + - - +
87E PHE 3.3 0.2 + - - -
88E ILE* 3.3 8.5 + - - +
89E LYS* 3.0 42.8 + - + +
99E GLN* 4.0 12.3 - - - +
100E LEU* 4.0 25.5 - - + +
101E PHE* 5.5 0.2 - - - -
102E ILE* 3.4 27.4 - - + +
112E PRO* 5.3 4.7 - - + -
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Residues in contact with ASP 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLN* 2.8 52.4 + - - +
83E GLY* 3.9 9.5 - - - +
84E LEU 3.3 0.2 - - - -
85E ILE* 1.3 77.5 - - - +
87E PHE* 1.3 61.6 + - - +
89E LYS* 3.6 11.8 + - - +
90E LYS* 3.3 43.2 + - - +
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Residues in contact with PHE 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E LEU* 5.9 0.4 - - + -
68E MET* 4.5 2.5 - - + -
73E TRP* 3.5 52.9 - + - -
79E ARG* 4.4 15.7 - - - +
83E GLY 3.3 12.8 + - - +
84E LEU* 3.5 15.7 - - + +
85E ILE 3.2 0.4 - - - -
86E ASP* 1.3 79.8 - - - +
88E ILE* 1.3 69.6 + - + +
90E LYS* 3.2 12.9 + - + +
91E PHE* 3.0 43.0 + + + +
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E LEU* 3.7 40.2 - - + -
68E MET* 3.9 13.0 - - + -
84E LEU* 3.2 22.5 + - + +
85E ILE* 3.3 1.5 + - - +
87E PHE* 1.3 80.7 - - + +
89E LYS* 1.3 63.6 + - - +
91E PHE* 3.2 6.4 + - - +
92E LEU* 2.9 43.5 + - + +
100E LEU* 3.3 24.7 - - + -
102E ILE* 4.1 22.9 - - + -
133E TYR* 4.6 9.2 - - + -
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLN* 5.5 0.9 - - - +
85E ILE* 3.0 40.8 + - + +
86E ASP* 3.9 12.1 - - - +
87E PHE 3.3 0.2 - - - -
88E ILE* 1.3 77.0 - - - +
90E LYS* 1.3 60.8 + - + +
93E LYS 3.2 1.7 + - - -
94E LEU* 2.8 51.9 + - + +
95E VAL 3.7 5.9 + - - -
96E ALA* 3.6 30.9 - - + +
97E SER 4.2 0.8 - - - +
98E GLU 3.1 27.1 + - - -
99E GLN* 3.4 23.8 + - - +
100E LEU* 4.1 15.1 - - + +
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Residues in contact with LYS 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASP* 3.3 33.0 + - - +
87E PHE* 3.2 12.0 + - + +
89E LYS* 1.3 74.6 - - + +
91E PHE* 1.3 63.0 + - - +
93E LYS* 2.8 23.9 + - - +
94E LEU 5.3 0.9 - - - -
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Residues in contact with PHE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E MET* 3.5 32.8 - - + -
69E LYS* 4.3 26.0 - - + -
70E THR* 4.4 14.1 - - - -
73E TRP* 3.7 26.9 - + - -
87E PHE* 3.0 36.4 + + + +
88E ILE 3.2 4.0 + - - +
90E LYS* 1.3 77.8 - - - +
92E LEU* 1.3 62.1 + - + +
93E LYS* 3.5 10.7 + - - +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 5.4 1.3 - - + -
66E PRO* 3.9 30.3 - - + +
67E ILE 3.7 24.9 - - - +
68E MET* 3.8 22.9 - - + -
88E ILE* 2.9 38.1 + - + +
91E PHE* 1.3 78.8 - - + +
93E LYS* 1.3 65.6 + - - +
94E LEU* 2.9 39.0 + - + +
100E LEU* 5.1 0.7 - - + -
133E TYR* 4.1 6.5 - - + -
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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