Contacts of the helix formed by residues 76 - 88 (chain N) in PDB entry 3LUE
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 GLY 76 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73N PHE* 3.0 17.6 + - - -
74N ARG 3.2 1.4 + - - -
75N ASN* 1.3 77.5 + - - +
77N LEU* 1.3 58.3 + - - +
78N LYS 3.6 1.1 - - - -
79N LEU* 3.4 11.6 - - - +
80N MET* 2.9 37.5 + - - +
106N ASN* 4.6 2.5 - - - -
107N VAL* 3.7 21.5 - - - +
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Residues in contact with LEU 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N ASN* 2.9 41.4 + - - +
76N GLY* 1.3 70.1 - - - +
78N LYS* 1.3 61.7 + - + +
79N LEU 3.1 0.2 - - - -
80N MET* 3.1 7.3 + - - +
81N LEU* 2.9 27.1 + - - +
94N PRO* 3.8 31.9 - - + -
95N ASP 5.1 2.0 - - - +
106N ASN* 4.1 15.7 - - - +
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Residues in contact with LYS 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N LEU* 3.6 8.9 - - + +
64N THR* 2.8 30.2 + - + +
65N GLN 2.8 29.0 + - - +
66N ILE* 3.9 14.1 - - + +
72N ASP* 4.1 14.9 + - + +
73N PHE* 3.6 18.0 - - + -
75N ASN* 4.3 2.5 + - - +
77N LEU* 1.3 77.3 - - + +
79N LEU* 1.3 59.7 + - - +
81N LEU* 3.6 11.7 - - + -
82N LEU* 2.8 29.5 + - - +
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Residues in contact with LEU 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N PHE* 3.6 24.3 - - + +
76N GLY* 3.3 16.3 + - - +
77N LEU 3.1 0.4 - - - -
78N LYS* 1.3 78.6 - - - +
80N MET* 1.3 62.3 + - - +
82N LEU* 3.4 5.6 + - + +
83N LEU* 3.2 24.5 + - + +
107N VAL* 4.7 7.9 - - + -
110N ALA* 3.7 24.0 - - + -
111N LEU* 5.4 0.2 - - + -
129N ILE* 4.5 12.3 - - + -
140N MET* 3.5 43.3 - - + -
141N ILE* 4.3 9.6 - - + -
144N ILE* 3.9 22.9 - - + -
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Residues in contact with MET 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N GLY 2.9 24.9 + - - +
77N LEU* 3.5 6.3 - - - +
79N LEU* 1.3 74.3 - - - +
81N LEU* 1.3 64.9 + - - +
83N LEU* 3.2 4.5 + - - +
84N GLU* 3.1 31.4 + - - +
91N LEU* 4.0 25.5 - - + +
92N PRO 3.1 27.6 - - - +
94N PRO* 4.3 18.2 - - + -
106N ASN* 3.5 36.8 - - - +
109N LYS* 3.8 23.6 - - + -
110N ALA* 4.1 10.8 - - + +
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Residues in contact with LEU 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N LEU* 4.3 3.6 - - + -
62N ALA* 3.9 26.5 - - + +
64N THR* 3.9 29.2 - - + -
77N LEU 2.9 17.4 + - - +
78N LYS* 3.6 12.8 - - + +
80N MET* 1.3 76.6 - - - +
82N LEU* 1.3 61.8 + - - +
84N GLU* 3.3 19.5 + - + +
85N VAL* 3.0 28.6 + - + +
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Residues in contact with LEU 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N TRP* 4.1 15.5 - - + -
55N CYS* 3.7 38.8 - - + +
58N HIS* 3.8 28.5 - - + -
59N LEU* 3.6 13.2 - - + +
73N PHE* 4.3 9.4 - - + -
78N LYS 2.8 21.7 + - - +
79N LEU* 3.5 8.5 - - + +
81N LEU* 1.3 73.8 - - - +
83N LEU* 1.3 57.4 + - + +
85N VAL* 3.3 3.4 + - - +
86N ILE* 3.1 42.1 + - + +
141N ILE* 4.3 10.5 - - + -
144N ILE* 4.9 7.9 - - + -
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Residues in contact with LEU 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N LEU* 3.2 16.4 + - + +
80N MET 3.2 6.9 + - - +
82N LEU* 1.3 75.4 - - + +
84N GLU* 1.3 63.3 + - - +
86N ILE* 3.7 4.1 - - + +
87N SER* 2.8 31.5 + - - -
91N LEU* 4.0 14.8 - - + -
110N ALA* 3.6 40.8 - - + +
113N PHE* 4.1 10.8 - - + -
114N ILE* 4.0 12.8 - - + -
144N ILE* 3.8 30.5 - - + -
148N PHE* 3.9 28.5 - - + -
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Residues in contact with GLU 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N MET* 3.1 19.2 + - - +
81N LEU* 3.8 22.6 - - + +
83N LEU* 1.3 76.9 - - - +
85N VAL* 1.3 59.0 + - + +
87N SER* 4.0 0.9 - - - -
88N GLY* 2.8 30.5 + - - -
89N GLU 3.3 21.5 + - - +
90N ARG* 3.4 37.2 + - - +
91N LEU* 3.0 37.2 + - + +
92N PRO 5.0 0.5 - - - +
93N ARG* 3.5 12.9 + - - -
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Residues in contact with VAL 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N HIS* 3.6 42.2 - - + +
59N LEU* 5.0 1.6 - - - -
61N LYS* 4.6 14.4 - - + +
62N ALA* 3.9 28.7 - - + +
81N LEU* 3.0 19.5 + - + +
82N LEU* 3.5 10.8 - - - +
83N LEU 3.3 0.2 - - - -
84N GLU* 1.3 79.0 - - + +
86N ILE* 1.3 63.9 + - + +
87N SER 3.5 0.2 + - - -
88N GLY* 3.7 5.7 + - - -
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Residues in contact with ILE 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N TRP* 4.1 10.5 - - + -
58N HIS* 3.5 46.0 - - + +
82N LEU* 3.1 24.4 + - + +
83N LEU* 3.7 10.8 - - + +
85N VAL* 1.3 75.7 - - - +
87N SER* 1.3 61.3 + - - +
144N ILE* 3.5 26.7 - - + -
148N PHE* 3.4 44.0 - - + +
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Residues in contact with SER 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N LEU 2.8 21.9 + - - -
84N GLU* 3.8 0.9 + - - -
86N ILE* 1.3 78.1 - - - +
88N GLY* 1.3 61.3 + - - +
89N GLU* 3.0 37.7 + - - +
113N PHE* 3.7 12.2 - - - -
148N PHE* 3.8 28.0 - - - -
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Residues in contact with GLY 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N GLU 2.8 13.9 + - - -
85N VAL 3.7 4.6 + - - -
86N ILE 3.5 1.8 - - - -
87N SER* 1.3 79.5 - - - +
89N GLU* 1.3 61.3 + - - +
90N ARG* 5.2 3.5 - - - -
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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