Contacts of the helix formed by residues 76 - 88 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73O PHE 3.0 18.2 + - - -
74O ARG 3.2 1.2 + - - -
75O ASN* 1.3 77.0 + - - +
77O LEU* 1.3 58.1 + - - +
78O LYS 3.6 0.9 - - - -
79O LEU* 3.4 11.0 - - - +
80O MET* 2.9 37.4 + - - +
106O ASN* 4.6 2.5 - - - -
107O VAL* 3.7 21.5 - - - +
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Residues in contact with LEU 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O ASN* 2.9 39.9 + - + +
76O GLY* 1.3 70.9 - - - +
78O LYS* 1.3 61.5 + - + +
80O MET* 3.1 8.4 + - - +
81O LEU* 2.9 27.1 + - - +
94O PRO* 3.8 31.9 - - + -
95O ASP 5.1 2.0 - - - +
106O ASN* 4.1 15.7 - - - +
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Residues in contact with LYS 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O LEU* 3.6 9.0 - - + +
64O THR* 2.8 30.9 + - + +
65O GLN 2.8 29.0 + - - +
66O ILE* 3.9 13.6 - - + +
72O ASP* 4.1 15.5 + - + +
73O PHE* 3.6 17.4 - - + -
75O ASN* 4.3 2.2 + - - +
76O GLY 3.6 0.2 - - - -
77O LEU* 1.3 76.6 - - + +
79O LEU* 1.3 58.9 + - - +
80O MET 3.3 0.2 - - - -
81O LEU* 3.6 12.6 - - + -
82O LEU* 2.8 30.1 + - - +
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Residues in contact with LEU 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73O PHE* 3.6 24.5 - - + +
76O GLY* 3.3 16.7 + - - +
77O LEU 3.1 0.4 - - - -
78O LYS* 1.3 79.6 - - - +
80O MET* 1.3 61.7 + - - +
82O LEU* 3.4 4.9 + - + +
83O LEU* 3.2 24.9 + - + +
107O VAL* 4.7 7.9 - - + -
110O ALA* 3.7 23.6 - - + -
129O ILE* 4.5 12.1 - - + -
140O MET* 3.5 43.5 - - + -
141O ILE* 4.3 9.4 - - + -
144O ILE* 3.9 22.9 - - + -
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Residues in contact with MET 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O GLY 2.9 26.9 + - - +
77O LEU* 3.5 6.1 - - - +
79O LEU* 1.3 73.9 - - - +
81O LEU* 1.3 63.3 + - - +
83O LEU* 3.2 4.8 + - - +
84O GLU* 3.1 31.4 + - - +
91O LEU* 4.0 25.6 - - + +
92O PRO 3.1 28.0 - - - +
94O PRO* 4.3 18.4 - - + -
106O ASN* 3.5 35.2 - - - +
109O LYS* 3.8 23.3 - - + -
110O ALA* 4.1 10.5 - - + -
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O LEU* 4.3 3.8 - - + -
62O ALA* 3.9 26.5 - - + +
64O THR* 3.9 29.8 - - + -
77O LEU 2.9 16.6 + - - +
78O LYS* 3.6 13.5 - - + +
80O MET* 1.3 77.7 - - - +
82O LEU* 1.3 61.8 + - - +
84O GLU* 3.3 19.8 + - + +
85O VAL* 3.0 28.0 + - + +
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Residues in contact with LEU 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O TRP* 4.1 14.6 - - + -
55O CYS* 3.7 38.4 - - + +
58O HIS* 3.8 28.5 - - + -
59O LEU* 3.6 14.1 - - + +
73O PHE* 4.3 9.9 - - + -
78O LYS 2.8 21.7 + - - +
79O LEU* 3.5 10.1 - - + +
80O MET 3.2 0.2 - - - -
81O LEU* 1.3 74.2 - - - +
83O LEU* 1.3 58.6 + - + +
85O VAL* 3.3 3.5 + - - +
86O ILE* 3.1 42.5 + - + +
141O ILE* 4.3 10.1 - - + -
144O ILE* 4.9 6.7 - - + -
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Residues in contact with LEU 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O LEU* 3.2 16.2 + - + +
80O MET 3.2 6.9 + - - +
82O LEU* 1.3 75.4 - - + +
84O GLU* 1.3 63.3 + - - +
86O ILE* 3.7 3.3 - - + +
87O SER* 2.8 30.9 + - - -
91O LEU* 4.0 14.4 - - + -
110O ALA* 3.6 40.6 - - + +
113O PHE* 4.1 11.3 - - + -
114O ILE* 4.0 13.0 - - + -
144O ILE* 3.8 30.5 - - + -
148O PHE* 3.9 28.9 - - + -
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Residues in contact with GLU 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O MET* 3.1 19.3 + - - +
81O LEU* 3.3 23.5 + - + +
83O LEU* 1.3 75.3 - - - +
85O VAL* 1.3 58.8 + - + +
87O SER* 4.0 0.9 - - - -
88O GLY* 2.8 31.0 + - - -
89O GLU 3.3 21.2 + - - +
90O ARG* 3.4 38.1 + - - +
91O LEU* 3.0 37.2 + - + +
92O PRO 5.0 0.5 - - - +
93O ARG* 3.5 13.3 + - - -
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Residues in contact with VAL 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O HIS* 3.6 41.5 - - + +
59O LEU* 5.0 1.6 - - - -
61O LYS* 4.6 14.6 - - + +
62O ALA* 3.9 28.5 - - + +
81O LEU* 3.0 19.5 + - + +
82O LEU* 3.5 10.1 - - - +
84O GLU* 1.3 80.3 - - + +
86O ILE* 1.3 64.4 + - + +
88O GLY* 3.7 5.7 + - - -
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Residues in contact with ILE 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O TRP* 4.1 9.9 - - + -
58O HIS* 3.5 45.3 - - + +
82O LEU* 3.1 24.7 + - + +
83O LEU* 3.7 11.4 - - + +
85O VAL* 1.3 75.3 - - - +
87O SER* 1.3 62.0 + - - +
144O ILE* 3.5 26.2 - - + -
148O PHE* 3.4 44.0 - - + +
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Residues in contact with SER 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O LEU 2.8 21.7 + - - -
84O GLU* 3.8 0.9 + - - -
86O ILE* 1.3 77.9 - - - +
88O GLY* 1.3 61.3 + - - +
89O GLU* 3.0 38.0 + - - +
113O PHE* 3.7 12.8 - - - -
148O PHE* 3.8 27.6 - - - -
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Residues in contact with GLY 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O GLU 2.8 13.7 + - - -
85O VAL 3.7 5.0 + - - -
86O ILE 3.5 1.6 - - - -
87O SER* 1.3 78.7 - - - +
89O GLU* 1.3 61.1 + - - +
90O 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