Contacts of the helix formed by residues 76 - 88 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73R PHE 3.0 18.0 + - - -
74R ARG 3.2 1.6 + - - -
75R ASN* 1.3 77.5 + - - +
77R LEU* 1.3 58.2 + - - +
78R LYS 3.6 1.6 - - - -
79R LEU* 3.3 11.4 + - - +
80R MET* 2.9 37.7 + - - +
106R ASN* 4.6 2.5 - - - -
107R VAL* 3.7 21.3 - - - +
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Residues in contact with LEU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R ASN* 2.9 40.6 + - - +
76R GLY* 1.3 71.0 - - - +
78R LYS* 1.3 61.6 + - + +
80R MET* 3.1 7.9 + - - +
81R LEU* 2.9 27.1 + - - +
94R PRO* 3.8 31.9 - - + -
95R ASP 5.1 1.8 - - - +
106R ASN* 4.1 15.5 - - - +
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Residues in contact with LYS 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R LEU* 3.6 8.5 - - + +
64R THR* 2.8 30.0 + - + +
65R GLN 2.8 28.8 + - - +
66R ILE* 3.9 13.4 - - + +
72R ASP* 4.1 15.6 + - + +
73R PHE* 3.6 17.6 - - + -
75R ASN* 4.3 2.2 + - - +
77R LEU* 1.3 77.5 - - + +
79R LEU* 1.3 60.2 + - - +
81R LEU* 3.6 12.6 - - + -
82R LEU* 2.8 29.6 + - - +
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Residues in contact with LEU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R PHE* 3.6 24.7 - - + +
76R GLY* 3.3 17.0 + - - +
77R LEU 3.1 0.6 - - - -
78R LYS* 1.3 79.2 - - - +
80R MET* 1.3 62.0 + - - +
82R LEU* 3.4 5.2 + - + +
83R LEU* 3.2 25.3 + - + +
107R VAL* 4.7 8.3 - - + -
110R ALA* 3.7 22.9 - - + -
111R LEU* 5.4 0.2 - - + -
129R ILE* 4.5 12.1 - - + -
140R MET* 3.5 44.0 - - + -
141R ILE* 4.3 9.2 - - + -
144R ILE* 3.9 22.7 - - + -
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Residues in contact with MET 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76R GLY 2.9 26.2 + - - +
77R LEU* 3.5 5.6 - - - +
79R LEU* 1.3 74.2 - - - +
81R LEU* 1.3 64.6 + - - +
83R LEU* 3.2 4.5 + - - +
84R GLU* 3.1 31.6 + - - +
91R LEU* 4.0 24.8 - - + +
92R PRO 3.1 28.0 - - - +
94R PRO* 4.3 18.8 - - + -
106R ASN* 3.5 36.8 - - - +
109R LYS* 3.8 23.3 - - + -
110R ALA* 4.1 10.1 - - + +
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Residues in contact with LEU 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R LEU* 4.3 3.4 - - + -
62R ALA* 3.9 26.0 - - + +
64R THR* 3.9 28.9 - - + -
77R LEU 2.9 17.3 + - - +
78R LYS* 3.6 13.5 - - + +
80R MET* 1.3 78.0 - - - +
82R LEU* 1.3 62.1 + - - +
84R GLU* 3.3 19.2 + - + +
85R VAL* 3.0 28.0 + - + +
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Residues in contact with LEU 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R TRP* 4.1 14.8 - - + -
55R CYS* 3.7 39.5 - - + +
58R HIS* 3.8 28.3 - - + -
59R LEU* 3.6 13.9 - - + +
73R PHE* 4.3 9.2 - - + -
78R LYS 2.8 21.5 + - - +
79R LEU* 3.5 9.2 - - + +
81R LEU* 1.3 74.4 - - - +
83R LEU* 1.3 57.7 + - + +
85R VAL* 3.3 3.4 + - - +
86R ILE* 3.1 41.6 + - + +
141R ILE* 4.3 10.1 - - + -
144R ILE* 4.9 7.2 - - + -
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Residues in contact with LEU 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R LEU* 3.2 15.9 + - + +
80R MET 3.2 6.5 + - - +
82R LEU* 1.3 75.9 - - + +
84R GLU* 1.3 62.2 + - - +
86R ILE* 3.7 4.0 - - + +
87R SER* 2.8 31.5 + - - -
91R LEU* 4.0 14.4 - - + -
110R ALA* 3.6 41.5 - - + +
113R PHE* 4.1 10.7 - - + -
114R ILE* 4.0 12.6 - - + -
144R ILE* 3.8 30.1 - - + -
148R PHE* 3.9 29.2 - - + -
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Residues in contact with GLU 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80R MET* 3.1 18.7 + - - +
81R LEU* 3.3 23.1 + - + +
83R LEU* 1.3 75.7 - - - +
85R VAL* 1.3 60.0 + - + +
87R SER* 4.0 0.9 - - - -
88R GLY* 2.8 30.8 + - - -
89R GLU 3.3 20.9 + - - +
90R ARG* 3.4 37.9 + - - +
91R LEU* 3.0 37.4 + - + +
92R PRO 5.0 0.5 - - - +
93R ARG* 3.5 12.9 + - - -
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Residues in contact with VAL 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58R HIS* 3.6 42.4 - - + +
59R LEU* 5.0 1.6 - - - -
61R LYS* 4.6 14.6 - - + +
62R ALA* 3.9 28.7 - - + +
81R LEU* 3.0 19.1 + - + +
82R LEU* 3.5 10.1 - - - +
83R LEU 3.3 0.2 - - - -
84R GLU* 1.3 79.3 - - + +
86R ILE* 1.3 63.5 + - + +
87R SER 3.5 0.2 + - - -
88R GLY* 3.7 5.7 + - - -
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Residues in contact with ILE 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R TRP* 4.1 10.1 - - + -
58R HIS* 3.5 46.2 - - + +
82R LEU* 3.1 23.5 + - + +
83R LEU* 3.7 11.2 - - + +
85R VAL* 1.3 76.1 - - - +
87R SER* 1.3 61.7 + - - +
144R ILE* 3.5 26.2 - - + -
148R PHE* 3.4 44.4 - - + +
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Residues in contact with SER 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83R LEU 2.8 22.1 + - - -
84R GLU* 3.8 0.9 + - - -
86R ILE* 1.3 76.8 - - - +
88R GLY* 1.3 61.8 + - - +
89R GLU* 3.0 37.9 + - - +
113R PHE* 3.7 12.2 - - - -
148R PHE* 3.8 27.6 - - - -
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Residues in contact with GLY 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R GLU 2.8 14.3 + - - -
85R VAL 3.7 4.8 + - - -
86R ILE 3.5 1.8 - - - -
87R SER* 1.3 78.9 - - - +
89R GLU* 1.3 62.1 + - - +
90R 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