Contacts of the helix formed by residues 76 - 88 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73S PHE* 3.0 17.6 + - - -
74S ARG 3.2 1.4 + - - -
75S ASN* 1.3 76.8 + - - +
77S LEU* 1.3 57.4 + - - +
78S LYS 3.6 1.3 - - - -
79S LEU* 3.4 10.5 - - - +
80S MET* 2.9 37.2 + - - +
106S ASN* 4.6 2.0 - - - -
107S VAL* 3.7 21.8 - - - -
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Residues in contact with LEU 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75S ASN* 2.9 39.9 + - + +
76S GLY* 1.3 71.4 - - - +
78S LYS* 1.3 62.9 + - + +
79S LEU 3.1 0.2 - - - -
80S MET* 3.1 7.7 + - - +
81S LEU* 2.9 26.9 + - - +
94S PRO* 3.8 32.8 - - + -
95S ASP 5.1 1.8 - - - +
106S ASN* 4.1 15.5 - - + +
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Residues in contact with LYS 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59S LEU* 3.6 8.9 - - + +
64S THR* 2.8 30.5 + - + +
65S GLN 2.8 28.8 + - - +
66S ILE* 3.9 14.3 - - + +
72S ASP* 4.1 14.9 + - + +
73S PHE* 3.6 17.2 - - + -
75S ASN* 4.3 2.3 + - - +
76S GLY 3.6 0.2 - - - -
77S LEU* 1.3 77.4 - - + +
79S LEU* 1.3 59.7 + - - +
81S LEU* 3.6 12.1 - - + -
82S LEU* 2.8 29.5 + - - +
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Residues in contact with LEU 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73S PHE* 3.6 24.5 - - + +
76S GLY* 3.3 16.8 + - - +
77S LEU 3.1 0.6 - - - -
78S LYS* 1.3 77.9 - - - +
80S MET* 1.3 62.0 + - - +
82S LEU* 3.4 5.3 + - + +
83S LEU* 3.2 24.9 + - + +
107S VAL* 4.7 7.9 - - + -
110S ALA* 3.7 22.9 - - + -
129S ILE* 4.5 12.3 - - + -
140S MET* 3.5 43.5 - - + -
141S ILE* 4.3 9.6 - - + -
144S ILE* 3.9 22.4 - - + -
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Residues in contact with MET 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S GLY 2.9 26.7 + - - +
77S LEU* 3.5 5.4 - - - +
79S LEU* 1.3 73.5 - - - +
81S LEU* 1.3 63.3 + - - +
83S LEU* 3.2 4.7 + - - +
84S GLU* 3.1 32.0 + - - +
91S LEU* 3.9 25.4 - - + +
92S PRO 3.1 27.8 - - - +
94S PRO* 4.3 18.6 - - + -
106S ASN* 3.5 36.1 - - - +
109S LYS* 3.8 23.3 - - + -
110S ALA* 4.1 10.3 - - + -
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Residues in contact with LEU 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59S LEU* 4.3 3.6 - - + -
62S ALA* 3.9 26.5 - - + +
64S THR* 3.9 29.2 - - + -
77S LEU 2.9 16.5 + - - +
78S LYS* 3.6 13.2 - - + +
80S MET* 1.3 77.2 - - - +
82S LEU* 1.3 62.2 + - - +
84S GLU* 3.3 19.5 + - - +
85S VAL* 3.0 28.0 + - + +
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Residues in contact with LEU 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S TRP* 4.1 15.0 - - + -
55S CYS* 3.7 37.9 - - + +
58S HIS* 3.8 27.8 - - + -
59S LEU* 3.6 14.3 - - + +
73S PHE* 4.3 10.1 - - + -
78S LYS 2.8 21.5 + - - +
79S LEU* 3.5 10.1 - - + +
80S MET 3.2 0.2 - - - -
81S LEU* 1.3 74.0 - - - +
83S LEU* 1.3 58.1 + - + +
85S VAL* 3.3 3.3 + - - +
86S ILE* 3.1 42.7 + - + +
141S ILE* 4.3 9.9 - - + -
144S ILE* 4.9 6.3 - - + -
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Residues in contact with LEU 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S LEU* 3.2 16.8 + - + +
80S MET 3.2 6.7 + - - +
82S LEU* 1.3 75.6 - - - +
84S GLU* 1.3 63.1 + - - +
86S ILE* 3.7 4.0 - - + +
87S SER* 2.8 31.6 + - - -
91S LEU* 4.0 14.6 - - + -
110S ALA* 3.6 40.2 - - + +
113S PHE* 4.1 11.2 - - + -
114S ILE* 4.0 13.0 - - + -
144S ILE* 3.8 29.4 - - + -
148S PHE* 3.9 29.2 - - + -
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Residues in contact with GLU 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80S MET* 3.1 19.1 + - - +
81S LEU* 3.3 22.8 + - - +
83S LEU* 1.3 75.1 - - - +
85S VAL* 1.3 58.8 + - + +
87S SER* 4.0 0.9 - - - -
88S GLY* 2.8 31.0 + - - -
89S GLU 3.3 21.3 + - - +
90S ARG* 3.4 38.7 + - - +
91S LEU* 3.0 36.9 + - + +
92S PRO 5.0 0.5 - - - +
93S ARG* 3.5 12.6 + - - -
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Residues in contact with VAL 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58S HIS* 3.6 42.2 - - + +
59S LEU* 5.0 1.6 - - - -
61S LYS* 4.6 14.1 - - + +
62S ALA* 3.9 28.7 - - + +
81S LEU* 3.0 18.8 + - + +
82S LEU* 3.5 10.8 - - - +
84S GLU* 1.3 81.0 - - + +
86S ILE* 1.3 63.3 + - + +
88S GLY* 3.7 5.9 + - - -
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Residues in contact with ILE 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S TRP* 4.1 10.5 - - + -
58S HIS* 3.5 45.3 - - + +
82S LEU* 3.1 24.4 + - + +
83S LEU* 3.7 10.8 - - + +
85S VAL* 1.3 77.0 - - - +
87S SER* 1.3 61.7 + - - +
144S ILE* 3.5 26.2 - - + -
148S PHE* 3.4 44.5 - - + +
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Residues in contact with SER 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S LEU 2.8 23.2 + - - -
84S GLU* 3.8 0.7 + - - -
86S ILE* 1.3 76.8 - - - +
88S GLY* 1.3 60.8 + - - +
89S GLU* 3.0 37.5 + - - +
113S PHE* 3.7 11.8 - - - -
148S PHE* 3.8 27.4 - - - -
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Residues in contact with GLY 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84S GLU 2.8 13.7 + - - -
85S VAL 3.7 5.0 + - - -
86S ILE 3.5 1.4 - - - -
87S SER* 1.3 78.9 - - - +
89S GLU* 1.3 61.0 + - - +
90S ARG* 5.2 3.3 - - - -
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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