Contacts of the helix formed by residues 76 - 88 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73L PHE 3.0 18.0 + - - -
74L ARG 3.2 1.4 + - - -
75L ASN* 1.3 77.0 + - - +
77L LEU* 1.3 58.0 + - - +
78L LYS 3.6 1.6 - - - -
79L LEU* 3.4 10.7 - - - +
80L MET* 2.9 36.8 + - - +
106L ASN* 4.6 2.0 - - - -
107L VAL* 3.7 21.8 - - - -
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Residues in contact with LEU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ASN* 2.9 40.3 + - + +
76L GLY* 1.3 70.5 - - - +
78L LYS* 1.3 62.8 + - + +
80L MET* 3.1 8.2 + - - +
81L LEU* 2.9 26.9 + - - +
94L PRO* 3.8 31.9 - - + -
95L ASP 5.1 1.8 - - - +
106L ASN* 4.1 15.5 - - + +
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Residues in contact with LYS 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L LEU* 3.6 8.8 - - + +
64L THR* 2.8 30.4 + - + +
65L GLN 2.8 29.7 + - - +
66L ILE* 3.9 13.4 - - + +
72L ASP* 4.1 15.7 + - + +
73L PHE* 3.6 18.0 - - + -
75L ASN* 4.3 2.1 + - - +
77L LEU* 1.3 77.6 - - + +
79L LEU* 1.3 59.4 + - - +
81L LEU* 3.6 11.9 - - + -
82L LEU* 2.8 29.8 + - - +
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Residues in contact with LEU 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L PHE* 3.6 24.5 - - + +
76L GLY* 3.3 16.7 + - - +
77L LEU 3.1 0.4 - - - -
78L LYS* 1.3 78.3 - - - +
80L MET* 1.3 62.1 + - - +
82L LEU* 3.4 4.8 + - + +
83L LEU* 3.2 25.6 + - + +
107L VAL* 4.7 8.7 - - + -
110L ALA* 3.7 22.7 - - + -
129L ILE* 4.5 11.7 - - + -
140L MET* 3.5 43.7 - - + -
141L ILE* 4.3 9.2 - - + -
144L ILE* 3.9 23.1 - - + -
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Residues in contact with MET 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L GLY 2.9 25.8 + - - +
77L LEU* 3.1 5.6 + - - +
79L LEU* 1.3 75.2 - - - +
81L LEU* 1.3 64.5 + - - +
83L LEU* 3.2 5.3 + - - +
84L GLU* 3.1 31.8 + - - +
91L LEU* 4.0 24.9 - - + +
92L PRO 3.1 27.6 - - - +
94L PRO* 4.3 18.6 - - + -
106L ASN* 3.5 36.1 - - - +
109L LYS* 3.8 23.3 - - + -
110L ALA* 4.1 10.3 - - + -
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Residues in contact with LEU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L LEU* 4.3 4.3 - - + -
62L ALA* 3.9 26.0 - - + +
64L THR* 3.9 29.2 - - + -
77L LEU 2.9 17.4 + - - +
78L LYS* 3.6 13.7 - - + +
80L MET* 1.3 77.0 - - - +
82L LEU* 1.3 62.1 + - - +
84L GLU* 3.3 19.0 + - - +
85L VAL* 3.0 28.5 + - + +
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Residues in contact with LEU 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L TRP* 4.1 14.8 - - + -
55L CYS* 3.7 39.0 - - + +
58L HIS* 3.8 28.3 - - + -
59L LEU* 3.6 13.4 - - + +
73L PHE* 4.3 10.1 - - + -
78L LYS 2.8 22.2 + - - +
79L LEU* 3.5 10.5 - - + +
80L MET 3.2 0.2 - - - -
81L LEU* 1.3 74.8 - - - +
83L LEU* 1.3 58.7 + - + +
85L VAL* 3.3 3.1 + - - +
86L ILE* 3.1 42.4 + - + +
141L ILE* 4.3 9.4 - - + -
144L ILE* 4.9 6.3 - - + -
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Residues in contact with LEU 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L LEU* 3.2 15.7 + - + +
80L MET 3.2 6.9 + - - +
82L LEU* 1.3 75.5 - - + +
84L GLU* 1.3 62.9 + - - +
86L ILE* 3.7 4.0 - - + +
87L SER* 2.8 31.5 + - - -
91L LEU* 4.0 13.9 - - + -
110L ALA* 3.6 40.4 - - + +
113L PHE* 4.1 11.2 - - + -
114L ILE* 4.0 13.0 - - + -
144L ILE* 3.8 30.7 - - + -
148L PHE* 3.9 28.5 - - + -
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Residues in contact with GLU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L MET* 3.1 19.5 + - - +
81L LEU* 3.3 24.4 + - + +
83L LEU* 1.3 75.5 - - - +
85L VAL* 1.3 58.6 + - + +
87L SER* 4.0 1.3 - - - -
88L GLY* 2.8 30.8 + - - -
89L GLU 3.3 22.0 + - - +
90L ARG* 3.4 39.2 + - - +
91L LEU* 3.0 35.8 + - + +
92L PRO 5.0 0.5 - - - +
93L ARG* 3.5 14.0 + - - -
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Residues in contact with VAL 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L HIS* 3.6 42.4 - - + +
59L LEU* 5.0 1.3 - - - -
61L LYS* 4.6 14.6 - - + +
62L ALA* 3.9 28.9 - - + +
81L LEU* 3.0 20.1 + - + +
82L LEU* 3.5 10.8 - - - +
84L GLU* 1.3 81.0 - - + +
86L ILE* 1.3 63.4 + - + +
87L SER 3.5 0.2 + - - -
88L GLY* 3.7 5.4 + - - -
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Residues in contact with ILE 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L TRP* 4.1 10.5 - - + -
58L HIS* 3.5 45.3 - - + +
82L LEU* 3.1 24.7 + - + +
83L LEU* 3.7 11.4 - - + +
85L VAL* 1.3 76.8 - - - +
87L SER* 1.3 61.0 + - - +
144L ILE* 3.5 26.5 - - + -
148L PHE* 3.4 44.3 - - + +
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Residues in contact with SER 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L LEU 2.8 22.8 + - - -
84L GLU* 3.8 0.7 + - - -
86L ILE* 1.3 77.5 - - - +
88L GLY* 1.3 61.5 + - - +
89L GLU* 3.0 37.1 + - - +
113L PHE* 3.7 12.0 - - - -
148L PHE* 3.8 26.9 - - - -
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Residues in contact with GLY 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L GLU 2.8 14.1 + - - -
85L VAL 3.7 4.8 + - - -
86L ILE 3.5 1.4 - - - -
87L SER* 1.3 77.9 - - - +
89L GLU* 1.3 61.1 + - - +
90L ARG* 5.2 3.7 - - - -
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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