Contacts of the helix formed by residues 66 - 78 (chain A) in PDB entry 2LPN
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 ALA 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR 4.3 12.3 - - - +
58A TYR 5.2 1.3 - - - +
60A GLY* 3.1 21.6 - - - -
61A ALA 4.4 0.2 + - - -
64A ASP 2.8 5.5 + - - +
65A ALA* 1.3 80.5 - - - +
67A THR* 1.3 64.2 + - - +
68A LYS 3.4 2.2 - - - +
69A ILE* 3.4 25.5 - - + +
70A LEU* 3.8 2.4 + - - +
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 5.7 0.2 - - - +
63A LYS* 4.3 21.1 - - - +
64A ASP* 4.5 10.8 - - - +
65A ALA 4.2 0.4 - - - -
66A ALA* 1.3 73.9 - - - +
68A LYS* 1.3 65.0 + - - +
69A ILE 3.5 0.2 - - - -
70A LEU* 3.3 23.1 - - + +
71A SER* 4.1 3.6 + - - -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA 3.4 0.4 - - - -
67A THR* 1.3 78.7 + - - +
69A ILE* 1.3 60.0 + - - +
70A LEU 3.0 5.1 + - - -
71A SER* 2.7 36.2 + - - +
72A GLU* 3.9 12.8 + - + +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR 3.3 20.9 - - - +
59A LEU* 3.2 20.4 - - - +
66A ALA* 3.4 32.3 - - + +
68A LYS* 1.3 76.5 - - - +
70A LEU* 1.3 67.2 + - - +
71A SER 3.2 0.2 - - - -
72A GLU* 2.9 26.4 + - + +
73A VAL* 3.3 12.6 + - + +
90A LEU* 3.6 28.9 - - + -
93A LEU* 3.7 26.0 - - + -
97A ILE* 5.0 0.9 - - + -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.5 37.5 - - + +
41A LEU* 3.5 23.8 - - + -
59A LEU 3.8 8.3 - - - -
61A ALA* 3.3 36.6 - - - +
63A LYS* 5.0 8.3 - - - +
66A ALA 3.9 7.9 - - - +
67A THR* 3.3 22.0 + - + +
69A ILE* 1.3 82.2 - - - +
71A SER* 1.3 63.6 + - - +
73A VAL* 3.0 13.9 + - - +
74A THR* 3.1 22.5 + - + -
75A ARG* 6.1 0.2 - - - +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR 4.1 2.4 + - - -
68A LYS* 2.7 30.4 + - - +
70A LEU* 1.3 79.7 - - - +
72A GLU* 1.3 61.8 + - - +
73A VAL 3.1 0.2 - - - -
74A THR* 3.3 8.7 - - - -
75A ARG* 3.0 60.0 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 4.3 16.3 - - + +
69A ILE* 2.9 27.0 + - + +
71A SER* 1.3 80.0 - - - +
73A VAL* 1.3 58.7 + - - +
75A ARG* 5.2 0.9 - - - -
76A PRO* 3.0 24.2 - - - +
86A ILE* 4.7 8.3 - - - +
90A LEU* 6.4 0.9 - - + -
93A LEU* 4.1 27.9 - - + +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 5.7 1.6 - - + -
18A LEU* 4.5 12.6 - - + -
21A PHE* 5.4 0.2 - - + -
41A LEU* 4.1 27.1 - - + -
59A LEU* 3.7 29.2 - - + +
69A ILE* 3.6 17.0 - - + +
70A LEU* 3.0 7.1 + - - +
72A GLU* 1.3 79.4 - - - +
74A THR* 1.3 67.0 + - - +
75A ARG 3.3 0.2 - - - -
76A PRO* 3.0 14.3 - - - +
77A MET* 3.0 43.0 + - + +
86A ILE* 5.9 3.8 - - + -
90A LEU* 5.6 6.1 - - + -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.4 17.4 - - - +
37A ILE* 3.1 29.0 - - + +
38A GLU* 3.6 28.9 - - + +
41A LEU* 3.7 5.2 - - + -
70A LEU* 3.1 25.5 + - + -
71A SER* 3.2 10.2 + - - -
73A VAL* 1.3 77.9 - - - +
75A ARG* 1.3 89.5 + - - +
77A MET 3.1 1.0 + - - -
78A SER 3.1 16.8 + - - -
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.5 48.9 + - + +
38A GLU* 6.1 1.2 - - - +
71A SER* 3.0 43.2 + - - +
72A GLU* 5.2 1.1 - - - -
74A THR* 1.3 102.9 + - - +
76A PRO* 1.4 64.5 - - + +
78A SER* 3.1 23.7 + - - -
79A VAL* 4.1 7.1 - - - +
81A MET* 5.0 0.4 - - - -
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.9 3.8 - - - -
72A GLU* 3.0 27.4 - - - +
73A VAL* 3.0 20.0 - - - +
75A ARG* 1.4 85.5 - - + +
77A MET* 1.3 56.0 + - - +
78A SER 3.1 4.9 - - - -
79A VAL 2.7 26.2 - - - +
81A MET* 3.3 35.0 - - + +
83A ALA* 5.5 0.3 - - - +
86A ILE* 3.4 32.6 - - + +
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Residues in contact with MET 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.5 52.5 - - + +
21A PHE* 4.3 22.9 - - + -
22A TYR* 3.6 37.0 - - + -
25A LEU* 5.5 0.7 - - + -
26A ILE* 4.3 1.2 - - - +
31A ASN* 2.9 25.5 + - - +
37A ILE* 3.8 14.4 - - + -
73A VAL* 3.0 35.1 + - + +
74A THR 3.1 6.5 + - - +
76A PRO* 1.3 81.4 - - - +
78A SER* 1.3 59.7 + - - +
79A VAL 3.2 2.1 + - - -
83A ALA* 4.3 13.0 - - + -
86A ILE* 5.4 2.9 - - + -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 5.5 1.1 - - - +
31A ASN* 3.1 16.4 - - - +
32A PHE* 3.6 41.2 + - - -
34A LEU* 3.6 24.3 - - - +
37A ILE* 3.7 5.4 - - - -
74A THR 3.1 2.9 + - - -
75A ARG 3.1 15.4 + - - -
77A MET* 1.3 79.5 - - - +
79A VAL* 1.3 59.6 + - - +
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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