Contacts of the helix formed by residues 54 - 69 (chain A) in PDB entry 2LBP
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 ASP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP 2.9 12.6 + - - +
52A ALA* 4.3 8.7 - - + +
53A CYS* 1.3 73.3 - - - +
55A PRO* 1.3 69.8 - - - +
56A LYS* 3.2 13.6 + - - +
57A GLN* 3.0 25.3 + - + +
58A ALA* 2.7 34.8 + - - +
81A SER* 3.9 5.2 - - - -
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Residues in contact with PRO 55 (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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53A CYS 4.2 5.6 - - - +
54A ASP* 1.3 91.8 - - - +
56A LYS* 1.3 55.5 + - - +
58A ALA* 3.8 8.6 - - + +
59A VAL* 3.3 27.0 - - - +
80A SER* 3.5 35.4 - - - +
81A SER* 4.3 1.1 - - - -
84A PRO* 4.3 8.9 - - + +
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Residues in contact with LYS 56 (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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54A ASP* 3.2 9.1 + - - +
55A PRO* 1.3 75.1 - - - +
57A GLN* 1.3 65.8 + - - +
58A ALA 3.4 0.2 - - - -
59A VAL* 3.9 14.8 - - + +
60A ALA* 3.3 21.1 + - - +
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Residues in contact with GLN 57 (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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12A SER* 5.4 0.4 + - - -
50A ASP* 4.4 16.4 + - - +
51A ASP* 3.4 17.2 - - - +
52A ALA* 3.4 25.8 - - - +
54A ASP* 3.0 21.2 + - + +
56A LYS* 1.3 81.1 - - - +
58A ALA* 1.3 50.4 + - - +
60A ALA* 3.2 8.0 + - + +
61A VAL* 2.7 43.1 + - + +
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Residues in contact with ALA 58 (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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51A ASP* 3.3 13.2 + - - +
54A ASP 2.7 19.7 + - - +
55A PRO 3.8 6.5 - - - +
57A GLN* 1.3 72.8 - - - +
59A VAL* 1.3 53.6 + - + +
61A VAL* 3.1 4.3 + - - +
62A ALA* 2.8 34.0 + - - +
76A HIS* 3.8 10.2 - - - +
81A SER* 3.1 41.7 - - - +
85A ALA* 4.7 2.0 - - - -
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Residues in contact with VAL 59 (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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55A PRO 3.3 21.3 - - - +
56A LYS* 3.9 18.4 - - + +
58A ALA* 1.3 74.6 - - - +
60A ALA* 1.3 64.7 + - - +
62A ALA* 4.6 0.9 - - - -
63A ASN* 3.1 34.9 + - - +
84A PRO* 3.3 34.3 - - + +
85A ALA* 5.1 1.1 - - - +
88A ILE* 3.5 19.2 - - + +
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Residues in contact with ALA 60 (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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56A LYS 3.3 11.9 + - - +
57A GLN* 3.2 13.5 + - + +
59A VAL* 1.3 78.9 - - + +
61A VAL* 1.4 70.5 + - + +
63A ASN* 3.4 5.9 + - - +
64A LYS* 3.1 21.0 + - - +
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Residues in contact with VAL 61 (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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8A VAL* 3.6 26.5 - - + -
49A TYR* 3.8 26.2 - - + -
50A ASP 3.1 28.7 - - - +
51A ASP* 4.4 1.1 - - - -
57A GLN* 2.7 30.4 + - + +
58A ALA* 3.1 10.5 + - - +
60A ALA* 1.4 78.3 - - + +
62A ALA* 1.3 58.2 - - - +
64A LYS* 3.0 10.7 + - - +
65A ILE* 3.0 34.8 + - + +
76A HIS* 4.2 2.2 - - + -
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Residues in contact with ALA 62 (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 ALA 2.8 15.4 + - - +
59A VAL 4.2 4.5 - - - +
60A ALA 3.4 0.2 - - - -
61A VAL* 1.3 73.0 - - - +
63A ASN* 1.3 62.6 + - - +
65A ILE* 3.7 3.4 - - - -
66A VAL* 3.2 28.4 + - - +
85A ALA* 4.3 5.4 - - - -
88A ILE* 3.8 21.6 - - + +
89A TYR* 3.3 41.8 + - + +
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Residues in contact with ASN 63 (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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59A VAL* 3.1 23.8 + - - +
60A ALA* 3.4 7.0 + - - +
61A VAL 3.1 1.2 - - - -
62A ALA* 1.3 78.5 - - - +
64A LYS* 1.3 59.0 + - - +
66A VAL* 3.4 9.6 + - - +
67A ASN* 3.1 32.9 + - - +
88A ILE* 3.3 25.8 - - - +
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Residues in contact with LYS 64 (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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49A TYR* 4.1 21.2 + - + -
60A ALA 3.1 12.3 + - - +
61A VAL* 3.0 10.9 + - - +
63A ASN* 1.3 77.7 - - - +
65A ILE* 1.3 58.8 + - - +
67A ASN* 4.4 8.5 - - - +
68A ASP* 2.6 42.5 + - + +
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Residues in contact with ILE 65 (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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6A ALA* 3.1 23.3 - - + -
8A VAL* 4.7 1.1 - - + -
49A TYR* 3.8 27.4 - - + +
61A VAL* 3.0 29.3 + - + +
62A ALA* 3.6 6.0 + - - -
63A ASN 3.2 0.4 - - - -
64A LYS* 1.3 76.5 - - - +
66A VAL* 1.3 69.6 + - - +
68A ASP 3.3 5.7 + - - -
69A GLY 3.3 0.5 + - - -
70A ILE* 3.2 39.2 + - + +
73A VAL* 2.8 40.6 - - + -
89A TYR* 3.9 13.7 - - + +
94A ILE* 5.1 1.8 - - + -
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Residues in contact with VAL 66 (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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62A ALA 3.2 20.5 + - - +
63A ASN* 3.5 12.1 - - - +
65A ILE* 1.3 74.2 - - - +
67A ASN* 1.3 59.3 + - + +
68A ASP 2.3 18.2 + - - -
69A GLY* 2.7 17.0 + - - -
70A ILE 5.0 0.2 - - - +
88A ILE* 4.2 11.9 - - + +
89A TYR* 4.8 4.9 - - + -
92A GLU* 4.1 35.4 - - + +
94A ILE* 3.2 31.8 - - + +
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Residues in contact with ASN 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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63A ASN 3.1 14.3 + - - +
64A LYS* 4.6 7.3 - - - +
66A VAL* 1.3 80.7 - - + +
68A ASP* 1.3 60.6 + - - +
69A GLY 3.7 0.4 - - - -
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Residues in contact with ASP 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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4A LYS* 5.1 8.0 + - - -
47A VAL* 5.8 0.7 - - - +
49A TYR* 3.6 14.6 + - - -
64A LYS* 2.6 51.8 + - + +
65A ILE 3.5 3.1 - - - +
66A VAL 2.3 19.6 + - - -
67A ASN* 1.3 73.1 - - - +
69A GLY* 1.3 58.2 + - - -
70A ILE* 3.4 15.4 + - - +
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Residues in contact with GLY 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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66A VAL 2.7 10.8 + - - -
67A ASN 3.7 0.4 - - - -
68A ASP* 1.3 77.7 - - - +
70A ILE* 1.3 59.5 + - - +
71A LYS* 3.1 26.8 + - - +
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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