Contacts of the helix formed by residues 67 - 82 (chain A) in PDB entry 1X47
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 LYS 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.6 17.0 - - - +
38A PHE* 3.5 47.6 - - + -
48A PHE* 4.1 18.6 - - + -
49A GLY 6.0 1.1 - - - +
50A ALA* 4.9 0.4 - - + +
66A SER* 1.3 73.0 + - - +
68A LYS* 1.3 57.3 + - + +
70A ALA* 3.0 10.4 + - + +
71A LYS* 2.7 37.7 + - + +
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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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10A VAL* 5.6 12.6 - - + +
12A ASN* 5.4 7.1 + - - -
19A VAL* 5.2 0.3 - - - +
66A SER* 3.4 4.4 - - - -
67A LYS* 1.3 76.8 - - + +
69A LEU* 1.3 63.3 + - + +
71A LYS* 2.6 11.3 + - + +
72A ASN* 2.5 38.0 + - - +
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Residues in contact with LEU 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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64A ALA* 3.0 26.2 - - + -
65A SER* 5.2 2.2 - - - +
66A SER* 3.9 18.5 + - - +
68A LYS* 1.3 83.1 - - + +
70A ALA* 1.3 50.2 + - - +
72A ASN* 3.0 14.3 + - + +
73A LYS* 2.7 48.1 + - + +
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Residues in contact with ALA 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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48A PHE 3.4 28.7 - - - +
49A GLY 4.1 0.4 - - - -
50A ALA* 3.9 22.1 - - + +
62A GLY 4.1 2.4 - - - +
63A THR* 4.0 7.6 - - - +
64A ALA* 3.4 8.4 - - - +
66A SER 3.3 8.7 + - - +
67A LYS* 3.0 11.8 + - + +
69A LEU* 1.3 78.0 - - - +
71A LYS* 1.3 51.1 + - - +
73A LYS* 3.0 5.0 + - - +
74A ALA* 2.7 35.3 + - - +
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Residues in contact with LYS 71 (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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9A PHE* 4.4 20.0 + - - +
10A VAL* 4.1 25.0 - - + +
19A VAL* 3.5 28.9 - - + +
36A TYR* 3.2 45.3 - - + -
38A PHE* 3.9 28.9 - - + -
50A ALA* 3.8 8.0 - - + +
67A LYS* 2.7 14.6 + - + +
68A LYS* 2.6 17.0 + - + +
70A ALA* 1.3 72.1 - - - +
72A ASN* 1.3 55.8 - - - +
74A ALA* 3.1 3.1 + - - +
75A ALA* 2.8 26.9 + - - +
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Residues in contact with ASN 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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17A SER* 5.8 1.4 - - - -
18A GLU* 3.5 27.2 + - - +
19A VAL* 3.8 13.1 - - + +
68A LYS 2.5 16.4 + - - +
69A LEU* 3.1 20.3 + - + +
71A LYS* 1.3 74.0 - - - +
73A LYS* 1.3 64.5 + - - +
75A ALA* 3.3 1.4 + - - +
76A ARG* 2.6 51.9 + - - +
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Residues in contact with LYS 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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46A GLU* 5.1 4.0 + - - -
62A GLY* 4.5 12.3 - - - -
63A THR 3.0 28.6 + - - +
64A ALA* 4.0 12.8 - - + +
69A LEU* 2.7 27.0 + - + +
70A ALA* 3.4 7.6 - - - +
72A ASN* 1.3 82.5 - - - +
74A ALA* 1.3 57.4 + - - +
76A ARG* 3.5 32.3 - - - +
77A ALA* 2.6 39.3 + - - +
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Residues in contact with ALA 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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36A TYR* 5.1 1.3 - - + -
50A ALA* 3.2 34.5 - - + +
51A SER* 3.8 3.6 - - - +
52A VAL* 3.3 17.7 - - + -
60A GLY 2.9 23.9 - - - +
61A SER* 4.1 2.0 - - - +
62A GLY 4.4 1.2 - - - +
70A ALA 2.7 13.2 + - - +
71A LYS* 3.3 12.3 - - - +
73A LYS* 1.3 73.6 - - - +
75A ALA* 1.3 60.7 + - - +
78A THR* 3.1 16.3 + - - -
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Residues in contact with ALA 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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18A GLU 4.1 1.3 - - - -
19A VAL* 3.6 32.3 - - - +
22A LEU* 3.8 18.7 - - + +
36A TYR* 3.9 8.3 - - - +
52A VAL* 3.5 8.0 - - + +
71A LYS 2.8 15.9 + - - +
72A ASN 3.7 2.7 - - - +
74A ALA* 1.3 73.6 - - - +
76A ARG* 1.3 66.6 + - - +
77A ALA 2.9 2.0 - - - -
78A THR* 2.8 15.1 + - - -
79A LEU* 2.8 15.1 + - - +
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Residues in contact with ARG 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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18A GLU* 4.1 21.5 - - + +
72A ASN* 2.6 35.2 + - - +
73A LYS* 3.5 37.4 - - - +
75A ALA* 1.3 72.5 - - - +
77A ALA* 1.3 63.5 + - - +
79A LEU* 3.5 7.0 + - - +
80A GLU* 3.2 32.4 + - + +
86A PHE* 5.4 7.3 - - + -
87A VAL* 6.1 2.0 - - + -
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Residues in contact with ALA 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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60A GLY* 3.2 26.5 - - - -
61A SER 3.7 8.1 - - - +
73A LYS 2.6 22.1 + - - +
74A ALA 3.5 0.4 - - - +
76A ARG* 1.3 74.2 - - - +
78A THR* 1.3 67.8 + - - +
79A LEU 3.0 2.6 + - - -
80A GLU* 3.0 17.4 + - - +
81A ILE* 3.1 15.2 + - - +
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Residues in contact with THR 78 (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 LEU* 3.3 24.7 - - + -
52A VAL* 3.1 31.4 - - + +
54A ILE* 4.0 17.0 - - + -
59A TYR* 3.3 5.9 - - + +
60A GLY* 2.8 26.8 + - - +
74A ALA 3.1 3.9 + - - -
75A ALA 2.8 11.8 + - - -
77A ALA* 1.3 74.3 - - - +
79A LEU* 1.3 64.1 + - - +
81A ILE* 3.3 6.9 - - - +
82A LEU* 3.1 31.1 + - + +
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Residues in contact with LEU 79 (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 GLU* 3.8 21.1 - - + +
21A ILE* 4.2 8.5 - - + -
22A LEU* 3.8 35.2 - - + +
25A TYR* 4.8 9.4 - - + -
75A ALA 2.8 11.3 + - - +
76A ARG* 3.5 9.2 - - - +
78A THR* 1.3 75.2 - - - +
80A GLU* 1.3 54.6 + - - +
82A LEU* 2.6 16.1 + - + -
83A ILE* 2.5 57.4 + - + -
86A PHE* 3.5 42.2 - - + -
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Residues in contact with GLU 80 (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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76A ARG* 3.2 24.4 + - + +
77A ALA* 3.0 10.4 + - - +
79A LEU* 1.3 77.9 - - + +
81A ILE* 1.3 66.7 + - + +
83A ILE 2.6 25.6 - - - +
84A PRO* 3.8 12.6 - - - +
86A PHE* 5.0 16.0 + - + +
87A VAL* 5.1 9.5 + - - +
93A SER 5.7 0.7 - - - +
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Residues in contact with ILE 81 (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 TYR* 3.2 69.8 - - + +
60A GLY* 3.7 4.0 - - - +
77A ALA 3.1 10.1 + - - +
78A THR* 3.3 8.1 - - - +
79A LEU 2.9 1.0 + - - -
80A GLU* 1.3 78.7 - - + +
82A LEU* 1.3 64.4 + - + +
84A PRO* 5.1 0.5 - - - +
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Residues in contact with LEU 82 (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 LEU* 4.1 10.8 - - + -
25A TYR* 3.5 44.0 - - + +
26A MET* 4.7 4.0 - - + -
30A LEU* 4.3 20.2 - - + -
54A ILE* 5.1 0.4 - - + -
59A TYR* 4.5 16.6 - - + +
78A THR* 3.1 36.6 - - + +
79A LEU* 2.6 11.0 + - + +
81A ILE* 1.3 79.1 - - + +
83A ILE* 1.3 60.3 + - + +
84A PRO* 3.1 14.9 - - - +
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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