Contacts of the helix formed by residues 60 - 76 (chain A) in PDB entry 1DXK
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A SER 3.1 0.4 + - - -
59A TRP* 1.3 82.7 - - + +
61A ASP* 1.3 57.3 + - - +
62A LYS* 3.9 13.1 - - - +
63A LEU* 2.8 32.9 + - - +
64A THR* 2.8 36.2 + - - -
93A GLY 3.9 12.6 - - - -
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Residues in contact with ASP 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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60A ASP* 1.3 73.8 - - - +
62A LYS* 1.3 58.0 + - - +
64A THR* 3.6 2.8 - - - -
65A LYS* 2.8 51.0 + - - +
93A GLY 3.8 9.8 - - - +
94A GLY* 3.4 10.2 - - - -
96A LYS* 3.5 26.6 - - - +
97A THR* 2.7 40.1 + - - +
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Residues in contact with LYS 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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13A THR* 6.5 0.9 - - - -
60A ASP* 3.4 14.2 + - - +
61A ASP* 1.3 78.5 - - - +
63A LEU* 1.3 65.7 + - + +
65A LYS* 3.7 9.5 - - - +
66A GLU* 3.3 47.4 + - - +
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Residues in contact with LEU 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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15A THR* 4.0 20.0 - - + +
16A ILE* 3.5 32.5 - - + +
30A GLU* 4.2 5.6 - - + -
31A LEU 3.6 20.6 - - - +
32A GLY* 5.1 1.1 - - - -
58A SER* 3.6 26.4 - - - +
59A TRP* 4.0 16.6 - - + -
60A ASP* 2.8 24.5 + - - +
62A LYS* 1.3 75.8 - - + +
64A THR* 1.3 61.4 + - - +
66A GLU* 3.4 9.3 + - - +
67A LEU* 2.9 29.8 + - - +
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Residues in contact with THR 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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54A LEU* 6.0 0.9 - - + -
57A SER* 4.3 7.9 - - - -
58A SER* 3.2 25.0 + - - -
60A ASP 2.8 22.4 + - - -
61A ASP* 3.6 4.3 - - - -
63A LEU* 1.3 74.5 - - - +
65A LYS* 1.3 63.9 + - - +
67A LEU* 3.4 8.4 + - + +
68A ILE* 3.0 46.5 + - + +
94A GLY* 3.3 28.9 - - - +
97A THR* 4.1 5.6 - - - -
98A LEU* 3.9 10.8 - - + -
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Residues in contact with LYS 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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61A ASP* 2.8 33.1 + - - +
62A LYS* 3.7 8.9 - - - +
64A THR* 1.3 73.3 - - - +
66A GLU* 1.3 64.6 + - + +
68A ILE* 3.1 3.7 + - - +
69A GLU* 2.9 34.7 + - - +
96A LYS* 6.1 2.2 - - - +
97A THR* 3.0 34.0 + - + -
100A GLU* 3.7 18.4 + - - -
101A ARG* 3.4 30.7 - - - +
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Residues in contact with GLU 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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11A ASN* 4.6 12.4 + - - +
12A GLU* 4.6 15.7 - - - +
13A THR* 4.7 7.8 + - - +
15A THR* 4.4 9.2 + - - -
16A ILE* 3.3 20.0 - - + +
62A LYS* 3.3 41.0 + - - +
63A LEU* 3.6 14.0 - - - +
65A LYS* 1.3 78.9 - - - +
67A LEU* 1.3 58.8 + - - +
69A GLU* 3.8 11.7 + - - +
70A MET* 2.9 31.4 + - - +
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Residues in contact with LEU 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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16A ILE* 3.4 24.0 - - + +
18A ILE* 4.7 2.2 - - + -
28A HIS* 3.6 55.0 - - + +
30A GLU* 4.2 7.6 - - - +
45A VAL* 4.9 1.8 - - + -
54A LEU* 4.0 21.5 - - + -
56A ASP 4.8 0.4 - - - +
57A SER* 4.6 9.6 - - - +
58A SER* 5.0 2.2 - - - -
63A LEU 2.9 17.7 + - - +
64A THR* 3.6 7.4 - - + +
66A GLU* 1.3 74.9 - - - +
68A ILE* 1.3 64.7 + - + +
70A MET* 3.3 5.2 + - + +
71A VAL* 3.1 35.3 + - + +
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Residues in contact with ILE 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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54A LEU* 4.5 15.9 - - + -
64A THR* 3.0 37.6 + - + +
65A LYS 3.5 5.6 - - - +
67A LEU* 1.3 75.9 - - + +
69A GLU* 1.3 58.6 + - - +
71A VAL* 3.2 10.6 + - - +
72A GLU* 2.8 56.7 + - - +
79A VAL* 4.0 10.5 - - + -
97A THR* 4.1 13.0 - - + -
98A LEU* 4.0 6.3 - - + -
101A ARG* 3.8 15.9 - - - +
103A ILE* 3.6 27.4 - - + -
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Residues in contact with GLU 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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65A LYS* 2.9 30.1 + - - +
66A GLU* 3.9 10.0 + - - +
68A ILE* 1.3 75.7 - - + +
70A MET* 1.3 62.6 + - - +
72A GLU* 4.1 7.3 - - - +
73A LYS* 3.2 26.2 + - - +
101A ARG* 3.0 35.6 + - - +
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Residues in contact with MET 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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9A ILE* 3.1 49.8 - - + +
10A LYS 3.5 3.6 - - - +
11A ASN* 2.2 47.3 - - - +
16A ILE* 3.9 8.7 - - - -
18A ILE* 3.7 22.2 - - + -
66A GLU 2.9 18.2 + - - +
67A LEU* 3.6 4.9 - - - +
68A ILE 3.2 0.2 - - - -
69A GLU* 1.3 78.4 - - - +
71A VAL* 1.3 60.1 + - + +
73A LYS* 4.0 2.6 - - - +
74A LYS* 3.1 28.3 + - + +
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Residues in contact with VAL 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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18A ILE* 4.4 13.0 - - + -
45A VAL* 4.0 21.5 - - + -
52A LEU* 3.4 8.8 - - + +
54A LEU* 4.4 9.2 - - + -
67A LEU* 3.1 28.4 + - + +
68A ILE* 3.3 11.0 - - - +
70A MET* 1.3 74.5 - - + +
72A GLU* 1.3 64.4 + - - +
74A LYS* 4.4 1.3 - - - -
75A PHE* 2.8 55.4 + - + -
79A VAL* 3.6 24.5 - - + -
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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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52A LEU* 4.0 0.4 - - - -
68A ILE* 2.8 39.4 + - - +
69A GLU* 4.1 7.2 - - - +
71A VAL* 1.3 75.9 - - - +
73A LYS* 1.3 56.9 + - - +
76A GLN* 2.9 31.0 + - - -
77A LYS 3.3 21.7 + - - +
78A ARG* 3.0 38.1 + - - +
79A VAL* 2.8 34.7 + - + +
101A ARG* 5.1 2.8 + - - -
103A ILE* 5.4 1.2 - - - +
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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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69A GLU 3.2 18.2 + - - +
70A MET* 4.0 3.1 - - - +
72A GLU* 1.3 74.6 - - - +
74A LYS* 1.3 64.3 + - - +
76A GLN* 2.7 31.6 + - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.4 31.6 - - + +
18A ILE* 3.7 24.7 - - + -
26A TRP* 3.6 22.2 - - - -
70A MET* 3.1 20.4 + - + +
71A VAL* 3.9 3.1 - - - +
73A LYS* 1.3 79.9 - - - +
75A PHE* 1.3 77.3 + - + +
76A GLN* 3.6 4.2 + - - +
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.4 3.4 - - + -
26A TRP* 3.5 52.3 - + - -
45A VAL* 4.0 12.3 - - + -
47A ASN* 3.2 29.5 + - + +
52A LEU* 3.7 28.9 - - + -
71A VAL* 2.8 49.8 + - + +
74A LYS* 1.3 96.4 - - + +
76A GLN* 1.3 71.8 + - - +
77A LYS* 3.4 12.0 + - + -
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Residues in contact with GLN 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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72A GLU 2.9 13.0 + - - -
73A LYS* 2.7 37.0 + - - +
74A LYS 3.3 4.2 - - - +
75A PHE* 1.3 81.4 - - - +
77A LYS* 1.3 61.4 + - - +
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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