Contacts of the helix formed by residues 63 - 77 (chain A) in PDB entry 1JD7
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 ASN 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TRP* 3.7 0.2 - - - -
57A LEU 3.2 6.7 - - - -
58A GLN* 3.2 25.1 - - - +
62A GLY* 1.3 73.6 - - - -
64A ARG* 1.3 58.8 + - - +
65A ALA* 3.2 10.8 + - - +
66A GLN* 2.7 55.2 + - - +
67A PHE* 2.9 27.5 + - - +
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Residues in contact with ARG 64 (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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57A LEU* 2.9 59.3 + - + +
58A GLN* 5.4 0.4 - - - -
63A ASN* 1.3 74.1 - - - +
65A ALA* 1.3 58.0 + - - +
67A PHE* 3.0 3.3 + - - +
68A ILE* 2.8 50.9 + - + +
162A ASP* 3.6 25.5 + - - -
166A ILE* 3.8 17.0 - - - +
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Residues in contact with ALA 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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63A ASN* 3.2 11.5 + - - +
64A ARG* 1.3 79.8 - - - +
66A GLN* 1.3 60.5 + - + +
68A ILE* 3.3 8.9 + - - +
69A ASP* 3.0 28.5 + - - +
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Residues in contact with GLN 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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13A TRP* 3.6 18.1 - - + +
14A GLN* 3.9 32.9 + - + +
61A GLY 5.4 0.9 - - - -
62A GLY* 3.3 10.4 - - - -
63A ASN* 2.7 57.3 + - - +
65A ALA* 1.3 71.6 - - + +
67A PHE* 1.3 64.6 + - - +
69A ASP* 3.5 7.3 + - - +
70A MET* 3.0 23.4 + - - +
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Residues in contact with PHE 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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13A TRP* 3.5 18.8 - + + +
34A VAL* 4.5 5.8 - - + -
37A PRO* 3.5 32.1 - - + -
57A LEU* 3.8 20.2 - - + -
63A ASN 2.9 14.3 + - - +
64A ARG* 3.0 12.1 + - - +
66A GLN* 1.3 77.4 - - - +
68A ILE* 1.3 68.3 + - + +
70A MET* 3.2 28.4 + - + +
71A VAL* 3.0 44.3 + - + +
81A ILE* 4.9 1.1 - - + -
83A VAL* 3.8 25.6 - - + -
163A LEU* 3.8 22.4 - - + -
166A ILE* 4.7 4.5 - - + -
168A VAL* 4.1 7.9 - - + -
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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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64A ARG* 2.8 46.4 + - + +
65A ALA* 3.7 7.4 - - - +
67A PHE* 1.3 74.8 - - + +
69A ASP* 1.3 66.2 + - - +
71A VAL* 3.0 4.8 + - - +
72A ASN* 2.9 40.5 + - - +
166A ILE* 3.8 40.2 - - + +
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Residues in contact with ASP 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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17A ALA* 5.2 0.2 - - - +
65A ALA 3.0 16.8 + - - +
66A GLN* 3.6 9.4 - - - +
67A PHE 3.3 0.2 - - - -
68A ILE* 1.3 77.5 - - - +
70A MET* 1.3 58.6 + - - +
72A ASN* 3.4 9.7 + - - +
73A ARG* 2.9 71.9 + - - +
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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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13A TRP* 3.5 44.0 - - + +
16A VAL* 3.6 36.3 - - + -
17A ALA* 4.1 13.9 - - - +
34A VAL* 4.1 12.8 - - + -
66A GLN 3.0 14.5 + - - +
67A PHE* 3.4 46.9 - - + +
68A ILE 3.1 0.2 - - - -
69A ASP* 1.3 76.7 + - - +
71A VAL* 1.3 67.5 + - + +
73A ARG* 4.0 0.2 - - - +
74A CYS* 3.0 27.4 + - - +
81A ILE* 4.5 7.0 - - + -
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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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67A PHE* 3.0 40.8 + - + +
68A ILE 3.0 8.5 + - - +
70A MET* 1.3 82.3 - - + +
72A ASN* 1.3 56.7 + - - +
74A CYS* 4.1 1.0 - - - +
75A SER* 3.0 31.8 + - - -
81A ILE* 4.4 18.1 - - + +
166A ILE* 3.8 19.5 - - + +
167A GLY* 3.7 31.6 - - - +
168A VAL* 4.1 8.1 - - + +
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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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68A ILE* 2.9 40.2 + - - +
69A ASP* 3.8 8.4 + - - +
71A VAL* 1.3 77.0 - - - +
73A ARG* 1.3 59.3 + - + +
75A SER* 3.3 7.0 + - - -
76A ALA* 2.9 30.8 + - - +
166A ILE 4.3 13.0 - - - +
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Residues in contact with ARG 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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14A GLN* 4.5 11.1 + - - +
17A ALA* 3.4 31.1 - - + +
18A GLN* 4.3 6.5 - - - +
21A GLU* 3.0 48.1 + - + +
69A ASP* 2.9 48.1 + - - +
70A MET 4.0 2.5 - - - +
72A ASN* 1.3 77.7 - - + +
74A CYS* 1.3 62.7 + - - +
76A ALA* 3.3 8.3 + - - +
77A ALA* 3.2 20.4 + - - +
901A CL 3.5 29.4 - - - +
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Residues in contact with CYS 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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16A VAL* 3.9 21.1 - - - -
17A ALA* 4.1 4.7 - - - -
20A CYS* 2.0 51.1 - - - -
70A MET 3.0 21.7 + - - +
71A VAL 4.1 2.2 - - - +
73A ARG* 1.3 73.1 - - - +
75A SER* 1.3 65.9 + - - +
77A ALA* 3.0 10.6 + - - +
78A GLY 3.1 0.2 + - - -
79A VAL* 2.8 35.7 + - + +
81A ILE* 4.2 13.0 - - + -
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Residues in contact with SER 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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71A VAL* 3.0 23.5 + - - -
72A ASN* 3.5 7.4 - - - -
74A CYS* 1.3 77.2 - - - +
76A ALA* 1.3 56.3 + - - +
78A GLY* 2.9 20.0 + - - -
79A VAL 3.5 10.9 + - - +
80A ASP* 5.8 2.2 + - - -
167A GLY 6.1 0.4 - - - -
169A LYS* 5.0 10.8 + - - -
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Residues in contact with ALA 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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21A GLU* 5.9 0.4 - - - +
72A ASN 2.9 17.2 + - - +
73A ARG* 3.5 9.2 - - - +
75A SER* 1.3 77.1 - - - +
77A ALA* 1.3 59.1 + - - +
78A GLY 3.2 1.0 + - - -
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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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20A CYS* 3.6 31.4 - - + +
21A GLU* 4.1 10.5 - - + +
25A GLY* 3.6 21.0 - - - +
26A PRO* 5.6 0.7 - - + -
73A ARG 3.2 10.6 + - - +
74A CYS 3.0 9.7 + - - +
76A ALA* 1.3 75.0 - - - +
78A GLY* 1.3 61.0 + - - +
79A VAL* 3.5 1.1 - - + -
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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