Contacts of the helix formed by residues 61 - 70 (chain A) in PDB entry 2DAT
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PHE 4.5 1.6 - - - +
41A ILE 3.3 19.3 - - - +
42A GLN* 5.0 0.9 - - - -
43A LEU* 4.4 18.8 - - + +
59A PRO 4.7 1.4 - - - +
60A VAL* 1.3 83.3 - - - +
62A PHE* 1.3 60.9 + - - +
63A LYS* 3.3 18.8 + - - +
64A LYS* 2.8 45.7 + - - +
65A ILE* 2.9 28.2 + - - +
87A LEU* 3.4 11.0 - - - -
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Residues in contact with PHE 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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22A ILE* 4.2 17.7 - - + -
25A VAL* 4.4 16.4 - - + -
26A ILE* 3.8 37.2 - - + -
37A SER* 4.1 19.1 - - - -
40A PHE* 3.0 49.2 + + + +
41A ILE* 3.9 10.5 + - + -
61A ASP* 1.3 72.4 - - - +
63A LYS* 1.3 66.5 + - + +
64A LYS 3.1 2.2 + - - -
65A ILE* 3.2 14.6 + - + +
66A LYS* 3.1 27.4 + - - +
84A VAL* 5.4 6.5 - - + -
87A LEU* 3.5 27.0 - - + +
88A CYS* 5.7 0.7 - - - -
108A LEU* 4.9 7.4 - - + -
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Residues in contact with LYS 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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41A ILE* 2.9 44.2 - - + +
42A GLN* 3.2 32.1 - - + +
43A LEU 4.8 1.8 - - - +
61A ASP* 3.3 12.3 + - - +
62A PHE* 1.3 78.1 - - + +
64A LYS* 1.3 58.5 + - + +
66A LYS* 4.1 4.4 - - - +
67A GLU* 3.1 27.6 + - - +
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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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60A VAL* 4.2 11.7 - - + -
61A ASP* 2.8 34.2 + - - +
62A PHE 3.1 0.2 - - - -
63A LYS* 1.3 74.7 - - + +
65A ILE* 1.3 65.8 + - - +
66A LYS 3.1 1.6 - - - -
67A GLU* 3.0 38.1 + - - +
68A ARG* 3.0 47.6 + - - +
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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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22A ILE* 4.4 13.7 - - + -
60A VAL* 4.0 12.1 - - + -
61A ASP 2.9 22.2 - - - +
62A PHE* 3.2 29.1 + - + +
64A LYS* 1.3 77.8 - - - +
66A LYS* 1.3 61.7 + - + +
68A ARG* 3.5 2.0 + - - -
69A ILE* 3.5 5.8 - - + +
74A TYR* 3.2 34.7 - - - +
80A LEU* 3.4 30.3 - - + -
83A ASP* 4.2 7.6 - - + -
84A VAL* 4.5 15.5 - - + +
87A LEU* 3.8 16.8 - - + -
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Residues in contact with LYS 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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19A ASN* 4.8 14.8 + - - +
22A ILE* 3.5 34.8 - - + -
23A ASP* 4.2 24.0 + - - +
26A ILE* 4.1 11.9 - - + +
62A PHE 3.1 16.5 + - - +
63A LYS* 4.1 4.5 - - - +
65A ILE* 1.3 73.4 - - + +
67A GLU* 1.3 66.8 + - - +
68A ARG 3.0 3.1 + - - -
69A ILE* 3.0 25.4 + - + +
70A ARG* 3.3 12.9 + - - +
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Residues in contact with GLU 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 LYS 3.1 21.1 + - - +
64A LYS* 3.0 34.8 + - + +
66A LYS* 1.3 76.4 - - - +
68A ARG* 1.3 61.8 + - - +
70A ARG* 3.0 26.6 - - + +
71A ASN* 2.9 46.2 + - - +
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Residues in contact with ARG 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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60A VAL* 6.2 1.8 - - - +
64A LYS* 3.2 53.1 + - - +
65A ILE 3.5 0.7 - - - +
66A LYS 3.0 0.6 - - - -
67A GLU* 1.3 81.1 + - - +
69A ILE* 1.3 60.9 + - - +
71A ASN* 2.8 18.2 + - - +
73A LYS* 3.1 53.3 + - + +
74A TYR* 3.4 40.7 + - + +
83A ASP* 5.4 6.1 + - - -
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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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10A ASN* 5.1 3.8 + - - +
15A THR* 3.7 38.0 + - + +
18A MET* 3.8 38.6 - - + +
19A ASN* 3.9 20.4 - - - +
22A ILE* 4.9 5.2 - - + -
65A ILE 3.5 16.8 - - - +
66A LYS* 3.0 19.4 + - + +
68A ARG* 1.3 76.6 - - - +
70A ARG* 1.3 61.2 + - - +
71A ASN 3.4 0.3 + - - -
72A HIS* 3.5 14.8 + - - +
73A LYS 5.2 0.2 - - - +
74A TYR* 3.8 18.6 - - + -
80A LEU* 4.2 10.5 - - + -
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Residues in contact with ARG 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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15A THR* 6.1 0.2 - - - -
66A LYS 3.3 4.0 + - - +
67A GLU* 3.0 40.1 - - - +
69A ILE* 1.3 79.9 - - - +
71A ASN* 1.3 84.8 + - - +
72A HIS* 3.3 16.3 + - - -
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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