Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 4DTR
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 3.5 31.3 + - + +
33A TYR 4.4 5.4 - - - -
35A PRO* 3.7 10.3 - - - +
62A PHE* 3.0 10.6 - - - +
63A ALA* 1.3 84.3 + - - +
65A MET* 1.3 64.0 + - - +
66A ARG* 3.4 5.0 + - - +
67A ASP* 2.9 48.1 + - - +
68A ALA 3.3 14.2 + - - -
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Residues in contact with MET 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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10A GLN* 3.6 34.1 - - + +
12A GLY 3.8 0.4 - - - +
13A ASP* 3.3 37.3 + - - +
14A SER 3.6 20.2 - - - +
15A ILE* 3.8 17.7 - - + +
33A TYR* 3.8 21.2 + - + +
35A PRO* 3.8 18.2 - - + -
64A ASN* 1.3 73.1 - - - +
66A ARG* 1.3 61.6 + - - +
68A ALA* 3.2 4.9 + - - +
69A SER* 3.0 24.8 + - - -
88A PHE* 3.6 34.9 - - + -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 5.7 2.0 - - - +
12A GLY* 3.3 34.0 - - - +
13A ASP* 2.9 34.9 + - - +
64A ASN* 3.4 3.6 - - - +
65A MET* 1.3 75.7 - - + +
67A ASP* 1.3 58.6 + - - +
69A SER* 3.3 7.3 + - - -
70A GLN* 2.9 37.5 + - + +
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 4.1 14.6 - - + -
63A ALA* 3.6 21.8 + - - +
64A ASN* 2.9 32.7 + - - +
65A MET 3.3 0.2 - - - -
66A ARG* 1.3 77.5 - - - +
68A ALA* 1.3 57.6 + - - +
70A GLN* 3.4 7.9 + - - +
71A TRP* 2.9 28.9 + - - +
74A ARG* 4.9 2.6 + - - -
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Residues in contact with ALA 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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35A PRO* 3.7 14.1 - - + -
37A LEU* 3.7 6.9 - - + +
62A PHE* 3.5 33.1 - - + -
64A ASN 3.3 2.8 + - - -
65A MET 3.2 6.0 + - - +
67A ASP* 1.3 78.3 - - - +
69A SER* 1.3 55.7 + - - +
71A TRP* 3.2 4.0 + - - +
72A ILE* 3.0 31.5 + - - +
88A PHE* 3.4 25.6 - - + -
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 5.6 1.6 + - - -
65A MET 3.0 9.7 + - - -
66A ARG* 3.3 11.4 + - - -
68A ALA* 1.3 71.4 - - - +
70A GLN* 1.3 67.2 + - - +
72A ILE* 3.2 14.7 + - - +
73A LYS* 3.1 32.0 + - - +
88A PHE* 3.6 18.7 - - - -
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Residues in contact with GLN 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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66A ARG* 2.9 21.9 + - + +
67A ASP* 3.7 9.9 - - - +
69A SER* 1.3 76.0 - - - +
71A TRP* 1.3 61.1 + - - +
73A LYS* 3.2 36.9 + - - +
74A ARG* 3.0 49.6 + - - +
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Residues in contact with TRP 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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37A LEU* 3.8 27.4 - - + -
38A PHE 3.4 26.9 - - - -
39A ALA* 4.2 5.4 - - + -
60A LYS* 3.6 36.6 - - + +
62A PHE* 3.5 29.4 - + + -
67A ASP 2.9 14.1 + - - +
68A ALA 3.4 7.0 - - - +
69A SER 3.2 0.2 - - - -
70A GLN* 1.3 74.4 - - - +
72A ILE* 1.3 76.0 + - - +
74A ARG* 3.1 25.4 + - + +
75A MET* 2.8 61.3 + - + +
82A ALA* 3.6 21.1 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 28.7 - - + -
68A ALA 3.0 16.4 + - - +
69A SER* 3.5 14.4 - - - +
71A TRP* 1.3 80.4 - - + +
73A LYS* 1.3 64.2 + - + +
75A MET* 3.1 3.5 + - - +
76A GLU* 3.0 23.1 + - + +
82A ALA* 4.2 15.2 - - + +
86A ASP* 3.9 27.6 - - + -
88A PHE* 4.6 4.0 - - + -
382A GLN* 3.7 23.9 + - - +
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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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69A SER* 3.1 20.9 + - - +
70A GLN* 3.2 33.8 + - - +
72A ILE* 1.3 77.1 - - + +
74A ARG* 1.3 59.1 + - + +
76A GLU* 3.1 12.3 + - - +
77A ASP* 2.9 32.8 + - - +
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Residues in contact with ARG 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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67A ASP 4.9 2.2 + - - -
70A GLN* 3.0 41.7 + - - +
71A TRP* 3.8 31.6 - - + +
73A LYS* 1.3 74.5 - - + +
75A MET* 1.3 60.7 + - - +
77A ASP* 3.2 18.3 + - + +
78A ILE* 2.9 41.2 + - + +
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Residues in contact with MET 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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39A ALA* 4.5 9.9 - - + -
71A TRP* 2.8 61.8 + - + +
72A ILE 3.4 8.5 - - - +
74A ARG* 1.3 76.2 - - - +
76A GLU* 1.3 58.3 + - - +
78A ILE* 3.4 11.4 + - - -
79A GLY 2.9 7.4 + - - -
80A LEU* 2.9 67.7 + - + +
81A GLU 3.3 26.0 - - - +
82A ALA* 3.9 9.4 - - + -
382A GLN* 6.0 0.2 - - - +
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Residues in contact with GLU 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 ILE* 3.0 13.6 + - - +
73A LYS* 3.1 12.5 + - - +
75A MET* 1.3 74.1 - - - +
77A ASP* 1.3 67.2 + - - +
79A GLY* 3.0 15.2 + - - -
80A LEU 4.8 1.8 - - - -
382A GLN* 5.6 9.1 + - - +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 2.9 20.3 + - - +
74A ARG* 3.4 24.6 - - + +
76A GLU* 1.3 77.5 - - - +
78A ILE* 1.3 61.5 + - + +
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Residues in contact with ILE 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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74A ARG* 2.9 27.4 + - + +
75A MET* 3.9 15.9 - - - +
77A ASP* 1.3 79.6 - - + +
79A GLY* 1.3 59.0 + - - +
80A LEU* 3.9 24.7 - - + +
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Residues in contact with GLY 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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75A MET 2.9 4.9 + - - -
76A GLU* 3.0 11.2 + - - -
78A ILE* 1.3 80.3 - - - +
80A LEU* 1.3 67.3 + - - +
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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