Contacts of the helix formed by residues 57 - 73 (chain A) in PDB entry 2DMT
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 SER 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ALA* 4.0 2.0 - - - -
56A LEU* 1.3 76.6 - - - +
58A GLN* 1.3 57.8 + - - +
59A LEU* 4.2 9.9 - - - -
60A GLN* 2.5 48.7 + - - +
61A VAL* 3.7 1.6 + - - +
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Residues in contact with GLN 58 (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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44A THR 5.2 0.2 + - - -
47A ARG* 3.3 24.5 - - - +
48A ILE* 3.3 52.2 - - + +
51A ALA* 3.8 13.2 - - + +
57A SER* 1.3 69.6 - - - +
59A LEU* 1.3 62.7 + - - +
60A GLN 3.3 0.2 + - - -
61A VAL* 3.4 2.7 + - - +
62A LYS* 3.3 16.9 + - - +
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Residues in contact with LEU 59 (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 ARG* 6.2 1.8 - - - +
57A SER* 2.7 12.2 + - - +
58A GLN* 1.3 76.7 - - - +
60A GLN* 1.3 66.0 + - + +
62A LYS* 3.0 31.0 + - - +
63A THR* 2.8 43.2 + - - +
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Residues in contact with GLN 60 (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 THR* 4.5 17.4 - - - +
23A VAL 4.9 5.5 + - - +
24A PHE* 2.8 47.8 - - + -
32A LEU* 5.3 0.4 - - + -
56A LEU* 3.9 16.8 - - + +
57A SER* 2.5 39.9 + - - +
59A LEU* 1.3 74.5 - - - +
61A VAL* 1.3 57.1 + - - +
63A THR* 4.9 3.4 - - - -
64A TRP* 2.6 40.4 + - - +
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Residues in contact with VAL 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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32A LEU* 4.1 11.6 - - + +
42A LEU* 3.2 23.1 - - + -
47A ARG* 3.6 30.7 - - + +
50A LEU* 3.5 24.0 - - + -
51A ALA* 4.9 6.5 - - + -
56A LEU* 5.4 2.0 - - + -
57A SER 4.6 4.7 - - - +
58A GLN 3.4 2.7 + - - +
59A LEU 3.3 0.6 - - - -
60A GLN* 1.3 74.1 - - + +
62A LYS* 1.3 64.9 + - - +
64A TRP* 4.4 2.7 - - - -
65A TYR* 2.8 66.1 + - + +
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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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15A LYS* 5.9 5.5 - - - +
47A ARG* 3.7 23.5 - - - +
58A GLN 3.3 9.4 + - - +
59A LEU* 3.0 33.4 + - + +
61A VAL* 1.3 81.1 - - - +
63A THR* 1.3 69.1 + - - +
65A TYR* 3.4 4.4 - - - +
66A GLN* 3.2 41.9 + - - +
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Residues in contact with THR 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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17A GLY* 6.1 3.4 - - - +
59A LEU* 2.8 40.0 + - - +
60A GLN* 3.9 3.8 - - - -
62A LYS* 1.3 71.8 - - - +
64A TRP* 1.3 69.2 + - - +
65A TYR 2.8 1.7 + - - -
66A GLN* 3.0 22.1 + - + +
67A ASN* 3.1 29.6 + - - +
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Residues in contact with TRP 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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24A PHE* 3.7 29.3 - + + -
29A LEU* 3.7 19.4 - - + +
32A LEU* 3.2 56.1 - - + -
33A GLU* 3.5 18.8 - - + -
36A PHE* 3.8 15.0 - - + -
60A GLN 2.6 26.2 + - - +
61A VAL* 4.0 1.1 - - - +
63A THR* 1.3 73.3 - - - +
65A TYR* 1.3 83.8 + + - +
67A ASN* 3.5 11.7 + - + +
68A ARG* 3.0 68.8 + - + +
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Residues in contact with TYR 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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32A LEU* 4.5 5.2 - - + -
35A ARG* 3.5 5.4 - - - +
36A PHE* 2.9 51.7 + + + -
39A GLN 3.6 9.4 - - - -
40A LYS 2.9 28.9 - - - -
41A TYR* 4.3 6.7 - + + -
42A LEU* 2.9 36.9 - - + +
47A ARG* 5.4 3.8 - - - +
50A LEU* 4.6 0.4 - - + +
61A VAL* 2.8 50.4 + - + +
62A LYS* 3.4 5.2 - - - +
63A THR 2.8 2.6 + - - -
64A TRP* 1.3 82.1 - + - +
66A GLN* 1.3 59.0 + - + +
68A ARG* 2.5 28.2 + - - +
69A ARG* 2.9 13.2 + - + -
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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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62A LYS* 3.2 39.8 + - - +
63A THR* 3.0 13.0 + - - +
65A TYR* 1.3 75.4 - - - +
67A ASN* 1.3 66.7 + - - +
69A ARG* 3.1 41.3 + - - +
70A MET* 3.5 10.5 + - - +
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Residues in contact with ASN 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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17A GLY 5.9 1.2 + - - -
63A THR* 3.1 32.4 + - - +
64A TRP* 3.5 12.3 - - + +
65A TYR 2.9 1.6 + - - -
66A GLN* 1.3 80.5 - - - +
68A ARG* 1.3 62.6 + - + +
70A MET* 3.3 22.6 - - - +
71A LYS* 4.1 2.1 + - - +
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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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29A LEU* 4.4 9.9 - - - +
33A GLU* 4.4 17.5 + - - +
36A PHE* 3.6 18.8 - - + -
64A TRP* 3.0 71.8 + - + +
65A TYR 2.5 13.2 + - - +
67A ASN* 1.3 69.7 - - + +
69A ARG* 1.3 67.5 + - - +
71A LYS* 3.0 31.6 + - - +
72A TRP* 3.0 10.8 + - - +
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Residues in contact with ARG 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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36A PHE* 3.9 12.7 - - + -
41A TYR* 3.0 54.8 + - + -
65A TYR* 2.9 14.7 + - - +
66A GLN* 3.1 33.6 + - - +
68A ARG* 1.3 74.7 - - - +
70A MET* 1.3 66.3 + - + +
72A TRP* 2.7 35.7 + - + +
73A LYS* 2.8 19.9 + - + +
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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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66A GLN 3.5 7.6 + - - +
67A ASN* 3.3 19.0 + - - +
68A ARG 3.1 0.2 - - - -
69A ARG* 1.3 79.7 - - - +
71A LYS* 1.3 61.7 + - - +
73A LYS* 3.2 39.7 + - - +
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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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67A ASN 4.1 2.2 + - - +
68A ARG* 3.0 23.3 + - - +
70A MET* 1.3 76.4 - - - +
72A TRP* 1.3 59.6 + - - +
73A LYS 2.7 21.3 - - - +
74A LYS* 5.6 1.0 - - - +
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Residues in contact with TRP 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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36A PHE* 5.0 9.2 - + + -
40A LYS* 3.8 37.5 - - + +
41A TYR* 3.3 28.7 - + - -
68A ARG 3.0 11.3 + - - +
69A ARG* 2.7 44.1 + - + +
71A LYS* 1.3 75.3 - - - +
73A LYS* 1.3 83.1 + - + +
74A LYS* 4.8 5.4 - - - +
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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 ARG* 2.8 16.9 + - + +
70A MET* 3.4 37.4 + - - +
71A LYS 2.7 16.9 + - - +
72A TRP* 1.3 103.2 - - + +
74A LYS* 1.3 68.8 - - - +
75A SER* 5.1 7.9 + - - -
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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