Contacts of the helix formed by residues 57 - 74 (chain A) in PDB entry 2DA3
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 LYS 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.0 41.5 - - + +
21A ARG* 3.3 25.3 + - - +
22A THR* 4.7 8.9 - - + +
56A LEU* 1.3 71.5 - - - +
58A LYS* 1.3 67.8 + - - +
59A ARG* 3.1 4.5 - - + +
60A VAL* 2.7 36.7 + - + +
61A VAL 2.9 9.5 + - - -
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Residues in contact with LYS 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 ARG* 4.1 23.7 - - - +
47A LEU* 3.9 8.5 - - + +
48A ASP* 3.4 50.3 - - - +
51A ALA* 3.4 15.0 - - + +
56A LEU 2.9 4.2 + - - -
57A LYS* 1.3 69.6 - - - +
59A ARG* 1.3 68.5 + - - +
61A VAL* 3.0 4.0 + - - +
62A GLN* 2.7 62.1 + - + +
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Residues in contact with ARG 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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57A LYS* 3.1 4.2 - - + -
58A LYS* 1.3 91.3 - - - +
60A VAL* 1.3 60.7 + - + +
62A GLN* 3.0 33.8 + - - +
63A VAL* 2.8 47.3 + - + +
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Residues in contact with VAL 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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21A ARG 4.7 0.2 - - - +
22A THR* 3.5 25.6 - - - +
24A ILE* 3.8 31.9 - - + -
56A LEU* 4.0 10.3 - - + -
57A LYS* 2.7 33.5 + - + +
59A ARG* 1.3 75.1 - - + +
61A VAL* 1.3 56.4 + - - +
63A VAL* 4.4 3.7 - - - +
64A TRP* 2.9 30.9 + - - +
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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* 3.9 24.0 - - + -
47A LEU* 4.0 12.0 - - + +
50A ILE* 4.3 6.1 - - + -
51A ALA* 3.5 24.7 - - + +
56A LEU* 3.5 50.7 - - + +
57A LYS 2.9 4.4 + - - -
58A LYS 3.4 6.1 - - - +
60A VAL* 1.3 76.0 - - - +
62A GLN* 1.3 61.9 + - - +
64A TRP* 3.9 4.8 - - - +
65A PHE* 3.0 41.1 + - + -
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Residues in contact with GLN 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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44A ARG* 3.8 27.1 - - - +
47A LEU* 3.9 27.6 - - + +
58A LYS* 2.7 41.4 + - + +
59A ARG* 3.0 34.3 + - - +
61A VAL* 1.3 72.0 - - - +
63A VAL* 1.3 73.1 + - + +
65A PHE* 3.3 13.5 + - - +
66A GLN* 3.4 20.2 + - - +
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Residues in contact with VAL 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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59A ARG* 2.8 39.9 + - + +
60A VAL* 4.4 3.4 - - - +
62A GLN* 1.3 71.2 - - + +
64A TRP* 1.3 64.9 + - - +
65A PHE 2.8 6.8 + - - -
66A GLN* 2.9 27.1 + - + +
67A ASN* 2.8 50.8 + - - +
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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 ILE* 3.3 26.0 - - + +
29A LEU* 3.5 21.5 - - + +
32A LEU* 4.0 13.7 - - + -
33A TYR* 3.3 60.1 + + - -
36A TYR* 3.9 19.7 - + + -
60A VAL* 2.9 22.4 + - + +
61A VAL* 3.9 6.7 - - - +
62A GLN 3.4 0.2 - - - -
63A VAL* 1.3 76.2 - - - +
65A PHE* 1.3 83.2 + + - +
67A ASN* 4.1 7.6 - - - +
68A THR* 2.7 47.5 + - - -
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Residues in contact with PHE 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* 3.8 26.0 - - + -
35A LYS* 4.4 10.3 - - + -
36A TYR* 3.7 22.8 - + + -
39A ASP* 3.4 21.5 - - + -
40A SER* 4.9 2.0 - - - +
42A PRO* 3.7 28.7 - - + -
47A LEU* 4.1 8.7 - - + -
50A ILE* 4.7 10.1 - - + -
61A VAL* 3.0 34.1 - - + -
62A GLN 3.3 10.3 + - - +
63A VAL 2.8 2.0 + - - -
64A TRP* 1.3 99.0 - + - +
66A GLN* 1.3 64.4 + - - +
67A ASN 3.1 1.3 + - - -
68A THR* 3.2 4.3 + - - -
69A ARG* 3.1 29.7 + - - +
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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 GLN* 3.4 15.6 + - - +
63A VAL* 2.9 37.9 + - - +
65A PHE* 1.3 79.1 - - - +
67A ASN* 1.3 74.0 + - - +
69A ARG* 3.8 20.6 + - - +
70A ALA* 3.5 20.3 + - - +
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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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63A VAL* 2.8 38.7 + - - +
64A TRP* 4.1 7.3 - - - +
66A GLN* 1.3 86.2 - - - +
68A THR* 1.3 66.3 + - - +
70A ALA* 3.3 8.3 + - - +
71A ARG* 3.3 27.0 + - - +
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Residues in contact with THR 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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33A TYR* 5.6 4.0 - - + -
36A TYR* 3.2 39.5 - - + +
64A TRP* 2.7 42.1 + - + -
65A PHE* 3.2 5.7 + - - -
67A ASN* 1.3 77.4 - - - +
69A ARG* 1.3 64.6 + - - +
71A ARG* 3.1 12.9 + - + +
72A GLU* 2.9 25.3 + - + +
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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 TYR* 3.4 19.5 - - + +
40A SER* 3.0 29.4 + - - +
41A ASN* 2.8 33.4 + - - +
65A PHE* 3.1 19.1 + - - +
66A GLN* 3.9 18.3 - - - +
67A ASN 3.3 0.2 - - - -
68A THR* 1.3 76.3 - - - +
70A ALA* 1.3 64.1 + - - +
72A GLU* 2.9 4.5 + - - +
73A ARG* 2.8 30.2 + - - +
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Residues in contact with ALA 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 10.3 + - - +
67A ASN* 3.3 12.0 + - - +
69A ARG* 1.3 77.4 - - - +
71A ARG* 1.3 58.8 + - + +
73A ARG* 2.9 17.8 - - - +
74A LYS* 2.8 31.2 + - - +
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Residues in contact with ARG 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* 3.3 13.6 + - - +
68A THR* 3.1 14.5 + - + +
69A ARG 3.0 0.6 - - - -
70A ALA* 1.3 76.3 - - + +
72A GLU* 1.3 66.2 + - + +
74A LYS* 3.3 41.8 + - + +
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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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36A TYR* 3.3 32.7 - - + +
68A THR* 2.9 12.9 + - + +
69A ARG* 2.9 8.6 + - - +
71A ARG* 1.3 77.8 - - + +
73A ARG* 1.3 61.4 + - - +
74A LYS 4.1 3.1 - - - +
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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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69A ARG* 2.8 17.7 + - - +
70A ALA* 2.9 36.8 - - - +
72A GLU* 1.3 71.8 - - - +
74A LYS* 1.3 70.7 + - - +
75A SER* 2.8 7.1 + - - -
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Residues in contact with LYS 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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70A ALA 2.8 20.7 + - - +
71A ARG* 3.4 35.0 - - + +
72A GLU 4.1 2.9 - - - +
73A ARG* 1.3 75.4 - - - +
75A SER* 1.3 77.0 + - - +
76A GLY* 3.4 7.4 + - - +
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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