Contacts of the helix formed by residues 62 - 80 (chain A) in PDB entry 2DKY
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PHE 4.8 3.2 - - - +
61A LEU* 1.3 77.1 - - - +
63A ARG* 1.3 61.6 + - - +
64A ASP* 3.2 11.4 - - + +
65A ALA* 3.2 12.2 + - + +
66A ILE* 2.8 32.2 + - - +
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Residues in contact with ARG 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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62A ASP* 1.3 72.9 + - - +
64A ASP* 1.3 64.1 + - - +
66A ILE* 3.7 4.5 - - - +
67A GLU* 2.8 52.8 + - + +
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Residues in contact with ASP 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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62A ASP* 3.2 7.1 - - + +
63A ARG* 1.3 81.5 + - - +
65A ALA* 1.3 67.3 + - - +
67A GLU* 3.7 4.6 - - - +
68A ALA* 2.9 27.4 + - - +
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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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61A LEU* 4.0 21.7 - - + +
62A ASP* 3.2 23.3 + - + +
64A ASP* 1.3 78.3 - - - +
66A ILE* 1.3 64.6 + - - +
68A ALA* 3.7 5.4 - - - +
69A LEU* 3.0 23.8 + - - +
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Residues in contact with ILE 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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54A VAL* 4.7 5.4 - - + +
55A LYS* 3.9 38.6 - - + +
58A HIS* 3.5 20.0 - - + +
59A ASP* 5.5 2.0 - - - +
61A LEU* 3.3 41.1 - - + +
62A ASP 2.8 26.1 + - - +
63A ARG* 3.7 4.9 - - - +
65A ALA* 1.3 69.2 - - - +
67A GLU* 1.3 70.4 + - + +
69A LEU* 2.9 10.8 + - + +
70A CYS* 2.8 22.3 + - + +
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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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55A LYS* 6.2 0.4 - - - +
63A ARG* 2.8 42.0 + - + +
64A ASP* 3.7 4.9 - - - +
66A ILE* 1.3 76.4 - - + +
68A ALA* 1.3 58.2 + - - +
70A CYS* 3.3 8.2 + - - +
71A ARG* 2.8 44.5 + - + +
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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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29A TRP* 5.0 1.8 - - + -
64A ASP 2.9 18.4 + - - +
65A ALA* 3.7 6.1 - - - +
67A GLU* 1.3 75.9 - - - +
69A LEU* 1.3 59.1 + - - +
71A ARG* 3.3 15.9 + - - +
72A ARG* 2.5 50.8 + - - +
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Residues in contact with LEU 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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29A TRP* 3.6 29.3 - - + -
30A LEU* 4.2 3.8 - - + -
35A PHE* 3.6 36.3 - - + -
38A TYR* 4.0 18.6 - - + -
54A VAL* 3.5 26.7 - - + -
58A HIS* 4.7 2.0 - - - +
61A LEU* 4.4 13.2 - - + -
65A ALA 3.0 14.0 + - - +
66A ILE* 2.9 13.5 + - + +
68A ALA* 1.3 77.0 - - - +
70A CYS* 1.3 62.7 + - - +
72A ARG* 3.2 12.5 + - - +
73A LEU* 3.3 24.1 + - + +
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Residues in contact with CYS 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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51A ILE* 3.2 34.1 - - + -
55A LYS* 3.7 24.0 - - + -
66A ILE* 2.8 19.0 + - + +
67A GLU* 3.7 11.0 - - - +
69A LEU* 1.3 68.1 - - - +
71A ARG* 1.3 55.9 + - - +
72A ARG 2.7 17.0 + - - -
73A LEU* 2.9 11.1 + - + -
74A ASN* 2.9 36.2 + - - -
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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 GLU* 2.8 32.4 + - - +
68A ALA* 3.3 16.6 - - - +
70A CYS* 1.3 71.0 - - - +
72A ARG* 1.3 92.5 + - - +
74A ASN* 2.9 14.5 + - - +
75A THR* 2.8 23.4 + - - -
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Residues in contact with ARG 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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26A ALA* 3.7 23.5 - - + +
29A TRP* 3.1 64.8 - - + +
30A LEU* 3.9 7.6 - - + -
68A ALA* 2.5 51.0 + - - +
69A LEU 3.2 7.8 + - - +
70A CYS 2.7 5.3 + - - -
71A ARG* 1.3 106.5 - - - +
73A LEU* 1.3 66.4 + - - +
74A ASN 3.3 0.2 - - - -
75A THR* 3.2 13.3 + - - -
76A LEU* 3.3 17.0 + - - +
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Residues in contact with LEU 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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30A LEU* 3.6 25.6 - - + -
38A TYR* 3.9 14.6 - - + -
47A PHE* 4.3 9.2 - - + -
49A ILE* 3.7 17.0 - - + -
51A ILE* 3.0 25.1 - - + -
54A VAL* 3.6 42.8 - - + -
69A LEU* 3.3 18.8 - - + +
70A CYS* 2.9 10.4 + - + +
72A ARG* 1.3 75.2 - - - +
74A ASN* 1.3 56.0 + - - +
76A LEU* 2.9 7.8 + - - +
77A ASN* 2.8 31.2 + - - -
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Residues in contact with ASN 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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51A ILE* 3.7 7.5 - - + +
70A CYS* 2.9 26.1 + - - +
71A ARG* 2.9 33.7 + - - +
73A LEU* 1.3 76.3 - - - +
75A THR* 1.3 77.6 + - - +
77A ASN* 2.7 35.7 + - - +
78A LYS* 3.3 16.1 + - - +
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Residues in contact with THR 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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22A GLU* 3.8 36.6 - - + +
26A ALA* 4.4 6.1 - - + -
71A ARG 2.8 19.9 + - - -
72A ARG* 3.2 12.6 + - - -
74A ASN* 1.3 89.3 + - - +
76A LEU* 1.3 56.2 + - - +
78A LYS* 3.4 24.0 + - - +
79A CYS* 3.3 18.5 - - - +
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Residues in contact with LEU 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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23A ALA* 3.4 35.4 - - + +
26A ALA* 3.4 22.7 - - + -
27A CYS* 3.8 11.4 - - - -
30A LEU* 3.4 33.4 - - + -
42A TYR* 3.6 22.4 - - + -
47A PHE* 3.5 24.0 - - + -
72A ARG 3.5 5.8 - - - +
73A LEU 2.9 6.6 + - - +
74A ASN 2.7 1.0 + - - -
75A THR* 1.3 76.7 - - - +
77A ASN* 1.3 56.2 + - - +
78A LYS 2.9 5.4 - - - -
79A CYS* 4.0 1.8 - - - -
80A ALA* 2.7 36.6 + - - +
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Residues in contact with ASN 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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47A PHE* 3.3 20.4 - - - -
48A PRO* 3.4 28.8 - - + +
49A ILE 2.9 21.9 - - - +
51A ILE* 3.2 28.6 - - - +
73A LEU 2.8 25.4 + - - -
74A ASN* 2.7 18.9 + - - +
76A LEU* 1.3 71.6 - - - +
78A LYS* 1.3 54.3 + - + +
81A VAL* 3.2 21.3 + - - +
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Residues in contact with LYS 78 (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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22A GLU* 5.9 1.2 + - - -
74A ASN* 3.3 10.5 + - - +
75A THR* 3.4 35.5 + - - +
76A LEU 2.9 0.6 - - - -
77A ASN* 1.3 80.3 - - + +
79A CYS* 1.3 64.7 + - - +
80A ALA 3.0 4.7 - - - -
81A VAL* 3.9 6.7 - - + -
82A MET* 2.6 39.8 + - + +
89A SER* 4.9 13.2 + - - +
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Residues in contact with CYS 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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19A THR* 4.1 24.7 - - - +
22A GLU* 3.5 33.0 - - - -
23A ALA* 4.1 15.9 - - + -
42A TYR* 3.4 13.2 + - + +
75A THR* 3.3 20.9 - - - +
76A LEU* 2.9 8.8 + - - +
78A LYS* 1.3 85.2 - - - +
80A ALA* 1.3 56.4 + - - +
82A MET* 2.8 25.8 - - - +
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Residues in contact with ALA 80 (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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42A TYR* 3.8 13.5 - - + -
45A PHE* 6.5 1.1 - - - -
47A PHE* 3.3 42.2 - - + +
48A PRO* 4.1 2.7 - - + +
76A LEU 2.7 15.4 + - - +
79A CYS* 1.3 81.0 - - - +
81A VAL* 1.3 57.8 + - - +
82A MET* 3.7 8.1 - - - +
83A LYS* 5.5 1.4 - - - +
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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