Contacts of the helix formed by residues 46 - 65 (chain D) in PDB entry 2DYY
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 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 3.2 5.8 - - + +
45D GLY* 1.3 77.9 - - - +
47D ILE* 1.3 71.0 + - - +
48D LYS* 2.6 40.7 + - - +
49D ASP* 3.3 26.4 - - - +
50D GLN* 3.0 24.3 + - - +
116D LEU* 4.4 0.7 - - - -
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLY 3.6 3.0 + - - -
46D ASP* 1.3 78.4 + - - +
48D LYS* 1.3 58.7 + - - +
50D GLN* 4.8 1.3 - - + -
51D THR* 2.5 48.0 + - - +
79D LEU* 4.4 18.4 - - + -
84D ASP* 3.8 39.0 - - + +
87D LYS* 3.5 27.6 - - + -
88D MET* 4.4 3.4 - - + -
116D LEU* 4.1 32.2 - - + +
117D ILE* 4.6 4.5 - - + -
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Residues in contact with LYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ASP* 2.6 21.9 + - - +
47D ILE* 1.3 77.5 - - + +
49D ASP* 1.3 70.6 + - - +
51D THR* 3.8 4.8 - - - -
52D ARG* 3.2 43.5 + - - +
87D LYS* 4.5 13.7 - - + +
90D GLU* 5.6 6.3 - - + -
91D VAL* 3.4 25.3 - - + +
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL* 4.1 4.1 - - + +
44D LYS* 3.8 47.7 + - + +
46D ASP* 3.2 29.7 + - + +
48D LYS* 1.3 85.5 - - - +
50D GLN* 1.3 61.9 + - - +
52D ARG* 3.3 15.7 + - - +
53D GLN* 3.0 23.0 + - - +
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PRO* 3.3 33.1 - - + +
42D ILE* 5.0 4.3 - - - +
43D VAL* 3.9 11.1 + - + +
44D LYS 3.3 24.1 + - - +
45D GLY* 3.3 18.6 - - - -
46D ASP 3.0 10.1 + - - +
47D ILE* 4.2 3.1 - - - +
49D ASP* 1.3 74.1 - - - +
51D THR* 1.3 67.3 + - - +
53D GLN* 3.1 1.7 + - - +
54D VAL* 2.9 27.7 + - - +
115D VAL* 3.7 2.7 - - - +
116D LEU* 2.9 50.9 + - + +
117D ILE* 4.1 10.3 + - + -
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Residues in contact with THR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 2.5 26.8 + - - +
48D LYS* 3.8 5.2 - - - -
49D ASP 3.3 0.2 - - - -
50D GLN* 1.3 76.9 - - - +
52D ARG* 1.3 58.4 + - - +
54D VAL* 3.4 4.1 + - - +
55D LEU* 3.1 44.0 + - + +
88D MET* 3.5 53.5 - - + +
91D VAL* 4.3 6.1 - - + -
117D ILE* 3.8 17.4 - - + +
119D ILE* 5.0 2.7 - - + -
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LYS* 3.2 42.5 + - - +
49D ASP* 3.7 13.1 + - - +
51D THR* 1.3 77.5 - - - +
53D GLN* 1.3 60.5 + - - +
55D LEU* 3.8 4.1 - - - +
56D GLU* 3.0 43.4 + - - +
91D VAL* 3.7 36.3 - - + +
94D GLU* 3.9 17.0 + - - -
95D TYR* 3.8 14.1 + - - +
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Residues in contact with GLN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D PRO* 3.7 15.9 - - + -
35D ILE 3.5 14.6 - - - +
36D ASP* 3.0 41.5 + - - +
37D PRO* 4.0 5.5 - - - +
43D VAL* 3.0 24.1 - - + +
49D ASP 3.0 13.7 + - - +
50D GLN 3.6 7.6 - - - +
52D ARG* 1.3 74.6 - - - +
54D VAL* 1.3 65.8 + - - +
56D GLU* 3.2 18.4 + - - +
57D ASN* 3.1 36.0 + - - +
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN* 3.5 20.3 - - + +
33D ILE 3.5 5.4 - - - -
34D PRO* 3.3 34.1 - - + -
50D GLN 2.9 18.9 + - - +
51D THR* 3.7 5.8 - - - +
53D GLN* 1.3 78.4 - - - +
55D LEU* 1.3 55.7 + - - +
57D ASN* 3.6 10.5 + - - +
58D ILE* 3.2 29.0 + - + +
117D ILE* 3.9 13.0 - - + +
119D ILE* 3.6 36.3 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D THR* 3.1 29.8 + - + +
52D ARG 3.8 1.6 - - - +
54D VAL* 1.3 75.8 - - - +
56D GLU* 1.3 59.1 + - - +
57D ASN 3.3 0.4 - - - -
58D ILE* 3.5 17.7 + - + +
59D LYS* 3.0 27.5 + - - +
69D LEU* 5.2 0.7 - - - +
91D VAL* 4.3 1.8 - - + +
92D TYR* 3.8 29.6 - - + +
95D TYR* 3.5 52.4 - - + -
96D PHE* 4.4 15.9 - - + -
119D ILE* 3.9 25.1 - - + -
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ASN 5.7 0.2 - - - -
52D ARG* 3.0 38.6 + - - +
53D GLN* 3.2 25.1 + - - +
55D LEU* 1.3 76.6 - - - +
57D ASN* 1.3 59.1 + - - +
59D LYS* 3.2 10.0 + - + +
60D ALA* 2.9 27.4 + - - +
95D TYR* 3.3 18.3 + - + +
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASN 4.3 2.1 - - - +
10D ALA* 4.4 1.8 - - + -
11D PRO* 3.3 23.2 - - + +
32D GLN* 3.6 18.2 - - + +
33D ILE 3.3 20.2 + - - -
35D ILE 3.2 18.6 + - - +
37D PRO* 3.6 22.0 - - - +
53D GLN* 3.1 20.0 + - - +
54D VAL* 3.7 6.7 - - - +
55D LEU 3.3 0.2 - - - -
56D GLU* 1.3 74.4 - - - +
58D ILE* 1.3 66.6 + - - +
60D ALA* 3.0 9.1 + - - +
61D ILE* 2.9 28.8 + - - +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 4.2 16.9 - - + +
32D GLN* 3.9 16.6 - - + -
54D VAL* 3.2 19.1 + - + +
55D LEU* 3.8 17.3 - - + +
56D GLU 3.4 0.2 - - - -
57D ASN* 1.3 77.6 - - - +
59D LYS* 1.3 58.7 + - - +
61D ILE* 3.4 8.3 + - - +
62D LEU* 2.9 45.5 + - + +
69D LEU* 5.2 1.3 - - + -
96D PHE* 4.7 13.0 - - + -
119D ILE* 3.4 43.7 - - + +
121D ALA* 4.7 13.9 - - + -
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Residues in contact with LYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU 3.0 15.2 + - - +
56D GLU* 3.3 14.1 - - + +
57D ASN 3.1 0.2 - - - -
58D ILE* 1.3 78.0 - - - +
60D ALA* 1.3 57.0 + - - +
62D LEU* 3.3 12.3 + - + +
63D GLU* 2.9 58.7 + - + +
69D LEU* 4.3 28.5 - - + -
95D TYR* 4.3 17.4 - - + -
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Residues in contact with ALA 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D THR* 4.4 3.5 + - - +
9D ASN* 3.5 45.5 + - + +
10D ALA 4.5 0.2 - - - +
56D GLU 2.9 13.7 + - - +
57D ASN 3.0 8.0 + - - +
59D LYS* 1.3 73.2 - - - +
61D ILE* 1.3 66.3 + - - +
63D GLU* 3.1 15.5 + - - +
64D ALA* 2.9 23.0 + - - +
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.3 8.9 - - + +
7D THR* 4.0 12.3 - - + -
10D ALA* 3.4 26.5 - - + -
19D GLN* 4.1 13.7 - - + +
20D ALA* 3.5 31.0 - - + -
27D LEU* 5.0 1.8 - - + -
29D ILE* 4.0 19.5 - - + -
32D GLN* 3.4 40.4 - - + +
57D ASN 2.9 17.6 + - - +
58D ILE 3.9 2.9 - - - +
60D ALA* 1.3 71.2 - - - +
62D LEU* 1.3 64.7 + - - +
64D ALA* 3.1 3.7 + - - +
65D ALA* 2.9 21.1 + - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 4.0 7.6 - - + -
29D ILE* 3.8 18.4 - - + -
58D ILE* 2.9 31.4 + - + +
59D LYS* 3.4 5.4 - - + +
61D ILE* 1.3 76.9 - - - +
63D GLU* 1.3 61.5 + - + +
65D ALA* 3.1 8.7 + - - +
67D TYR* 2.9 51.7 + - + +
68D SER 4.1 9.2 - - - +
69D LEU* 3.7 30.5 - - + -
72D VAL* 3.8 20.4 - - + -
123D ALA* 3.9 20.0 - - + -
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN* 2.8 22.9 + - - -
59D LYS* 2.9 50.7 + - + +
60D ALA* 3.1 14.8 + - - +
62D LEU* 1.3 75.6 - - + +
64D ALA* 1.3 60.5 + - - +
66D GLY* 3.3 6.6 + - - -
67D TYR 3.8 10.8 - - - +
68D SER* 6.0 1.3 - - - -
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE 5.1 0.4 - - - +
7B THR* 2.5 36.1 + - - +
8B GLU 2.8 13.0 + - - -
9B ASN* 3.7 1.6 + - - +
64B ALA* 4.6 5.8 - - + -
5D ILE* 4.4 9.6 - - + -
7D THR* 3.7 33.4 - - + +
9D ASN* 5.8 0.4 - - - +
60D ALA 2.9 8.9 + - - +
61D ILE 3.6 7.2 - - - +
63D GLU* 1.3 77.6 - - - +
65D ALA* 1.3 58.9 + - - +
66D GLY 3.5 0.3 + - - -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.0 26.4 - - - +
5D ILE* 4.0 17.2 - - + +
22D LYS* 4.5 0.6 - - + +
27D LEU* 3.4 42.0 - - + -
61D ILE 2.9 11.6 + - - +
62D LEU 3.1 3.1 + - - +
64D ALA* 1.3 77.6 - - - +
66D GLY* 1.3 56.2 + - - +
67D TYR* 3.3 16.8 - - + -
125D LYS* 5.3 0.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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