Contacts of the helix formed by residues 46 - 65 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY* 1.3 75.2 - - - -
47B ILE* 1.3 70.2 + - + +
48B LYS* 2.9 31.8 + - - +
49B ASP* 2.7 44.6 + - - +
50B GLN* 3.1 10.7 + - - +
116B LEU* 4.2 4.0 - - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 1.3 74.0 - - + +
48B LYS* 1.3 72.3 + - + +
50B GLN* 4.5 1.6 - - - -
51B THR* 2.8 32.8 + - + +
79B LEU* 6.0 7.2 - - + -
89B ASN* 5.7 5.2 - - - +
116B LEU* 3.6 42.5 - - + +
117B ILE* 3.9 27.4 - - + -
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 2.9 16.8 + - - +
47B ILE* 1.3 86.1 - - + +
49B ASP* 1.3 63.0 + - - +
51B THR* 2.9 23.0 - - + +
52B ARG* 3.1 19.1 + - - +
89B ASN* 5.2 12.0 - - - +
90B GLU 5.6 2.2 - - - +
91B VAL* 4.4 16.0 - - + +
48J LYS* 4.9 11.0 - - - +
52J ARG* 4.6 8.3 - - - +
90J GLU* 4.8 9.4 - - - -
94J GLU* 3.8 34.2 + - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.5 7.2 - - + +
45B GLY* 4.5 9.9 - - - -
46B ASP* 2.7 34.5 + - - +
48B LYS* 1.3 77.1 - - - +
50B GLN* 1.3 64.0 + - - +
52B ARG* 3.1 33.3 + - - +
53B GLN* 3.2 22.0 + - - +
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 3.4 26.6 - - + +
42B ILE* 5.7 0.2 - - - +
43B VAL* 3.1 36.7 + - + -
44B LYS* 4.7 1.6 - - - +
45B GLY 3.3 25.2 + - - +
46B ASP 3.1 10.2 + - - +
47B ILE* 4.0 4.5 - - - +
49B ASP* 1.3 76.2 - - - +
51B THR* 1.3 64.8 + - - +
53B GLN 3.2 1.7 + - - -
54B VAL* 3.0 26.2 + - - +
115B VAL* 3.9 3.1 - - - +
116B LEU* 2.8 52.0 + - - +
117B ILE* 4.0 8.0 + - + -
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Residues in contact with THR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 2.8 30.2 + - + +
48B LYS* 2.9 28.3 - - + +
50B GLN* 1.3 75.8 - - - +
52B ARG* 1.3 57.5 + - - +
54B VAL* 3.3 4.4 + - - +
55B LEU* 3.0 36.3 + - - +
89B ASN* 4.9 6.5 - - - +
91B VAL* 4.4 15.5 - - + -
92B TYR* 3.3 28.6 + - - -
117B ILE* 3.9 22.4 - - - +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LYS* 3.1 22.4 + - - +
49B ASP* 3.1 39.5 + - - +
50B GLN 3.2 0.2 - - - -
51B THR* 1.3 76.0 - - - +
53B GLN* 1.3 61.7 + - - +
55B LEU* 3.4 3.3 + - - +
56B GLU* 2.9 57.4 + - + +
91B VAL* 4.2 22.0 - - + -
95B TYR* 4.9 7.4 - - + +
93J ALA* 5.3 16.1 - - - +
94J GLU* 5.6 10.0 + - - +
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 4.2 5.6 - - + -
35B ILE 3.7 32.5 - - - +
36B ASP* 4.0 19.9 + - - +
37B PRO* 3.7 7.8 - - - +
43B VAL* 4.0 19.8 - - + +
49B ASP 3.2 14.1 + - - +
50B GLN 3.2 8.8 + - - +
52B ARG* 1.3 79.4 - - - +
54B VAL* 1.3 63.2 + - - +
56B GLU* 3.2 21.9 + - - +
57B ASN* 2.9 50.6 + - - +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 4.1 11.4 - - + +
33B ILE* 3.5 30.7 - - - -
34B PRO* 3.5 7.9 - - + -
50B GLN 3.0 19.5 + - - +
51B THR* 3.5 9.0 - - - +
53B GLN* 1.3 76.5 - - - +
55B LEU* 1.3 62.6 + - - +
57B ASN* 3.0 10.3 + - - +
58B ILE* 2.9 28.5 + - + +
117B ILE* 4.0 12.8 - - + +
119B ILE* 3.6 38.1 - - + -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 3.0 21.9 + - - +
52B ARG 3.9 1.6 - - - +
54B VAL* 1.3 76.1 - - + +
56B GLU* 1.3 61.7 + - - +
58B ILE* 3.8 11.4 - - + +
59B LYS* 3.1 23.7 + - - +
69B LEU* 5.7 0.7 - - - +
91B VAL* 4.0 23.3 - - + +
92B TYR* 4.1 24.0 - - + -
95B TYR* 3.3 48.1 - - + -
96B PHE* 4.6 11.2 - - + -
119B ILE* 3.4 31.4 - - + -
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Residues in contact with GLU 56 (chain B).
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 5.0 0.4 - - - +
52B ARG* 2.9 47.7 + - + +
53B GLN* 3.4 30.0 + - - +
54B VAL 3.1 0.2 - - - -
55B LEU* 1.3 76.6 - - - +
57B ASN* 1.3 62.3 + - - +
59B LYS* 3.4 8.2 + - - +
60B ALA* 3.1 20.8 + - - +
95B TYR* 3.4 20.0 + - - +
97J GLY 5.7 1.0 - - - +
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Residues in contact with ASN 57 (chain B).
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 4.1 2.0 + - - -
10B ALA* 4.3 1.1 - - + -
11B PRO* 3.2 23.3 - - + +
32B GLN* 3.7 16.6 - - - +
33B ILE 3.4 13.2 - - - +
35B ILE 3.1 16.6 + - - +
37B PRO* 3.6 18.4 - - - +
53B GLN* 2.9 37.2 + - - +
54B VAL* 3.0 7.1 + - - +
56B GLU* 1.3 75.5 - - - +
58B ILE* 1.3 66.6 + - - +
60B ALA* 2.9 18.6 + - - +
61B ILE* 3.0 18.2 + - - +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 4.0 20.6 - - + -
32B GLN* 3.8 16.4 - - + -
54B VAL* 2.9 24.3 + - + +
55B LEU* 3.8 14.8 - - + +
57B ASN* 1.3 74.9 - - - +
59B LYS* 1.3 59.0 + - - +
61B ILE* 3.2 12.9 + - - +
62B LEU* 2.9 38.7 + - + +
69B LEU* 5.8 1.6 - - + -
72B VAL* 5.7 0.4 - - + -
96B PHE* 5.2 13.5 - - + -
119B ILE* 3.8 40.2 - - + +
121B ALA* 4.4 15.7 - - + +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU 3.1 15.1 + - - +
56B GLU* 3.6 6.1 - - - +
58B ILE* 1.3 79.4 - - - +
60B ALA* 1.3 64.8 + - - +
62B LEU* 3.2 13.0 + - + +
63B GLU* 2.9 49.6 + - + +
69B LEU* 4.5 15.0 - - + -
95B TYR* 4.0 19.7 + - + +
98J GLU* 2.7 52.9 + - - +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B THR* 4.2 3.8 + - + +
9B ASN* 3.4 45.0 + - + +
10B ALA* 4.4 2.0 - - + -
56B GLU 3.1 11.5 + - - +
57B ASN 2.9 10.0 + - - +
59B LYS* 1.3 78.5 - - - +
61B ILE* 1.3 57.5 + - - +
63B GLU* 3.2 12.6 + - - +
64B ALA* 2.8 28.9 + - - +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.3 10.0 - - + +
7B THR* 4.4 7.6 - - + -
10B ALA* 3.6 19.7 - - + -
19B GLN* 4.0 14.8 - - + +
20B ALA* 3.5 30.5 - - + -
27B LEU* 5.0 1.1 - - + -
29B ILE* 3.6 23.3 - - + -
32B GLN* 3.6 34.3 - - + +
57B ASN 3.0 13.6 + - - +
58B ILE* 3.5 5.8 - - - +
60B ALA* 1.3 73.6 - - - +
62B LEU* 1.3 66.7 + - - +
64B ALA* 3.2 1.5 + - - +
65B ALA* 2.8 27.3 + - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.0 9.4 - - + -
29B ILE* 3.8 20.9 - - + -
58B ILE* 2.9 26.5 + - + +
59B LYS* 3.5 8.3 - - + +
61B ILE* 1.3 75.5 - - - +
63B GLU* 1.3 54.7 + - + +
65B ALA* 3.3 1.6 + - - +
66B GLY 3.0 7.8 + - - -
67B TYR* 2.6 47.4 + - + +
68B SER 4.0 7.9 - - - +
69B LEU* 3.7 24.5 - - + +
72B VAL* 3.5 28.0 - - + -
121B ALA* 6.1 0.4 - - + -
122B ILE 6.0 0.2 - - - -
123B ALA* 3.8 26.9 - - + -
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS* 2.9 46.4 + - + +
60B ALA* 3.5 12.3 - - - +
62B LEU* 1.3 74.0 - - + +
64B ALA* 1.3 60.7 + - - +
65B ALA 3.1 1.6 - - - -
66B GLY* 2.9 13.3 + - - -
67B TYR 3.7 11.2 - - - +
68B SER* 5.9 1.8 - - - -
9D ASN* 2.8 22.4 + - - +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.2 10.9 - - + +
7B THR* 3.5 36.6 - - + +
60B ALA 2.8 17.7 + - - +
61B ILE 3.8 2.7 - - - +
63B GLU* 1.3 73.1 - - - +
65B ALA* 1.3 57.9 + - - +
66B GLY 3.1 0.6 + - - -
6D PHE 4.5 3.8 - - - +
7D THR* 3.0 13.0 + - - +
8D GLU 2.9 25.6 + - - -
9D ASN* 3.8 6.0 + - - +
64D ALA* 4.6 7.9 - - + +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.9 22.2 - - + +
27B LEU* 3.4 40.2 - - + -
61B ILE 2.8 18.0 + - - +
62B LEU 3.6 1.8 - - - +
64B ALA* 1.3 76.0 - - - +
66B GLY* 1.3 60.6 + - - +
67B TYR* 3.4 12.3 - - + -
125B LYS* 5.3 0.7 + - - -
8D GLU* 3.1 22.5 - - - +
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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
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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