Contacts of the helix formed by residues 42 - 56 (chain B) in PDB entry 2IOY
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B SER* 2.9 15.1 + - - +
40B GLN* 3.8 9.0 - - + +
41B ASN* 1.3 77.2 - - - +
43B SER* 1.3 59.4 + - - +
44B SER* 2.4 48.2 + - - -
45B LYS* 2.9 10.5 + - + -
46B GLU* 2.9 27.4 + - - +
66B VAL* 3.8 4.3 - - - +
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Residues in contact with SER 43 (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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42B ASP* 1.3 73.2 + - - +
44B SER* 1.3 57.2 + - - +
46B GLU* 3.4 14.8 + - - +
47B LEU* 3.0 27.5 + - - +
66B VAL* 3.2 24.3 - - - +
67B ASP* 3.8 5.9 + - - +
70B ALA* 3.6 31.0 - - - +
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Residues in contact with SER 44 (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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42B ASP* 2.4 31.9 + - - -
43B SER* 1.3 73.1 - - - +
45B LYS* 1.3 54.9 + - - -
47B LEU* 3.3 9.6 + - - +
48B SER* 3.1 27.0 + - - -
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Residues in contact with LYS 45 (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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38B ASP 3.8 13.7 - - - +
39B SER 3.3 22.4 - - - +
40B GLN* 3.7 32.3 - - - +
42B ASP* 2.9 15.9 + - + +
44B SER* 1.3 74.4 + - - +
46B GLU* 1.3 61.1 + - - +
48B SER* 3.2 13.9 + - - -
49B ASN* 2.8 50.6 + - - +
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Residues in contact with GLU 46 (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 VAL* 4.2 2.4 - - + +
39B SER* 3.4 25.5 + - - +
42B ASP 2.9 13.1 + - - +
43B SER* 3.4 17.3 + - - +
45B LYS* 1.3 76.7 - - - +
47B LEU* 1.3 56.9 + - - +
49B ASN* 3.1 4.4 + - - +
50B VAL* 2.9 35.1 + - + +
63B ILE* 4.2 16.0 - - + +
64B ASN 4.1 2.8 - - - +
65B PRO* 3.4 8.8 - - - +
66B VAL* 2.8 35.6 + - + +
67B ASP 5.0 0.2 + - - -
70B ALA 4.7 0.5 - - - +
71B VAL* 3.5 35.5 + - + +
74B ALA* 5.0 3.1 - - + +
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Residues in contact with LEU 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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43B SER 3.0 17.5 + - - +
44B SER* 3.6 9.4 - - - +
45B LYS 3.3 0.2 - - - -
46B GLU* 1.3 75.4 - - - +
48B SER* 1.3 58.6 + - - +
50B VAL* 3.4 1.6 + - - +
51B GLU* 2.9 58.3 + - + +
73B THR* 4.2 12.3 - - + -
74B ALA* 3.7 40.2 - - + +
77B GLU* 3.9 12.6 - - - +
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Residues in contact with SER 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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44B SER 3.1 13.8 + - - -
45B LYS* 3.2 21.5 + - - -
47B LEU* 1.3 77.6 - - - +
49B ASN* 1.3 59.5 + - - +
51B GLU* 3.3 12.1 + - - +
52B ASP* 2.9 30.5 + - - +
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Residues in contact with ASN 49 (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 VAL* 4.3 8.3 - - + -
37B GLU* 3.0 43.2 - - + +
38B ASP 3.0 35.8 + - - +
39B SER* 3.4 13.9 + - - +
45B LYS* 2.8 36.4 + - - +
46B GLU* 3.1 8.7 + - - +
48B SER* 1.3 74.4 + - - +
50B VAL* 1.3 62.2 + - - +
52B ASP* 3.3 2.7 + - - +
53B LEU* 3.0 25.6 + - - +
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Residues in contact with VAL 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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7B VAL* 4.3 11.7 - - + -
46B GLU 2.9 20.2 + - - +
47B LEU 3.8 4.0 - - - +
49B ASN* 1.3 74.0 - - - +
51B GLU* 1.3 58.0 + - + +
53B LEU* 3.2 9.3 + - - +
54B ILE* 2.8 45.8 + - + +
61B LEU* 4.0 20.6 - - + +
63B ILE* 3.8 28.7 - - + -
74B ALA* 3.8 31.4 - - + +
77B GLU* 5.6 0.4 - - + -
78B ALA* 4.7 0.2 - - + -
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Residues in contact with GLU 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 LEU* 2.9 37.5 + - + +
48B SER* 3.6 11.1 - - - +
50B VAL* 1.3 75.5 - - + +
52B ASP* 1.3 55.9 + - - +
54B ILE* 3.5 10.7 + - + +
55B GLN* 3.0 35.2 + - + +
77B GLU* 2.6 40.8 - - - +
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Residues in contact with ASP 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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37B GLU* 2.6 29.6 - - - +
48B SER* 2.9 14.7 + - - +
49B ASN* 3.4 8.7 - - - +
51B GLU* 1.3 75.7 - - - +
53B LEU* 1.3 56.9 + - - +
55B GLN* 3.3 8.4 + - - +
56B GLN* 2.9 46.1 + - - +
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Residues in contact with LEU 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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5B GLY* 3.9 11.7 - - - -
6B LEU 4.3 0.9 - - - +
7B VAL* 3.2 35.2 - - + -
35B ILE* 3.9 35.4 - - + -
37B GLU* 4.1 15.3 - - + +
49B ASN 3.0 14.7 + - - +
50B VAL 3.7 5.8 - - - +
52B ASP* 1.3 72.6 - - - +
54B ILE* 1.3 65.8 + - - +
56B GLN* 3.2 7.6 + - - +
57B LYS 3.1 16.8 + - - -
58B VAL* 3.2 35.2 + - + -
61B LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 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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50B VAL* 2.8 36.3 + - + +
51B GLU* 3.7 10.8 - - + +
53B LEU* 1.3 76.2 - - - +
55B GLN* 1.3 58.9 + - + +
57B LYS* 3.0 20.8 + - - +
58B VAL* 4.7 0.2 - - - +
61B LEU* 4.4 5.8 - - + -
77B GLU* 3.8 15.7 - - + +
78B ALA* 3.7 29.8 - - - +
81B LYS* 3.9 31.2 - - + -
83B ILE* 3.8 23.4 - - + +
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Residues in contact with GLN 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 GLU* 3.0 21.5 + - + +
52B ASP* 3.6 8.7 - - - +
54B ILE* 1.3 73.0 - - + +
56B GLN* 1.3 61.2 + - + +
57B LYS* 3.1 20.8 + - - +
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Residues in contact with GLN 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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35B ILE* 3.1 32.0 - - + +
37B GLU* 4.3 4.8 + - - -
52B ASP* 2.9 46.6 + - - +
53B LEU* 3.2 10.1 + - - +
55B GLN* 1.3 74.8 - - + +
57B LYS* 1.3 73.3 + - - +
58B VAL* 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