Contacts of the helix formed by residues 42 - 56 (chain B) in PDB entry 1SFU
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 ASN 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER* 4.2 0.9 - - - -
41B ILE* 1.3 78.2 - - - +
43B LYS* 1.3 66.7 + - - +
44B LYS* 4.3 8.3 - - + +
45B LYS* 3.1 48.0 + - + +
46B ILE* 3.1 9.4 + - - +
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Residues in contact with LYS 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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32B ALA* 3.9 22.0 - - + -
33B ILE* 4.0 34.3 - - + +
36B SER* 3.3 18.8 + - - +
42B ASN* 1.3 71.8 - - - +
44B LYS* 1.3 64.0 + - - +
46B ILE* 2.9 5.6 + - - +
47B ASN* 2.9 27.1 + - - +
2D G 5.8 3.9 + - - -
3D C 4.7 7.1 + - - +
4D G 3.5 21.8 + - - -
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Residues in contact with LYS 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 ASN* 3.2 5.9 - - + +
43B LYS* 1.3 78.5 - - - +
45B LYS* 1.3 60.2 + - + +
47B ASN* 3.2 3.6 + - - +
48B GLN* 2.9 47.2 + - + +
6C G 6.0 1.3 - - - +
4D G 3.3 31.9 + - - +
5D C 3.6 23.5 + - - -
6D G 4.7 9.7 + - - -
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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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8B VAL 5.0 5.7 + - - -
10B ASP* 5.9 3.8 - - - +
13B ILE* 3.6 27.7 - - + +
41B ILE* 3.5 17.0 - - + -
42B ASN* 3.1 36.0 + - + +
44B LYS* 1.3 79.4 - - + +
46B ILE* 1.3 64.0 + - - +
48B GLN* 3.2 17.7 + - - +
49B GLN* 3.2 30.2 + - - +
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Residues in contact with ILE 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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13B ILE* 4.7 0.2 - - + -
17B VAL* 3.7 24.4 - - + +
32B ALA* 3.8 18.2 - - + +
35B LEU* 3.9 16.4 - - + +
36B SER* 3.9 20.4 - - - -
39B LEU* 4.0 20.0 - - + -
41B ILE* 3.9 20.0 - - + +
42B ASN 3.1 13.1 + - - +
43B LYS 2.9 8.8 + - - +
45B LYS* 1.3 76.8 - - - +
47B ASN* 1.3 57.9 + - - +
49B GLN* 3.0 7.1 + - - +
50B LEU* 2.9 45.7 + - + +
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Residues in contact with ASN 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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32B ALA* 3.3 25.0 - - - +
43B LYS* 2.9 18.6 + - - +
44B LYS 3.7 1.8 - - - +
46B ILE* 1.3 72.9 - - - +
48B GLN* 1.3 66.8 + - - +
50B LEU* 3.9 10.0 - - - +
51B TYR* 3.1 38.6 + - + -
69B TRP* 4.3 4.2 + - - -
3D C 3.7 30.0 + - - -
4D G 2.7 44.2 + - - +
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Residues in contact with GLN 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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10B ASP* 4.9 10.8 + - - +
44B LYS* 2.9 33.5 + - + +
45B LYS* 3.2 30.8 + - - +
47B ASN* 1.3 77.3 - - - +
49B GLN* 1.3 76.2 + - - +
51B TYR* 4.5 2.3 - - - +
52B LYS* 3.3 31.0 + - - +
4D G 3.6 17.2 - - - +
5D C 2.9 28.8 + - - +
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Residues in contact with GLN 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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10B ASP* 3.5 30.5 + - - +
13B ILE* 3.8 16.9 - - + +
14B PHE* 3.2 40.3 - - + +
17B VAL* 4.0 17.5 - - + -
45B LYS* 3.2 19.3 + - - +
46B ILE 3.0 6.4 + - - +
48B GLN* 1.3 92.2 + - - +
50B LEU* 1.3 59.3 + - - +
52B LYS* 3.1 15.8 + - - +
53B LEU* 2.8 33.6 + - + +
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Residues in contact with LEU 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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17B VAL* 3.5 24.9 - - + -
21B VAL* 4.1 17.7 - - + -
32B ALA* 4.2 7.2 - - - -
35B LEU* 4.1 9.9 - - + -
46B ILE* 2.9 43.0 + - + +
47B ASN* 3.2 17.4 + - - +
49B GLN* 1.3 76.7 - - - +
51B TYR* 1.3 57.6 + - - +
53B LEU* 3.1 8.7 + - + +
54B GLN 2.9 23.7 + - - -
59B VAL* 3.6 2.8 - - + +
69B TRP* 3.4 52.7 - - + +
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Residues in contact with TYR 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 ASN* 3.1 33.1 + - - +
48B GLN 4.6 2.5 - - - +
50B LEU* 1.3 78.0 - - - +
52B LYS* 1.3 62.3 + - + +
54B GLN* 3.4 17.3 + - - +
55B LYS* 3.2 31.1 + - - +
61B MET* 3.6 27.2 - - + +
67B PRO* 4.6 0.2 - - - +
69B TRP* 3.6 27.5 - + - -
2D G 4.0 1.9 + - - +
3D C 2.6 43.9 + - - -
4D G 3.5 43.8 + + + +
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Residues in contact with LYS 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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10B ASP* 5.2 15.0 + - - +
14B PHE* 4.1 14.4 - - + -
48B GLN* 3.3 20.3 + - - +
49B GLN* 3.1 20.8 + - - +
51B TYR* 1.3 76.4 - - + +
53B LEU* 1.3 66.6 + - - +
55B LYS* 3.1 25.9 + - + +
56B GLU* 3.1 23.6 + - - +
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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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14B PHE* 3.1 34.5 - - + +
17B VAL* 3.7 30.1 - - + +
18B LYS* 4.1 29.6 - - + +
49B GLN* 2.8 24.0 + - + +
50B LEU* 3.4 12.6 - - + +
52B LYS* 1.3 76.6 - - - +
54B GLN* 1.3 61.6 + - - +
56B GLU* 3.3 5.6 + - - +
57B ASP 3.3 3.3 + - - -
58B THR* 2.9 42.0 + - + -
59B VAL* 3.7 22.7 - - + -
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Residues in contact with GLN 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 LEU 2.9 12.4 + - - +
51B TYR* 3.6 29.0 - - - +
52B LYS 3.1 0.2 - - - -
53B LEU* 1.3 76.2 - - - +
55B LYS* 1.3 65.4 + - + +
56B GLU 3.1 0.2 - - - -
57B ASP* 3.0 17.8 + - - +
59B VAL* 3.5 23.9 - - + +
60B LYS* 4.1 15.5 - - + +
61B MET* 3.2 44.3 + - - +
69B TRP* 4.1 2.6 - - + -
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Residues in contact with LYS 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 TYR* 3.2 20.1 + - - +
52B LYS* 3.1 19.1 + - + +
54B GLN* 1.3 78.0 - - + +
56B GLU* 1.3 62.3 + - + +
57B ASP* 3.3 8.0 + - - +
6D G 5.7 4.0 + - - -
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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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14B PHE* 3.0 37.9 - - - -
18B LYS* 4.7 5.9 + - - -
52B LYS* 3.1 18.2 + - - +
53B LEU* 3.3 8.1 + - - +
54B GLN 3.1 0.8 - - - -
55B LYS* 1.3 79.6 - - + +
57B ASP* 1.3 71.3 + - - +
58B THR* 3.2 11.4 + - - +
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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