Contacts of the helix formed by residues 42 - 56 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER* 4.2 0.4 - - - -
41A ILE* 1.3 79.9 - - - +
43A LYS* 1.3 66.4 + - - +
44A LYS* 4.2 9.2 - - + +
45A LYS* 2.9 38.4 + - + +
46A ILE* 3.0 10.4 + - - +
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Residues in contact with LYS 43 (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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32A ALA* 3.8 23.6 - - + -
33A ILE* 4.0 31.6 - - + +
36A SER* 3.5 17.4 + - - +
41A ILE 3.4 2.6 + - - -
42A ASN* 1.3 71.8 - - - +
44A LYS* 1.3 57.2 + - - +
46A ILE* 3.2 3.2 + - - +
47A ASN* 2.9 34.5 + - - +
2C G 4.1 21.5 + - - +
3C C 4.4 7.9 + - - +
4C G 3.7 18.0 + - - -
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Residues in contact with LYS 44 (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 ASN* 3.1 7.5 - - + +
43A LYS* 1.3 78.5 - - - +
45A LYS* 1.3 64.1 + - + +
47A ASN* 3.3 2.8 + - - +
48A GLN* 3.0 40.3 + - - +
4C G 3.1 34.0 + - - +
5C C 3.9 21.3 + - - -
6C G 4.9 7.9 + - - -
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Residues in contact with LYS 45 (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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10A ASP* 4.3 14.1 + - - +
13A ILE* 4.0 23.3 - - + +
41A ILE* 3.5 24.0 - - + -
42A ASN* 2.9 27.6 + - + +
44A LYS* 1.3 79.0 - - + +
46A ILE* 1.3 65.2 + - - +
48A GLN* 3.2 28.4 + - - +
49A GLN* 3.3 19.0 + - - +
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Residues in contact with ILE 46 (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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13A ILE* 4.8 0.9 - - + -
17A VAL* 4.0 23.2 - - + +
32A ALA* 3.9 9.4 - - - +
35A LEU* 3.8 21.5 - - + -
36A SER* 3.7 26.5 - - - +
39A LEU* 4.1 17.7 - - + -
41A ILE* 4.1 18.6 - - + +
42A ASN 3.0 16.6 + - - +
43A LYS* 3.5 9.2 - - - +
45A LYS* 1.3 76.5 - - - +
47A ASN* 1.3 56.8 + - - +
49A GLN* 3.3 4.7 + - - +
50A LEU* 2.9 45.5 + - + +
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Residues in contact with ASN 47 (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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32A ALA* 3.4 20.0 - - - +
43A LYS* 2.9 27.2 + - - +
44A LYS 3.7 0.4 - - - +
45A LYS 3.2 0.2 - - - -
46A ILE* 1.3 72.9 - - - +
48A GLN* 1.3 67.0 + - - +
49A GLN 3.1 2.0 - - - -
50A LEU* 4.0 8.2 - - - +
51A TYR* 3.1 38.6 + - + -
69A TRP* 4.5 2.3 + - - -
3C C 3.6 30.6 + - - -
4C G 2.6 44.3 + - - +
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Residues in contact with GLN 48 (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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10A ASP* 4.9 9.2 + - - +
13A ILE* 6.1 0.2 - - - +
44A LYS* 3.0 35.4 + - + +
45A LYS* 3.2 27.0 + - - +
47A ASN* 1.3 77.6 - - - +
49A GLN* 1.3 72.2 + - - +
51A TYR* 4.6 1.7 - - - +
52A LYS* 3.0 36.5 + - - +
4C G 3.5 26.8 - - - +
5C C 2.7 22.3 + - - +
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Residues in contact with GLN 49 (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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10A ASP* 3.6 28.7 - - - +
13A ILE* 4.1 13.0 - - + +
14A PHE* 3.1 56.3 - - + +
17A VAL* 4.1 12.8 - - + -
45A LYS 3.3 11.8 + - - +
46A ILE 3.8 5.8 - - - +
47A ASN 3.1 0.4 - - - -
48A GLN* 1.3 92.2 + - - +
50A LEU* 1.3 56.0 + - - +
51A TYR 3.3 0.4 - - - -
52A LYS* 3.1 20.3 + - - +
53A LEU* 2.7 37.6 + - - +
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Residues in contact with LEU 50 (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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17A VAL* 3.7 21.1 - - + -
21A VAL* 4.3 12.3 - - + -
32A ALA* 4.1 5.2 - - + -
35A LEU* 3.9 15.3 - - + -
46A ILE* 2.9 38.1 + - + +
47A ASN* 3.2 14.5 + - - +
49A GLN* 1.3 76.9 - - - +
51A TYR* 1.3 57.5 + - - +
53A LEU* 3.3 7.2 + - + +
54A GLN 3.0 22.0 + - - -
59A VAL* 3.6 4.6 - - + +
69A TRP* 3.3 64.6 - - + +
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Residues in contact with TYR 51 (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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47A ASN* 3.1 33.3 + - - +
48A GLN 4.6 2.2 - - - +
50A LEU* 1.3 72.8 - - - +
52A LYS* 1.3 65.5 + - + +
54A GLN* 3.3 15.7 + - - +
55A LYS* 3.3 29.6 + - - +
61A MET* 3.9 25.3 - - + +
67A PRO* 4.1 4.3 - - - +
69A TRP* 3.4 30.4 - + - -
2C G 4.2 0.2 + - - -
3C C 2.6 37.5 + - - -
4C G 3.6 47.1 + + + +
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Residues in contact with LYS 52 (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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10A ASP* 6.0 2.0 - - - -
14A PHE* 4.4 12.1 - - + -
48A GLN* 3.0 28.4 + - - +
49A GLN* 3.1 34.0 + - - +
51A TYR* 1.3 78.6 - - + +
53A LEU* 1.3 63.2 + - - +
55A LYS* 3.1 29.5 + - + +
56A GLU* 3.4 12.5 + - - +
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Residues in contact with LEU 53 (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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14A PHE* 3.7 28.7 - - + +
17A VAL* 4.5 8.7 - - + -
18A LYS* 3.9 24.7 - - + +
21A VAL* 3.6 34.3 - - + -
49A GLN 2.7 16.4 + - - +
50A LEU* 3.5 6.5 - - + +
52A LYS* 1.3 75.6 - - - +
54A GLN* 1.3 63.6 + - - +
56A GLU* 3.0 15.9 + - - +
57A ASP 3.3 7.6 + - - -
58A THR* 3.3 40.8 + - + +
59A VAL* 3.8 14.6 - - + -
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Residues in contact with GLN 54 (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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50A LEU 3.0 13.3 + - - +
51A TYR* 3.6 23.6 - - - +
52A LYS 3.2 0.6 - - - -
53A LEU* 1.3 76.7 - - - +
55A LYS* 1.3 58.6 + - + +
57A ASP* 2.9 24.4 + - - +
59A VAL* 3.5 23.3 - - + +
60A LYS* 3.8 17.7 - - + +
61A MET* 2.8 48.1 + - - +
69A TRP* 4.1 2.2 - - + -
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Residues in contact with LYS 55 (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 TYR* 3.4 17.9 - - - +
52A LYS* 3.1 18.2 + - + +
54A GLN* 1.3 79.5 - - + +
56A GLU* 1.3 60.9 + - + +
57A ASP* 3.2 8.2 + - - +
6C G 5.9 1.0 + - - -
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Residues in contact with GLU 56 (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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14A PHE* 3.4 34.0 - - - -
18A LYS* 4.8 7.3 + - - -
52A LYS* 3.6 10.9 - - - +
53A LEU* 3.0 12.1 + - - +
55A LYS* 1.3 78.2 - - + +
57A ASP* 1.3 73.2 + - - +
58A THR* 3.2 11.9 + - - +
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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