Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 1SJ1
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A TRP* 5.2 0.2 - - - -
40A ILE* 3.4 6.5 - - - +
41A GLU* 1.3 76.4 - - - +
43A GLU* 1.3 62.1 + - - +
44A GLU* 3.2 25.7 + - - +
45A LEU* 3.2 30.3 + - + +
46A TYR* 2.9 25.2 + - - +
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Residues in contact with GLU 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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2A TRP* 5.2 5.6 - - + -
41A GLU 3.4 5.9 + - - +
42A ASP* 1.3 76.8 + - - +
44A GLU* 1.3 54.8 + - - +
46A TYR* 3.3 11.6 + - + +
47A ASN* 2.9 54.9 + - - +
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Residues in contact with GLU 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 ASP* 3.2 17.9 + - - +
43A GLU* 1.3 77.1 - - - +
45A LEU* 1.3 61.1 + - + +
47A ASN* 3.4 10.1 + - - +
48A CYS* 3.0 29.3 + - - +
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Residues in contact with LEU 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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21A CYS* 4.1 1.2 - - - -
23A ASP* 3.8 35.9 - - + +
24A VAL* 4.1 19.5 - - + -
37A VAL* 5.5 6.5 - - + -
40A ILE* 4.1 20.2 - - + +
42A ASP* 3.2 30.0 + - + +
44A GLU* 1.3 77.7 - - + +
46A TYR* 1.3 67.5 + - - +
48A CYS* 3.3 13.5 + - - -
49A ALA* 2.9 24.3 + - - +
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Residues in contact with TYR 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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2A TRP* 3.3 74.2 + + + -
40A ILE* 3.7 6.2 - - + +
42A ASP 2.9 14.3 + - - +
43A GLU* 3.6 11.0 - - + +
45A LEU* 1.3 75.0 - - - +
47A ASN* 1.3 73.6 + - - +
49A ALA* 3.1 8.3 + - + +
50A LYS* 2.9 47.7 + - + +
63A ILE* 4.3 13.7 - - + -
65B GLU* 2.9 25.3 + - - -
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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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43A GLU* 2.9 44.6 + - - +
44A GLU* 3.6 8.8 - - - +
46A TYR* 1.3 93.9 - - - +
48A CYS* 1.3 57.0 + - - +
50A LYS* 3.4 6.3 + - - +
51A GLU* 3.1 25.2 + - - +
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Residues in contact with CYS 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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20A LEU* 4.0 12.0 - - - +
21A CYS* 2.0 54.6 - - + +
23A ASP* 6.0 0.2 - - - -
44A GLU 3.0 17.1 + - - +
45A LEU* 3.3 17.9 + - - -
47A ASN* 1.3 74.4 - - - +
49A ALA* 1.3 63.5 + - - +
51A GLU* 3.6 14.7 + - + +
52A ALA* 3.1 22.2 + - - +
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Residues in contact with ALA 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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4A VAL* 4.3 10.1 - - + -
21A CYS* 3.6 5.5 - - - -
24A VAL* 4.5 5.2 - - + -
25A PHE* 4.2 11.1 - - + -
40A ILE* 4.3 15.3 - - + -
45A LEU 2.9 15.1 + - - +
46A TYR* 3.3 12.1 - - + +
48A CYS* 1.3 77.0 - - - +
50A LYS* 1.3 60.5 + - - +
52A ALA* 3.3 3.1 + - - +
53A MET* 2.9 27.5 + - - +
61A ILE* 4.8 0.2 - - - +
63A ILE* 3.9 17.3 - - + +
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Residues in contact with LYS 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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46A TYR* 2.9 43.9 + - + +
47A ASN* 3.7 7.9 - - - +
49A ALA* 1.3 74.2 - - - +
51A GLU* 1.3 64.6 + - - +
53A MET* 3.2 27.2 + - + +
54A GLU* 3.0 25.7 + - + +
63A ILE* 3.9 8.4 - - + +
2B TRP* 6.5 1.3 - - - -
65B GLU* 4.4 7.0 - - - +
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Residues in contact with GLU 51 (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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20A LEU* 3.4 32.3 - - + +
47A ASN 3.1 13.0 + - - +
48A CYS* 3.7 17.2 - - - +
49A ALA 3.3 0.2 - - - -
50A LYS* 1.3 77.2 - - - +
52A ALA* 1.3 57.7 + - - +
54A GLU* 3.3 8.2 + - + +
55A ALA* 3.0 27.1 + - + +
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Residues in contact with ALA 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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16A ILE* 5.3 0.3 - - - +
17A CYS* 3.8 26.3 - - + +
20A LEU* 4.0 13.4 - - + +
25A PHE* 3.6 28.5 - - + -
48A CYS 3.1 15.3 + - - +
49A ALA 3.6 1.3 - - - +
50A LYS 3.3 0.2 - - - -
51A GLU* 1.3 74.9 - - - +
53A MET* 1.3 65.6 + - - +
55A ALA* 3.1 2.5 + - - +
56A CYS* 3.1 20.6 + - - +
61A ILE* 3.7 8.9 - - - +
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Residues in contact with MET 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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49A ALA 2.9 13.8 + - - +
50A LYS* 3.6 40.4 - - + +
51A GLU 3.2 0.4 - - - -
52A ALA* 1.3 78.6 - - - +
54A GLU* 1.4 61.0 + - + +
55A ALA 3.4 0.3 + - - -
56A CYS* 3.7 6.2 + - - +
59A SER* 5.5 1.0 - - - -
61A ILE* 3.4 41.2 + - + +
62A THR* 4.0 6.3 - - - -
63A ILE* 4.0 11.4 - - + -
71A NCO 3.1 16.6 + - - -
65B GLU* 3.6 36.1 - - + +
66B ALA* 3.8 22.8 - - - +
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Residues in contact with GLU 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 LYS* 3.0 19.9 + - + +
51A GLU* 3.8 7.6 - - + +
53A MET* 1.4 78.7 - - + +
55A ALA* 1.3 58.3 + - + +
56A CYS 3.6 0.2 - - - -
71A NCO 2.9 39.5 + - - -
66B ALA* 6.1 0.2 - - - -
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Residues in contact with ALA 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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16A ILE* 4.1 15.5 - - + +
20A LEU* 3.9 20.6 - - + -
51A GLU* 3.0 17.1 + - + +
52A ALA 3.1 3.1 + - - +
54A GLU* 1.3 77.2 - - + +
56A CYS* 1.3 65.8 + - - +
57A PRO* 3.1 9.5 - - - +
71A NCO 4.1 3.6 + - - -
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Residues in contact with CYS 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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16A ILE* 4.5 0.2 - - - +
52A ALA 3.1 13.6 + - - +
53A MET 3.7 6.7 + - - +
54A GLU 3.6 1.4 - - - -
55A ALA* 1.3 73.4 - - - +
57A PRO* 1.3 70.6 - - - +
58A VAL 3.2 4.3 + - - -
59A SER* 3.5 8.2 + - - +
60A ALA* 3.4 32.1 - - - +
61A ILE* 4.1 8.7 - - + +
70A F3S 2.2 46.7 - - - -
71A NCO 3.1 23.0 + - - -
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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