Contacts of the helix formed by residues 44 - 58 (chain A) in PDB entry 5M72
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.7 7.5 + - - -
37A ILE* 5.0 1.8 - - + -
38A LEU* 4.1 0.6 - - - +
41A ASN* 3.2 35.3 + - + +
42A LYS 3.5 0.8 + - - -
43A ASP* 1.3 75.1 - - - +
45A VAL* 1.3 65.4 + - - +
46A THR* 3.1 8.0 + - - -
47A ALA* 2.9 35.2 + - + +
48A LEU* 3.0 25.6 + - - +
606B LYS* 2.9 32.5 + - - -
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Residues in contact with VAL 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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43A ASP 3.1 10.0 + - - +
44A ASP* 1.3 73.4 + - - +
46A THR* 1.3 58.3 + - - +
48A LEU* 3.3 2.8 + - - +
49A HIS* 2.8 31.1 + - + +
74A VAL* 3.5 29.6 - - + +
75A LEU* 3.8 19.9 - - + +
78A ASN* 3.2 45.3 - - + +
80A LEU* 5.4 0.9 - - + -
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Residues in contact with THR 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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15A TRP* 3.7 7.6 - - + -
44A ASP* 3.1 9.0 + - - -
45A VAL* 1.3 81.6 - - - +
47A ALA* 1.3 56.3 + - - +
49A HIS* 3.3 6.3 + - - +
50A CYS* 2.9 28.9 + - - -
78A ASN* 5.6 2.3 + - - -
601B PRO* 4.0 14.0 - - + +
602B PRO 4.8 3.1 - - - +
603B LEU* 3.6 31.4 - - + -
606B LYS* 3.9 25.9 + - + +
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Residues in contact with ALA 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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15A TRP* 3.5 20.6 - - + -
34A VAL* 3.2 17.4 - - + +
37A ILE* 4.0 10.5 - - + -
38A LEU* 3.6 26.2 - - + -
44A ASP* 2.9 21.9 + - + +
45A VAL 3.2 0.2 - - - -
46A THR* 1.3 73.9 - - - +
48A LEU* 1.3 60.7 + - - +
50A CYS* 3.3 1.4 + - - -
51A LYS* 2.9 25.1 + - - +
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Residues in contact with LEU 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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38A LEU* 3.9 26.2 - - + -
42A LYS 4.4 7.6 - - - +
43A ASP 4.6 0.2 - - - -
44A ASP 3.0 21.8 + - - +
45A VAL 3.7 3.8 - - - +
47A ALA* 1.3 75.5 - - - +
49A HIS* 1.3 64.1 + - - +
51A LYS* 3.3 5.6 + - + +
52A VAL* 3.0 29.4 + - - +
67A VAL* 4.2 11.6 - - + +
71A HIS* 3.9 46.9 - - + +
74A VAL* 3.7 29.6 - - + -
75A LEU* 4.0 16.4 - - + -
80A LEU* 4.7 0.7 - - - -
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Residues in contact with HIS 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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45A VAL* 2.8 18.5 + - + +
46A THR* 3.5 6.5 - - - +
48A LEU* 1.3 76.7 - - - +
50A CYS* 1.3 63.1 + - - +
52A VAL* 3.2 3.2 + - + +
53A VAL* 3.0 29.1 + - + +
78A ASN 5.5 1.2 + - - -
79A SER 5.5 1.8 - - - -
80A LEU* 3.5 35.5 - - + +
83A GLU* 2.7 35.3 + - + -
110A LYS* 5.6 3.8 - - - -
599B ALA 4.5 3.4 + - - -
601B PRO* 3.5 34.7 - - + +
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Residues in contact with CYS 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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15A TRP* 4.0 7.9 - - - -
18A VAL* 4.5 1.3 - - - -
34A VAL* 3.8 17.3 - - + -
46A THR 2.9 20.9 + - - +
47A ALA* 3.8 4.0 - - - +
49A HIS* 1.3 76.9 - - - +
51A LYS* 1.3 57.8 + - - +
53A VAL* 3.2 0.7 + - - -
54A CYS* 2.9 34.2 + - - -
600B PHE* 3.5 40.5 - - + -
601B PRO* 4.0 7.9 - - - -
603B LEU* 3.9 24.2 - - - -
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Residues in contact with LYS 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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31A LEU* 3.7 21.1 - - + -
34A VAL* 3.8 11.3 - - + +
35A ASN* 2.9 33.5 + - - +
38A LEU* 3.8 15.1 - - + +
47A ALA 2.9 18.2 + - - +
48A LEU* 3.3 7.4 + - + +
50A CYS* 1.3 75.0 - - - +
52A VAL* 1.3 64.5 + - - +
54A CYS* 3.3 3.3 + - - +
55A LEU* 3.0 34.8 + - + +
63A GLU* 5.4 5.2 - - - -
67A VAL* 3.9 29.1 - - + +
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Residues in contact with VAL 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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48A LEU 3.0 18.3 + - - +
49A HIS 3.2 7.8 + - - +
51A LYS* 1.3 75.5 - - - +
53A VAL* 1.3 62.0 + - - +
55A LEU* 3.3 4.3 + - - +
56A ILE* 3.0 33.4 + - + +
64A ALA* 3.9 15.7 - - + +
67A VAL* 3.8 19.1 - - + -
68A ILE* 3.7 31.2 - - + -
80A LEU* 4.0 9.9 - - + -
83A GLU* 3.7 31.9 - - + -
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Residues in contact with VAL 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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27A PHE* 4.1 3.4 - - + -
49A HIS* 3.0 27.7 + - + +
50A CYS 3.6 6.7 - - - +
52A VAL* 1.3 76.8 - - - +
54A CYS* 1.3 58.0 + - - +
56A ILE* 3.3 2.4 + - - +
57A GLN* 2.8 39.2 + - + +
83A GLU* 4.4 7.0 - - + +
598B VAL* 3.9 18.2 - - + +
599B ALA* 3.5 40.8 - - - +
600B PHE* 3.6 24.0 - - + +
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Residues in contact with CYS 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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27A PHE* 3.5 36.5 - - - +
30A ALA* 3.7 4.3 - - - -
31A LEU* 3.6 31.2 - - + -
34A VAL* 4.9 1.1 - - - -
50A CYS 2.9 21.3 + - - -
51A LYS* 3.5 8.3 - - - +
53A VAL* 1.3 76.6 - - - +
55A LEU* 1.3 63.4 + - - +
57A GLN* 3.3 3.1 + - - +
58A ASN* 3.1 28.2 + - - +
600B PHE* 3.7 22.9 - - - -
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Residues in contact with LEU 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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31A LEU* 3.9 24.0 - - + -
51A LYS* 3.0 33.8 + - + +
52A VAL* 3.7 3.8 - - - +
54A CYS* 1.3 74.8 - - - +
56A ILE* 1.3 63.1 + - - +
58A ASN* 3.2 6.0 + - + -
59A GLY 3.1 4.3 + - - -
60A SER* 2.8 46.0 + - - +
63A GLU* 3.6 45.1 - - + +
64A ALA* 3.7 10.5 - - + -
67A VAL* 3.8 24.5 - - + -
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Residues in contact with ILE 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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52A VAL* 3.0 36.8 + - + +
53A VAL 3.7 2.9 - - - +
55A LEU* 1.3 75.5 - - - +
57A GLN* 1.3 64.2 + - - +
59A GLY* 3.0 11.4 + - - -
61A PHE* 3.6 20.0 - - + -
64A ALA* 3.8 4.3 - - + -
83A GLU* 4.0 21.3 - - + +
86A TYR* 3.8 31.4 - - + -
87A CYS* 3.7 32.1 - - - -
595B LEU* 4.4 8.1 - - + +
598B VAL* 3.7 24.7 - - + -
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Residues in contact with GLN 57 (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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27A PHE* 3.6 50.3 - - + -
53A VAL* 2.8 22.2 + - + +
54A CYS 3.6 4.3 - - - +
56A ILE* 1.3 75.8 - - - +
58A ASN* 1.3 55.8 + - - +
59A GLY 3.4 0.6 + - - -
203A K 2.8 21.1 - - - -
595B LEU* 4.3 16.1 + - - +
598B VAL* 2.8 37.4 + - + +
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Residues in contact with ASN 58 (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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27A PHE* 4.1 9.7 + - - +
28A THR* 3.0 42.0 + - - +
31A LEU* 5.4 6.3 - - - +
54A CYS 3.1 16.6 + - - +
55A LEU* 3.2 4.5 + - + +
56A ILE 3.2 0.4 - - - -
57A GLN* 1.3 74.9 - - - +
59A GLY* 1.3 60.7 + - - +
60A SER* 3.4 12.0 + - - +
203A K 2.8 27.9 - - - -
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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