Contacts of the helix formed by residues 42 - 57 (chain A) in PDB entry 6ABP
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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40A VAL 3.2 0.4 - - - +
41A PRO* 1.3 79.8 - - - +
43A GLY* 1.3 54.7 - - - +
44A GLU* 3.2 9.2 + - - +
45A LYS* 2.9 43.6 + - - +
46A THR* 2.7 30.1 + - - -
66A PRO* 3.6 9.6 - - - -
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Residues in contact with GLY 43 (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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42A ASP* 1.3 73.1 - - - +
44A GLU* 1.3 65.2 + - - +
46A THR* 3.2 2.5 + - - -
47A LEU* 2.9 31.0 + - - +
66A PRO* 4.1 1.8 - - - +
67A ASP* 5.8 1.2 - - - +
70A LEU* 3.5 31.4 - - - +
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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 11.9 + - - +
43A GLY* 1.3 76.8 - - - +
45A LYS* 1.3 68.9 + - + +
47A LEU* 3.3 5.6 + - - +
48A ASN* 2.9 52.8 + - - +
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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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39A ALA 4.8 2.9 - - - +
40A VAL* 4.2 4.6 - - - +
41A PRO* 3.6 40.8 - - + +
42A ASP* 2.9 31.0 + - - +
44A GLU* 1.3 84.1 - - + +
46A THR* 1.3 52.5 + - - +
48A ASN* 3.9 7.9 - - - +
49A ALA* 2.8 35.7 + - - +
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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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8A LEU* 4.8 0.4 - - + +
40A VAL* 3.4 17.6 - - - +
42A ASP 2.7 19.6 + - - -
43A GLY* 3.4 12.1 - - - -
44A GLU 3.1 0.2 - - - -
45A LYS* 1.3 75.6 - - - +
47A LEU* 1.4 65.4 + - + +
49A ALA* 3.3 3.6 + - - +
50A ILE* 3.2 28.6 + - + +
63A ILE* 3.8 28.0 - - + -
66A PRO* 3.3 17.3 - - + +
70A LEU* 4.3 6.5 - - + -
74A ILE* 4.0 25.4 - - + -
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Residues in contact with LEU 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 GLY 2.9 17.3 + - - +
44A GLU* 4.0 4.0 - - - +
46A THR* 1.4 79.6 - - + +
48A ASN* 1.3 64.9 + - - +
50A ILE* 3.2 28.2 + - + +
51A ASP* 3.2 9.9 + - - -
70A LEU* 4.4 12.1 - - + -
73A ALA* 4.3 36.6 - - + +
74A ILE* 4.4 7.6 - - + -
77A LYS* 3.4 33.7 - - + -
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Residues in contact with ASN 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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44A GLU* 2.9 51.1 + - - +
45A LYS* 3.9 7.5 - - - +
47A LEU* 1.3 74.9 - - - +
49A ALA* 1.3 62.4 - - - +
51A ASP* 3.2 15.1 + - - +
52A SER* 2.9 26.6 + - - -
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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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8A LEU* 4.2 6.7 - - + -
38A ILE* 3.7 31.9 - - + +
39A ALA 5.4 0.2 - - - +
40A VAL* 3.8 10.3 - - + -
45A LYS 2.8 19.0 + - - +
46A THR 3.6 5.2 - - - +
47A LEU 3.2 0.2 - - - -
48A ASN* 1.3 74.1 - - - +
50A ILE* 1.3 63.0 - - - +
52A SER* 3.1 9.6 + - - -
53A LEU* 2.8 32.7 + - - +
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Residues in contact with ILE 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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8A LEU* 4.4 10.1 - - + -
46A THR* 3.2 17.9 + - + +
47A LEU* 3.2 25.6 + - + +
49A ALA* 1.3 77.0 - - - +
51A ASP* 1.3 67.8 + - - +
53A LEU* 3.1 8.8 + - - +
54A ALA* 3.0 21.3 + - - +
61A PHE* 3.9 39.9 - - + -
63A ILE* 5.4 0.4 - - + -
74A ILE* 4.1 24.9 - - + +
77A LYS* 4.0 13.2 - - + -
78A ALA 4.6 2.7 - - - +
81A TYR* 4.0 20.4 - - + -
83A MET* 4.2 5.1 - - - +
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Residues in contact with ASP 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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47A LEU 3.2 5.1 + - - +
48A ASN* 3.4 15.5 - - - +
50A ILE* 1.3 78.8 - - - +
52A SER* 1.3 63.3 + - - +
54A ALA* 3.2 4.7 + - - +
55A ALA* 3.1 21.5 + - - +
77A LYS* 2.6 37.8 + - - -
81A TYR* 2.6 33.5 + - - +
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Residues in contact with SER 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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38A ILE* 5.3 7.1 - - - +
48A ASN 2.9 13.6 + - - -
49A ALA* 3.1 12.5 + - - -
51A ASP* 1.3 77.1 - - - +
53A LEU* 1.3 62.7 + - - +
55A ALA* 3.2 11.6 + - - +
56A SER* 3.1 26.1 + - - -
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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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6A GLY* 4.0 11.0 - - - +
8A LEU* 3.8 15.0 - - + -
36A ILE* 3.9 20.4 - - + -
38A ILE* 3.8 21.1 - - + -
49A ALA 2.8 19.7 + - - +
50A ILE* 3.1 10.1 + - - +
52A SER* 1.3 72.5 - - - +
54A ALA* 1.3 62.5 + - - +
56A SER* 3.2 5.9 + - - -
57A GLY 3.1 4.7 + - - -
58A ALA* 3.0 41.7 + - + +
60A GLY 4.6 1.8 - - - +
61A PHE* 3.6 44.9 - - + -
83A MET* 3.7 9.2 - - + -
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Residues in contact with ALA 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 ILE 3.0 12.1 + - - +
51A ASP 3.2 8.9 + - - +
53A LEU* 1.3 76.1 - - - +
55A ALA* 1.3 58.3 + - - +
57A GLY* 3.0 20.0 + - - +
58A ALA 4.9 0.9 - - - +
81A TYR* 3.6 42.6 - - + -
83A MET* 3.4 12.1 - - + +
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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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51A ASP 3.1 11.2 + - - +
52A SER* 3.4 13.5 - - - +
54A ALA* 1.3 76.9 - - - +
56A SER* 1.3 58.7 + - - +
57A GLY* 3.4 0.9 + - - -
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Residues in contact with SER 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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4A LYS* 3.0 28.0 + - - -
36A ILE* 4.1 26.1 - - - +
52A SER* 3.1 15.5 + - - -
53A LEU* 3.5 11.8 - - - -
54A ALA 3.2 0.2 - - - -
55A ALA* 1.3 75.4 - - - +
57A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 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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4A LYS* 4.1 12.9 + - - +
53A LEU 3.1 0.4 + - - -
54A ALA 3.0 16.2 + - - -
55A ALA 3.2 1.4 - - - -
56A SER* 1.3 79.8 - - - +
58A ALA* 1.3 66.8 + - - +
59A LYS* 3.4 17.0 - - - +
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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