Contacts of the helix formed by residues 47 - 56 (chain A) in PDB entry 2M72
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 LEU 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.3 38.1 - - + -
43A CYS* 3.4 33.2 - - + +
44A LYS* 3.4 16.6 - - + +
45A PRO 3.1 1.5 - - - -
46A CYS* 1.3 79.7 - - + +
48A ARG* 1.3 58.5 + - - +
49A GLU* 3.2 11.9 - - - +
50A LEU* 3.8 19.7 - - + -
51A LYS* 2.9 30.8 + - + +
89A ASN* 5.6 0.7 - - - +
91A TRP* 3.7 33.4 - - + -
112A ILE* 6.5 0.2 - - + -
113A PRO* 5.7 2.0 - - + -
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Residues in contact with ARG 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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45A PRO 3.8 13.0 + - - +
46A CYS 2.9 8.8 + - - +
47A LEU* 1.3 76.5 - - - +
49A GLU* 1.3 64.0 + - - +
51A LYS* 4.0 8.1 - - - +
52A ALA* 3.2 25.5 + - - +
113A PRO* 4.8 1.3 - - + -
131A TYR* 3.3 13.7 + - + +
133A GLU* 4.3 29.5 + - + +
134A GLY 5.5 0.6 - - - +
136A GLU* 2.7 42.8 + - - +
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Residues in contact with GLU 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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35A ILE* 5.9 0.3 - - - +
37A SER* 2.7 37.6 + - - -
47A LEU* 3.2 20.3 - - - +
48A ARG* 1.3 70.7 + - - +
50A LEU* 1.3 80.9 + - - +
52A ALA* 3.3 1.1 + - - +
53A ILE* 2.8 50.5 + - + +
113A PRO* 3.6 15.4 - - + +
114A ALA 5.0 0.4 - - - +
115A VAL* 3.6 13.3 - - + +
131A TYR* 2.8 38.7 + - + +
136A GLU* 4.5 7.6 - - + -
139A LEU* 4.2 14.1 - - + -
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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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37A SER* 3.8 21.5 - - - +
39A PHE* 5.0 4.0 - - + -
47A LEU* 3.8 21.5 - - + -
49A GLU* 1.3 95.9 + - - +
51A LYS* 1.3 56.5 + - - +
53A ILE* 3.8 3.8 - - - +
54A GLN* 2.8 31.9 + - - +
68A LEU* 3.8 16.8 - - + +
70A ALA* 4.9 8.5 - - + -
91A TRP* 3.8 35.4 - - + +
93A TYR* 3.2 38.8 + - + +
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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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44A LYS 5.3 7.0 - - - +
45A PRO* 6.1 2.9 - - + -
47A LEU* 2.9 21.2 + - + +
48A ARG* 4.0 9.9 - - - +
50A LEU* 1.3 76.3 - - - +
52A ALA* 1.3 62.4 + - - +
54A GLN* 3.3 12.1 + - - +
55A GLU* 3.2 47.2 + - + +
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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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48A ARG* 3.2 18.0 + - - +
49A GLU 3.8 2.0 - - - +
51A LYS* 1.3 75.9 - - - +
53A ILE* 1.3 68.7 + - + +
55A GLU* 3.2 23.8 + - - +
56A VAL* 3.3 17.9 + - - +
60A TRP* 6.0 0.2 - - - -
136A GLU* 4.1 22.0 - - + -
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Residues in contact with ILE 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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35A ILE* 4.3 4.5 - - + -
49A GLU* 2.8 38.6 + - + +
50A LEU* 4.6 0.7 - - - +
52A ALA* 1.3 73.9 - - + +
54A GLN* 1.3 52.7 + - - +
56A VAL* 3.1 7.4 + - - -
57A TYR* 2.6 47.6 + - + -
60A TRP* 3.6 48.2 - - + -
66A VAL* 5.9 0.4 - - + -
68A LEU* 3.4 41.1 - - + -
139A LEU* 3.9 23.3 - - + -
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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 2.8 19.3 + - - +
51A LYS* 3.4 11.7 - - - +
53A ILE* 1.3 78.0 - - - +
55A GLU* 1.3 64.4 + - + +
57A TYR* 3.3 19.9 + - + +
68A LEU* 4.6 0.6 - - - +
89A ASN* 4.1 10.0 + - - +
90A GLY 3.2 28.8 + - - +
91A TRP* 3.0 26.4 + - - -
92A GLU* 5.4 7.0 - - + +
93A TYR* 3.2 18.9 + - + +
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Residues in contact with GLU 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 LYS* 3.2 36.8 + - + +
52A ALA* 3.5 13.5 - - - +
53A ILE 3.2 0.8 - - - -
54A GLN* 1.3 79.0 - - + +
56A VAL* 1.3 64.7 + - + +
57A TYR 3.4 0.6 + - - -
58A ALA 5.3 0.3 + - - -
59A ASP* 5.4 0.5 - - - +
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Residues in contact with VAL 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 ALA 3.3 16.8 - - - +
53A ILE* 3.1 5.4 + - - +
55A GLU* 1.3 82.6 - - + +
57A TYR* 1.3 63.6 + - - +
58A ALA 3.3 2.7 - - - -
59A ASP* 3.1 28.4 + - + +
60A TRP* 3.1 46.4 + - + +
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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