Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 1MUS
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 SER 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER* 2.7 23.9 + - - -
51A GLU* 3.2 2.4 - - - -
52A GLY* 1.3 70.7 - - - -
54A LYS* 1.3 58.1 + - - +
55A ALA* 3.5 6.8 + - - +
56A ALA* 3.0 26.1 + - - +
57A GLN* 2.8 31.7 + - - +
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Residues in contact with LYS 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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52A GLY 3.4 6.1 + - - -
53A SER* 1.3 72.4 + - - +
55A ALA* 1.3 61.2 + - - +
57A GLN* 3.0 18.9 + - - +
58A GLU* 2.7 58.9 + - + +
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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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30A ARG* 4.1 6.1 + - - +
53A SER* 3.2 5.5 + - - +
54A LYS* 1.3 83.5 - - - +
56A ALA* 1.3 58.6 + - - +
58A GLU* 3.8 5.1 - - - +
59A GLY* 2.8 27.4 + - - -
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Residues in contact with ALA 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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30A ARG* 4.2 13.1 + - - +
37A GLN* 4.1 18.7 + - - +
50A SER* 4.0 11.3 + - - +
53A SER* 3.0 25.6 + - - +
55A ALA* 1.3 77.3 - - - +
57A GLN* 1.3 59.9 + - - +
60A ALA* 2.8 31.4 + - - +
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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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46A ILE* 5.0 0.4 - - + -
47A THR* 2.8 39.4 + - - +
50A SER* 3.5 19.2 + - - +
53A SER 2.8 18.1 + - - +
54A LYS* 3.7 22.0 + - - +
56A ALA* 1.3 80.0 - - - +
58A GLU* 1.3 65.0 + - - +
60A ALA* 3.3 2.7 + - - +
61A TYR* 3.1 43.2 + - + -
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Residues in contact with GLU 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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54A LYS* 2.7 50.7 + - + +
55A ALA* 3.8 4.9 - - - +
57A GLN* 1.3 78.5 + - - +
59A GLY* 1.3 60.7 + - - +
61A TYR* 3.5 4.6 + - - +
62A ARG* 3.0 67.4 + - - +
65A ARG* 4.7 10.7 + - - -
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Residues in contact with GLY 59 (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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30A ARG* 3.7 32.7 - - - +
55A ALA 2.8 17.9 + - - -
56A ALA 3.7 0.2 - - - -
57A GLN 3.2 0.2 - - - -
58A GLU* 1.3 72.8 - - - +
60A ALA* 1.3 65.7 + - - +
62A ARG* 3.7 10.5 - - - +
63A PHE* 3.0 24.4 + - - +
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Residues in contact with ALA 60 (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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30A ARG* 4.3 1.6 - - - +
34A VAL* 3.9 28.3 - - + -
37A GLN* 4.5 9.9 - - - +
46A ILE* 3.7 28.0 - - + -
56A ALA 2.8 18.2 + - - +
57A GLN 3.8 0.7 - - - +
59A GLY* 1.3 76.6 - - - +
61A TYR* 1.3 62.4 + - - +
63A PHE* 3.2 4.0 + - - +
64A ILE* 3.0 27.3 + - - +
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Residues in contact with TYR 61 (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 SER* 5.7 1.9 - - - -
46A ILE* 3.6 44.5 + - + +
47A THR* 4.1 13.2 + - - -
57A GLN* 3.1 41.8 + - + +
58A GLU* 4.2 4.9 - - - +
60A ALA* 1.3 75.9 - - - +
62A ARG* 1.3 64.4 + - - +
64A ILE* 3.1 38.4 + - + +
65A ARG* 3.2 28.0 + - - +
343A MET* 4.5 7.2 - - + +
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Residues in contact with ARG 62 (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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58A GLU* 3.0 53.0 + - + +
59A GLY* 3.7 8.1 - - - +
61A TYR* 1.3 77.0 - - - +
63A PHE* 1.3 61.7 + - - +
65A ARG* 3.4 30.4 + - - +
66A ASN* 3.2 23.3 + - - +
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Residues in contact with PHE 63 (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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22A LEU* 4.2 4.3 - - + -
27A ARG* 3.4 25.6 - - - -
30A ARG* 3.8 25.4 - - + -
31A LEU* 3.5 38.1 - - + -
34A VAL* 4.5 7.9 - - + -
59A GLY 3.0 17.9 + - - +
60A ALA 3.5 4.0 - - - +
62A ARG* 1.3 79.1 - - - +
64A ILE* 1.3 74.8 + - + +
66A ASN* 3.0 25.2 + - - +
69A VAL* 3.9 35.2 - - + +
74A ILE* 4.0 12.6 - - + -
351A ARG* 3.9 8.4 - - + -
355A ILE* 4.1 10.5 - - + -
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Residues in contact with ILE 64 (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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34A VAL* 5.3 4.0 - - + -
46A ILE* 4.3 4.3 - - + -
60A ALA* 3.0 17.5 + - + +
61A TYR* 3.1 34.1 - - + +
63A PHE* 1.3 87.3 - - + +
65A ARG* 1.3 58.5 + - + +
66A ASN 3.5 0.2 - - - -
343A MET* 3.5 45.3 - - + -
348A ASN* 3.2 23.1 - - + +
351A ARG* 2.8 22.0 + - - +
352A MET* 4.0 30.7 - - + +
355A ILE* 4.7 5.6 - - + -
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Residues in contact with ARG 65 (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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58A GLU* 4.7 10.5 + - - -
61A TYR* 3.2 39.8 + - - +
62A ARG* 3.6 29.0 - - - +
63A PHE 3.0 0.2 - - - -
64A ILE* 1.3 79.2 - - + +
66A ASN* 1.3 62.3 + - - +
67A PRO* 3.2 9.5 - - - +
348A ASN* 3.3 29.0 - - + +
351A ARG* 3.6 6.5 + - - -
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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