Contacts of the strand formed by residues 52 - 59 (chain A) in PDB entry 3MB8
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 TYR 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 3.7 29.2 - - + -
13A ILE* 3.9 28.5 - - + +
47A ALA 3.9 2.4 - - - +
48A TYR* 3.3 4.6 + - - -
49A ASN 2.8 37.3 + - - +
50A ARG* 3.3 6.4 - - + -
51A GLU* 1.3 96.5 - - + +
53A ARG* 1.3 60.2 + - - +
54A SER* 5.1 0.3 + - - -
67A ILE* 4.5 4.9 - - + +
68A SER 3.3 19.3 - - - +
69A HIS 3.8 11.0 - - - -
75A GLY* 2.7 38.7 + - - -
78A ILE* 3.6 14.8 - - + +
79A ALA* 3.7 22.0 - - + -
71B ILE* 3.8 13.7 - - + +
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Residues in contact with ARG 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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30A PRO* 3.7 19.8 + - + +
31A ALA* 4.5 4.6 - - - +
33A THR* 3.3 20.1 - - - +
34A GLU* 2.8 44.2 + - - +
45A GLU* 2.9 42.7 + - - +
47A ALA 3.5 3.8 - - - +
48A TYR* 3.7 36.9 - - + -
51A GLU 3.7 0.2 + - - -
52A TYR* 1.3 72.5 - - - +
54A SER* 1.3 63.0 + - - +
55A PHE* 3.7 12.7 - - + -
67A ILE* 3.1 4.1 - - - -
68A SER* 2.9 35.5 + - - +
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Residues in contact with SER 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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13A ILE 4.7 1.0 + - - -
15A LEU* 3.4 32.0 - - - +
45A GLU* 3.6 5.4 - - - +
46A LEU* 2.8 32.0 + - - +
47A ALA* 2.9 25.0 + - - +
52A TYR 5.1 0.8 + - - -
53A ARG* 1.3 75.5 - - - +
55A PHE* 1.3 65.8 + - - +
65A THR* 5.1 1.3 - - - -
66A VAL 3.2 8.1 - - - -
67A ILE* 3.9 16.6 - - - -
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Residues in contact with PHE 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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33A THR* 3.3 35.4 - - - -
34A GLU* 3.9 19.3 - - + -
37A ALA* 3.7 19.5 - - + -
43A LYS* 4.3 14.1 - - + -
44A GLN 3.2 13.5 - - - -
45A GLU* 3.6 45.1 - - + -
46A LEU* 3.5 10.4 - - - +
53A ARG* 3.7 21.8 - - - -
54A SER* 1.3 76.5 - - - +
56A ARG* 1.3 59.4 + - - +
57A VAL* 4.0 16.4 - - + -
65A THR* 3.6 5.0 - - - +
66A VAL* 2.8 33.9 + - + +
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Residues in contact with ARG 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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18A GLU 2.6 30.5 + - - -
19A ASP* 3.6 19.4 + - - +
20A VAL 4.0 1.8 - - - +
21A GLU* 2.7 32.9 + - + +
43A LYS* 3.4 2.6 - - - -
44A GLN* 2.8 43.6 + - + +
46A LEU* 3.5 26.1 - - + +
55A PHE* 1.3 72.8 - - - +
57A VAL* 1.3 72.1 + - - +
58A VAL* 5.2 6.3 - - + -
63A PRO* 4.3 11.2 - - + -
64A ILE 3.6 7.9 - - - +
65A THR* 4.8 1.1 - - - +
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Residues in contact with VAL 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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37A ALA* 3.8 32.5 - - + -
40A CYS* 3.6 22.7 - - - -
42A LYS 3.4 8.1 - - - +
43A LYS* 4.7 0.4 - - + -
55A PHE* 4.0 5.8 - - + -
56A ARG* 1.3 79.1 - - - +
58A VAL* 1.3 65.2 + - - +
63A PRO* 3.2 5.2 - - - +
64A ILE* 2.8 53.8 + - + +
66A VAL* 3.8 28.9 - - + -
240A LEU* 4.5 7.2 - - + -
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Residues in contact with VAL 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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40A CYS* 3.2 3.8 - - - +
41A GLU* 3.0 49.3 + - - +
42A LYS* 2.9 44.0 + - + -
56A ARG* 5.2 6.5 - - + +
57A VAL* 1.3 77.5 - - - +
59A TYR* 1.3 60.9 + - - +
61A SER* 3.7 22.9 - - - +
62A GLN 3.3 3.4 - - - +
63A PRO* 4.5 12.8 - - + -
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Residues in contact with TYR 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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39A MET* 3.7 25.4 - - + -
40A CYS* 4.1 13.2 - - - -
41A GLU* 4.2 3.1 - - + -
57A VAL* 4.1 0.8 - - + -
58A VAL* 1.3 74.3 - - - +
60A ASP* 1.3 84.8 + - + +
61A SER 3.1 0.4 - - - -
62A GLN* 2.9 26.3 + - - +
64A ILE* 4.2 15.5 - - + -
150A LEU* 6.0 0.9 - - - +
237A LYS* 4.7 10.5 + - - +
240A LEU* 3.6 43.5 - - + -
241A LYS* 3.9 30.0 + - + +
244A ALA* 3.5 5.0 - - + +
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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