Contacts of the strand formed by residues 55 - 64 (chain A) in PDB entry 1MU5
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 ASN 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.3 1.6 + - - +
54A PRO* 1.3 71.0 - - - +
56A ILE* 1.3 58.6 + - - +
57A LYS* 4.7 14.7 + - - +
75A VAL 3.7 1.0 - - - +
76A ASP* 3.6 14.9 - - - -
77A ASN* 2.7 41.1 + - + +
202A GLU* 3.4 24.2 - - - +
217A ARG* 2.7 39.4 + - - +
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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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40A ILE* 4.4 5.8 - - + +
43A SER* 3.7 26.5 - - - +
44A LEU* 3.4 37.5 - - + +
47A THR* 5.4 0.2 - - + -
54A PRO* 4.1 11.7 - - + -
55A ASN* 1.3 79.1 - - - +
57A LYS* 1.3 66.8 + - - +
58A ILE* 4.0 19.2 - - + +
74A VAL* 4.0 20.0 - - + -
75A VAL 3.4 5.6 - - - +
76A ASP* 4.2 7.0 - - + -
202A GLU 2.9 8.9 + - - +
203A PHE* 3.3 23.4 - - + +
204A ILE 3.0 23.6 + - - +
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Residues in contact with LYS 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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55A ASN* 4.7 18.9 + - - +
56A ILE* 1.3 77.2 - - - +
58A ILE* 1.3 63.6 + - - +
59A THR* 4.2 6.7 - - + -
73A ASN 3.5 0.9 - - - +
74A VAL* 3.2 6.1 - - - +
75A VAL* 2.9 55.7 + - + +
202A GLU* 4.9 6.2 + - - +
204A ILE* 3.6 38.8 - - + +
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Residues in contact with ILE 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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36A VAL* 4.6 17.9 - - + -
40A ILE* 3.6 32.8 - - + -
56A ILE* 4.0 17.5 - - + -
57A LYS* 1.3 76.1 - - - +
59A THR* 1.3 69.9 + - - +
60A ILE* 4.7 4.5 - - + -
72A VAL* 5.3 1.3 - - + -
73A ASN 3.5 3.6 - - - +
74A VAL* 4.2 13.2 - - + -
191A ILE* 4.3 12.3 - - + -
203A PHE* 4.1 17.9 - - + -
204A ILE* 2.8 17.6 + - - +
205A PHE* 3.3 25.4 - - + -
206A LYS 2.9 24.4 + - - -
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Residues in contact with THR 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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57A LYS* 5.2 6.5 - - + -
58A ILE* 1.3 83.0 - - - +
60A ILE* 1.3 64.8 + - - +
61A ASP* 4.2 15.3 + - - -
71A LYS 3.6 1.3 - - - +
72A VAL* 3.6 2.6 - - - +
73A ASN* 2.9 57.5 + - - +
204A ILE* 6.4 1.8 - - + -
206A LYS* 3.3 24.7 - - + -
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Residues in contact with ILE 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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32A LEU* 4.0 16.2 - - + -
36A VAL* 3.7 29.8 - - + -
58A ILE* 4.7 1.6 - - + -
59A THR* 1.3 79.9 - - - +
61A ASP* 1.3 68.1 + - - +
70A TYR* 4.0 17.3 - - + -
71A LYS 3.4 7.4 - - - +
72A VAL* 4.4 6.3 - - + -
180A TRP* 3.8 22.2 - - + -
187A ILE* 4.3 6.1 - - + -
205A PHE* 3.8 24.7 - - + -
206A LYS 3.0 7.3 + - - +
207A ASP 3.3 2.9 - - - -
208A PRO* 3.1 41.6 - - + +
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Residues in contact with ASP 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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59A THR* 4.6 13.2 + - - -
60A ILE* 1.3 84.6 + - - +
62A LEU* 1.3 62.5 + - - +
63A ILE* 3.4 13.1 + - + -
70A TYR* 3.1 7.6 - - - -
71A LYS* 2.7 48.2 + - + +
73A ASN* 6.1 0.2 - - - +
206A LYS* 5.0 12.6 + - - +
207A ASP 4.9 2.6 - - - +
208A PRO* 4.5 2.7 - - - +
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Residues in contact with LEU 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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61A ASP* 1.3 70.6 - - - +
63A ILE* 1.3 62.9 + - - +
64A ASP 3.5 21.1 - - - +
65A ASP* 3.9 31.4 - - + +
68A GLN* 4.2 9.2 - - - +
69A ILE 3.4 15.3 - - - +
70A TYR* 3.8 34.8 - - + +
208A PRO* 4.2 14.9 + - + +
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Residues in contact with ILE 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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61A ASP* 3.6 10.8 - - + +
62A LEU* 1.3 78.9 - - - +
64A ASP* 1.3 60.8 + - + +
65A ASP 4.2 0.7 - - - -
69A ILE* 2.8 39.7 + - + +
71A LYS* 3.5 32.8 - - + +
125A LYS* 5.2 15.7 - - + -
175A SER* 3.6 26.5 - - - +
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Residues in contact with ASP 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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62A LEU* 3.5 2.7 - - - +
63A ILE* 1.3 81.5 - - + +
65A ASP* 1.3 55.1 + - - +
66A ALA* 3.3 6.4 + - - +
67A ARG* 2.7 64.5 + - + +
68A GLN* 2.6 32.7 + - - -
69A ILE* 3.0 23.8 + - + +
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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