Contacts of the strand formed by residues 57 - 61 (chain A) in PDB entry 1MC9
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 LYS 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 2.7 34.6 + - - +
26A ASP* 2.9 21.2 + - - +
52A ARG* 3.2 6.6 - - - +
53A VAL* 2.9 47.5 + - + +
54A TYR* 3.9 15.7 - - + -
56A ASP* 1.3 100.9 - - - +
58A CYS* 1.3 59.2 + - - +
72A ILE* 4.6 9.2 - - + -
73A TYR* 3.5 7.6 - - - +
74A SER* 3.2 22.9 + - - +
75A CYS* 3.4 4.1 - - - -
136A GOL 2.8 31.8 + - - -
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Residues in contact with CYS 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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43A TRP* 4.8 2.5 - - - -
50A GLU* 3.5 32.5 - - - -
51A LEU 3.6 2.7 - - - -
52A ARG* 4.0 1.8 - - - -
57A LYS* 1.3 72.7 - - - +
59A LEU* 1.3 67.9 + - - +
60A ASP* 3.4 1.4 + - - +
72A ILE* 3.4 6.8 - - - -
73A TYR 2.7 36.4 + - - +
75A CYS* 2.0 46.2 - - - -
81A GLN* 3.7 23.3 - - + +
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Residues in contact with LEU 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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17A LEU* 4.4 12.1 - - + -
30A LEU* 3.2 32.8 - - + -
43A TRP* 4.1 15.9 - - + -
51A LEU* 2.9 46.2 + - + +
58A CYS* 1.3 72.0 - - - +
60A ASP* 1.3 58.9 + - - +
70A VAL* 3.4 11.9 - - + -
71A GLN 3.7 2.2 - - - -
72A ILE* 5.0 0.2 - - - +
81A GLN* 3.5 13.7 - - - +
83A TRP* 3.0 48.6 + - + +
100A LEU* 4.2 20.2 - - + -
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Residues in contact with ASP 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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58A CYS 3.7 7.6 - - - +
59A LEU* 1.3 78.4 - - - +
61A ALA* 1.3 62.9 + - - +
70A VAL* 3.5 3.1 - - - -
71A GLN* 2.8 58.8 + - + +
73A TYR* 3.3 15.1 - - + +
80A ASN* 3.4 10.0 + - - -
81A GLN* 3.0 19.3 + - + -
83A TRP* 4.2 3.4 - - - -
3B XYP 2.5 46.7 + - - -
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Residues in contact with ALA 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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60A ASP* 1.3 73.7 - - - +
62A ALA* 1.3 60.1 + - - +
63A GLY 3.2 21.0 + - - +
69A LYS 3.8 4.9 - - - -
70A VAL* 4.7 1.6 - - - +
80A ASN* 2.9 46.5 + - + +
83A TRP* 3.9 16.4 - - + -
93A GLY* 6.2 1.3 - - - -
96A SER* 5.5 1.8 - - - +
115A LEU* 3.7 20.4 - - + -
3B XYP 3.1 0.9 + - - -
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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