Contacts of the strand formed by residues 45 - 54 (chain C) in PDB entry 3MTS
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 VAL 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 2.7 38.1 + - - +
43C GLY 4.3 0.2 + - - -
44C GLU* 1.3 72.1 - - - +
46C GLU* 1.3 57.9 + - - +
47C TYR* 3.8 26.5 - - - +
48C LEU* 4.0 14.8 - - + -
62C VAL* 3.7 20.4 - - + -
63C LYS 4.0 3.4 - - - -
64C TRP* 4.1 9.6 - - + -
65C ARG* 5.0 0.4 - - - -
80C LEU* 4.2 14.4 - - + -
82C CYS* 3.8 28.9 - - + -
85C ILE* 4.0 6.0 - - + +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 4.6 8.6 + - - +
87B LYS* 3.5 33.1 + - + +
88B GLN* 4.8 0.3 - - - +
44C GLU 3.3 3.2 + - - -
45C VAL* 1.3 74.9 - - - +
47C TYR* 1.3 80.6 + - + +
63C LYS* 2.8 46.9 + - + +
64C TRP 3.8 3.1 - - - +
65C ARG* 3.7 42.8 + - + +
66C GLY 4.6 1.4 + - - -
85C ILE* 4.4 8.5 - - - +
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Residues in contact with TYR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 4.3 12.1 - - + -
88B GLN* 3.1 27.1 - - - +
91B LYS* 3.5 51.8 + - + -
95B ARG* 5.1 0.4 - - - -
45C VAL* 4.0 7.8 - - - +
46C GLU* 1.3 101.3 - - + +
48C LEU* 1.3 66.7 + - - +
49C CYS* 3.8 17.3 - - - -
62C VAL* 3.9 1.2 - - - -
63C LYS* 2.9 67.8 + - + +
69C ASP* 3.8 9.5 + - - -
85C ILE* 4.8 1.1 - - - -
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLN* 2.8 25.1 + - - +
95B ARG* 3.3 9.9 + - - -
45C VAL* 4.0 12.1 - - + -
47C TYR* 1.3 75.2 - - - +
49C CYS* 1.3 61.3 + - - +
50C ASP 5.0 0.2 - - - +
60C TYR* 4.0 19.1 - - + -
61C LEU 3.5 3.4 - - - +
62C VAL* 3.9 27.1 - - + -
80C LEU* 4.4 6.5 - - + -
82C CYS* 4.9 2.2 - - - -
85C ILE* 3.8 33.0 - - + +
86C LEU* 3.6 30.1 - - + -
89C PHE* 3.7 26.3 - - + -
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Residues in contact with CYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG* 3.8 30.7 + - - +
47C TYR* 3.8 28.7 - - - -
48C LEU* 1.3 76.7 - - - +
50C ASP* 1.3 64.2 + - - +
61C LEU* 2.8 34.9 + - + +
63C LYS* 3.9 16.4 - - - -
69C ASP* 5.9 1.3 - - - -
72C SER* 4.8 4.5 - - - -
89C PHE* 4.1 5.2 - - - -
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU 3.8 0.8 - - - -
49C CYS* 1.3 81.4 + - - +
51C TYR* 1.3 85.3 + - - +
60C TYR* 3.4 7.6 - - - +
61C LEU* 2.9 38.3 + - + +
74C TRP* 3.7 23.8 - - + -
89C PHE* 3.8 11.2 - - - -
93C LEU* 6.4 0.2 - - - -
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Residues in contact with TYR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ASP* 1.3 88.4 + - - +
52C LYS* 1.3 76.3 + - - +
53C LYS* 3.8 20.0 - - + +
58C GLU* 2.6 41.5 + - + +
59C TYR 3.3 8.7 - - - -
60C TYR* 3.4 36.6 - + + -
74C TRP* 3.8 4.4 - - - -
89C PHE* 3.6 19.5 - - + -
90C HIS* 3.6 17.5 - + - -
93C LEU* 4.4 11.2 - - + -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 1.3 84.9 + - - +
53C LYS* 1.3 62.8 + - - +
54C ILE* 3.8 30.1 - - + -
58C GLU* 3.5 1.0 - - - -
59C TYR* 2.7 46.2 + - + +
74C TRP* 4.0 31.8 - - + -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.8 24.4 - - + +
52C LYS* 1.3 76.4 - - - +
54C ILE* 1.3 65.0 + - - +
55C ARG 3.6 18.8 - - - +
56C GLU* 3.5 34.2 + - - +
57C GLN 3.3 10.5 - - - +
58C GLU* 3.8 15.8 + - + +
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS* 3.8 27.3 - - + -
53C LYS* 1.3 77.5 - - - +
55C ARG* 1.3 77.2 + - + +
57C GLN* 2.9 32.8 + - - +
59C TYR* 4.0 22.6 - - + +
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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