Contacts of the strand formed by residues 57 - 64 (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 GLN 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C LYS* 3.3 2.1 - - - -
54C ILE 2.9 40.3 + - - +
55C ARG* 5.6 0.7 - - + -
56C GLU* 1.3 77.3 - - - +
58C GLU* 1.3 83.4 + - - +
59C TYR* 3.1 38.8 - - + +
76C PRO* 3.7 10.5 - - - +
77C ARG* 3.8 0.6 - - - +
78C GLN* 2.5 40.2 + - - +
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Residues in contact with GLU 58 (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* 2.6 40.1 + - + +
52C LYS 3.5 2.7 - - - -
53C LYS* 3.8 22.4 + - + +
56C GLU 3.8 4.4 + - - +
57C GLN* 1.3 83.5 + - - +
59C TYR* 1.3 62.1 + - - +
60C TYR* 4.2 14.2 + - + -
77C ARG* 3.0 50.5 + - + +
90C HIS* 4.9 2.6 + - - -
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Residues in contact with TYR 59 (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* 3.3 6.6 - - - -
52C LYS* 2.7 43.5 + - + +
54C ILE* 4.0 31.8 - - + +
57C GLN* 3.1 45.7 - - + +
58C GLU* 1.3 73.1 - - - +
60C TYR* 1.3 67.6 + - - +
74C TRP* 3.6 21.3 - - + -
75C GLU* 3.2 8.5 - - - +
76C PRO* 3.8 31.6 - - + -
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Residues in contact with TYR 60 (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* 4.0 14.6 - - + -
50C ASP 3.4 10.8 - - - +
51C TYR* 3.4 19.3 - + - -
58C GLU* 4.2 6.7 - - + -
59C TYR* 1.3 81.0 - - - +
61C LEU* 1.3 61.1 - - - +
62C VAL* 3.6 3.7 + - + +
73C THR 3.6 0.2 - - - +
74C TRP* 3.3 6.0 - - - -
75C GLU* 2.8 36.4 + - - -
77C ARG* 2.7 50.3 + - + -
80C LEU* 3.9 27.4 - - + -
86C LEU* 3.5 21.1 - - + -
89C PHE* 4.0 15.5 - + - -
90C HIS* 2.6 33.6 + - - -
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Residues in contact with LEU 61 (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* 3.5 4.7 - - - +
49C CYS* 2.8 48.7 + - + +
50C ASP* 2.9 34.8 + - + +
60C TYR* 1.3 69.8 - - - +
62C VAL* 1.3 61.3 + - - +
72C SER* 4.0 25.6 - - - +
73C THR 3.7 21.3 - - - -
74C TRP* 3.4 31.6 - - + +
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Residues in contact with VAL 62 (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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45C VAL* 3.7 20.9 - - + -
47C TYR 3.9 2.9 - - - -
48C LEU* 3.9 17.7 - - + -
49C CYS* 4.7 0.2 - - - -
60C TYR 3.8 11.9 - - - +
61C LEU* 1.3 75.1 - - - +
63C LYS* 1.3 67.3 - - - +
64C TRP* 3.5 37.5 - - + -
72C SER* 3.3 9.6 - - - -
73C THR 2.8 32.9 + - - +
75C GLU* 4.0 7.6 - - + -
80C LEU* 3.9 23.3 - - + -
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Residues in contact with LYS 63 (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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46C GLU* 2.8 55.3 + - - +
47C TYR* 2.9 55.7 + - + +
49C CYS* 3.9 5.0 - - - -
61C LEU 4.1 1.2 + - - -
62C VAL* 1.3 74.1 - - - +
64C TRP* 1.3 61.9 + - - +
66C GLY 4.9 1.0 - - - +
67C TYR 2.8 31.3 + - - +
68C PRO* 3.7 14.1 - - - -
69C ASP* 3.4 25.8 - - - +
72C SER* 3.5 16.6 - - - +
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Residues in contact with TRP 64 (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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43C GLY* 3.7 33.0 - - - -
44C GLU 3.6 26.0 - - - +
45C VAL* 4.1 13.5 - - + -
46C GLU* 4.1 1.6 - - - -
62C VAL* 3.5 33.2 + - + -
63C LYS* 1.3 86.9 + - - +
65C ARG* 1.3 65.2 + - - +
66C GLY 3.2 0.7 + - - -
67C TYR* 3.2 43.9 + + + +
68C PRO 5.6 0.6 + - - -
71C GLU 3.8 18.6 - - - -
72C SER* 4.8 0.8 + - - +
73C THR* 3.1 23.5 + - + +
75C GLU* 3.7 31.0 - - + -
79C ASN 6.0 0.7 - - - -
80C LEU* 4.6 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