Contacts of the strand formed by residues 46 - 51 (chain C) in PDB entry 3TDM
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 GLU 46 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLN 5.8 2.2 - - - +
4C VAL 3.3 2.7 + - - +
5C VAL* 3.3 28.0 - - + +
6C VAL* 2.9 24.8 + - - +
44C ALA* 4.6 0.5 - - - +
45C GLY* 1.3 79.2 + - - +
47C ILE* 1.3 68.7 + - - +
75C LEU* 4.4 4.0 - - - -
76C PRO* 3.1 29.8 - - + +
78C ILE* 3.7 22.2 - - + +
99C LYS* 3.0 36.2 + - - +
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Residues in contact with ILE 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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5C VAL* 4.6 1.6 - - - -
6C VAL 3.2 6.3 - - - +
8C ILE* 3.6 27.6 - - + -
36C VAL* 4.3 15.9 - - + +
39C VAL* 4.2 26.5 - - + -
46C GLU* 1.3 83.7 - - - +
48C LEU* 1.3 64.8 + - - +
49C LEU* 4.0 13.2 - - + +
69C VAL* 5.5 2.5 - - + -
73C THR* 4.2 25.4 - - + +
75C LEU* 4.2 14.8 - - + -
76C PRO 3.0 7.5 + - - +
77C ILE* 3.5 9.9 - - + -
78C ILE* 2.7 35.4 + - - +
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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
----------------------------------------------------------
5C VAL* 4.1 13.6 - - + +
6C VAL 2.9 7.1 + - - -
7C ALA* 3.8 23.1 - - + +
8C ILE* 2.7 33.8 + - - +
47C ILE* 1.3 72.3 - - - +
49C LEU* 1.3 55.4 + - - +
50C THR* 3.9 7.1 + - - +
78C ILE* 3.5 35.4 - - + +
80C SER* 3.5 24.9 - - - +
101C SER* 4.4 6.7 - - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.8 14.6 - - + +
10C ALA* 5.1 0.4 - - + -
32C LEU* 4.4 14.6 - - + -
36C VAL* 5.8 0.2 - - + -
47C ILE* 3.6 10.0 + - + -
48C LEU* 1.3 70.9 - - - +
50C THR* 1.3 62.9 + - - +
51C SER 4.4 0.2 + - - -
65C MET* 3.8 41.5 - - + +
66C ILE* 4.3 21.8 - - + +
69C VAL* 4.0 28.0 - - + -
77C ILE* 4.2 15.0 - - + -
78C ILE 2.8 16.3 + - - +
79C ALA* 3.6 3.8 - - + +
80C SER* 3.3 23.9 + - - +
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Residues in contact with THR 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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7C ALA* 6.1 0.3 - - - +
8C ILE 3.1 8.2 + - - +
9C ASP* 3.7 21.8 + - - +
10C ALA 3.3 24.9 + - - +
48C LEU* 4.6 8.8 + - - +
49C LEU* 1.3 73.2 - - - +
51C SER* 1.3 71.8 + - - +
52C ILE* 3.5 4.3 + - + +
55C ASP* 4.0 23.8 - - + +
65C MET* 4.1 7.8 - - - +
80C SER* 3.4 29.8 + - - +
81C GLY* 4.4 1.3 - - - -
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Residues in contact with SER 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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10C ALA 3.8 5.0 + - - -
11C LYS* 5.5 1.0 - - - +
50C THR* 1.3 74.0 - - - +
52C ILE* 1.3 52.1 + - - +
53C ASP* 4.0 2.9 + - - +
54C ARG* 3.6 19.2 + - - +
55C ASP* 2.3 43.2 + - - +
62C ASP* 3.2 46.4 + - - +
65C MET* 4.1 9.2 - - - +
80C SER 3.7 9.0 + - - -
81C GLY* 4.7 0.2 - - - -
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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