Contacts of the strand formed by residues 132 - 136 (chain C) in PDB entry 3L43
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 LEU 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C ILE* 4.1 15.9 - - + -
51C PHE* 4.2 25.4 - - + -
71C LEU 3.9 1.0 - - - +
72C GLN* 4.3 1.3 - - - +
73C LEU* 2.8 39.9 + - + +
130C LEU* 2.8 28.1 + - + +
131C ASN* 1.3 80.7 - - - +
133C THR* 1.3 62.9 + - - +
134C LEU* 4.1 2.7 - - + -
278C GLN* 4.1 15.9 - - + +
281C LEU* 3.4 31.4 - - + +
282C ASN* 3.6 15.0 - - - +
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Residues in contact with THR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN* 3.4 29.0 - - + +
34C ILE* 2.7 37.3 + - - +
70C VAL* 3.8 29.2 - - + -
71C LEU 3.4 8.7 - - - +
72C GLN* 3.4 24.6 - - + +
132C LEU* 1.3 71.1 - - - +
134C LEU* 1.3 57.4 + - - +
135C ILE* 5.0 0.9 - - + -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 3.3 33.7 - - + -
36C VAL* 4.2 7.0 - - + -
47C VAL* 5.4 0.2 - - + -
48C LEU* 3.7 35.7 - - + -
51C PHE* 3.6 41.5 - - + -
69C LEU 3.3 1.4 - - - +
70C VAL* 3.6 1.7 - - - -
71C LEU* 2.7 50.3 + - + +
73C LEU* 3.8 20.6 - - + -
132C LEU* 5.3 2.2 - - + -
133C THR* 1.3 75.9 - - - +
135C ILE* 1.4 60.9 + - - +
136C ASP 4.0 0.4 - - - -
172C LEU* 4.5 4.3 - - + -
281C LEU* 4.3 3.6 - - + -
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Residues in contact with ILE 135 (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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33C GLN* 3.5 45.1 - - + +
34C ILE 2.7 16.4 + - - +
35C ALA* 3.7 6.7 - - + +
36C VAL* 2.8 30.9 + - - +
68C PRO* 4.5 5.2 - - + -
69C LEU 3.4 6.5 - - - +
70C VAL* 4.2 17.7 - - + -
133C THR* 5.0 0.4 - - + -
134C LEU* 1.4 75.3 - - - +
136C ASP* 1.3 64.3 + - - +
137C LEU* 3.3 21.5 + - + +
163C PHE* 3.7 42.6 - - + -
169C CYS* 5.5 1.8 - - - -
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Residues in contact with ASP 136 (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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36C VAL* 4.5 5.2 - - - +
44C LYS* 3.8 17.3 - - - +
45C SER* 3.1 23.3 + - - -
48C LEU* 3.6 25.5 - - + +
57C LEU* 4.2 10.7 - - - +
65C THR* 4.1 9.7 + - + +
67C ARG 4.2 2.6 - - - +
68C PRO* 3.3 6.6 - - - +
69C LEU* 2.9 44.5 + - + +
134C LEU 4.0 1.2 - - - -
135C ILE* 1.3 68.3 - - - +
137C LEU* 1.3 62.5 + - - +
307C UNX 3.3 18.3 - - - -
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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