Contacts of the strand formed by residues 42 - 48 (chain C) in PDB entry 3K75
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 THR 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C SER* 4.5 2.9 + - - -
40C GLU* 4.0 10.0 - - - +
41C LYS* 1.3 94.0 + - - +
43C ILE* 1.3 68.1 + - - +
44C SER* 5.4 2.5 - - - -
131C VAL* 3.3 33.9 - - + -
132C CYS 3.3 4.0 - - - +
133C SER* 3.2 15.9 + - - -
303E VAL* 6.3 1.8 - - + -
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Residues in contact with ILE 43 (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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13C SER* 3.8 6.3 - - - +
14C SER* 3.8 20.0 - - - +
33C TRP* 3.2 40.2 - - + +
34C ARG 4.3 0.2 - - - -
35C ALA* 3.5 41.3 - - + +
40C GLU* 4.2 5.8 - - + -
42C THR* 1.3 80.6 - - - +
44C SER* 1.3 63.7 + - - +
131C VAL* 3.6 6.2 - - - +
132C CYS* 2.9 36.5 + - + +
142C PHE* 3.8 27.1 - - + +
143C GLY* 4.3 7.9 - - - -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C CYS* 3.6 3.0 - - - -
13C SER* 3.2 37.9 + - - -
33C TRP* 3.7 6.8 - - - -
42C THR* 5.4 2.2 - - - -
43C ILE* 1.3 79.3 - - - +
45C VAL* 1.3 65.0 + - - +
46C VAL* 5.3 0.2 - - - +
129C LYS* 3.5 28.0 + - - -
130C ILE 3.4 10.6 + - - -
131C VAL* 3.8 12.7 - - - +
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Residues in contact with VAL 45 (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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9C VAL* 3.8 11.2 - - + -
11C SER 3.7 13.7 - - - +
12C CYS* 4.2 2.7 - - - +
21C ALA* 3.8 17.0 - - + -
24C LEU* 3.8 8.3 - - + -
33C TRP* 3.4 32.1 - - + -
44C SER* 1.3 78.1 + - - +
46C VAL* 1.3 62.7 + - - +
47C LEU* 3.2 26.9 + - + +
128C VAL 3.5 3.6 - - - +
129C LYS* 4.6 0.2 - - - -
130C ILE* 3.0 42.3 + - + +
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Residues in contact with VAL 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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9C VAL* 3.6 2.9 - - - +
10C VAL* 3.0 46.4 + - + -
11C SER* 3.1 26.9 + - - +
45C VAL* 1.3 71.6 - - - +
47C LEU* 1.3 62.2 + - - +
84C TYR* 3.1 28.5 - - + +
127C ARG* 3.7 13.0 - - + +
128C VAL 4.0 2.9 - - - -
129C LYS* 3.6 36.3 - - + +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.5 36.3 - - + +
8C HIS 3.7 5.4 - - - +
9C VAL* 4.5 6.7 - - + -
10C VAL* 4.3 1.3 - - - -
24C LEU* 3.8 20.0 - - + -
25C LEU* 3.8 17.5 - - + -
45C VAL* 3.2 46.2 - - + +
46C VAL* 1.3 74.7 - - - +
48C GLN* 1.3 64.3 + - - +
126C ASP 4.0 0.2 - - - +
127C ARG* 3.5 3.3 - - - -
128C VAL* 3.1 46.7 + - + +
130C ILE* 4.9 5.4 - - + -
147C VAL* 4.8 6.5 - - + -
149C PHE* 5.6 0.2 - - + -
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Residues in contact with GLN 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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6C LEU* 4.3 5.5 - - - +
7C ARG 3.4 15.2 + - - -
8C HIS* 2.6 61.1 + - + +
10C VAL* 4.0 10.5 - - + +
46C VAL 4.0 1.6 + - - -
47C LEU* 1.3 76.6 - - - +
49C LEU* 1.3 93.9 + - - +
50C GLU* 3.8 7.7 - - + +
75C SER* 3.8 22.2 + - - -
126C ASP* 3.9 6.7 + - - -
127C ARG* 2.4 44.8 + - - +
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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