Contacts of the strand formed by residues 35 - 43 (chain C) in PDB entry 6B0Z
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 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LYS* 4.4 0.2 - - - -
5C ILE* 3.5 15.7 - - + +
7C GLY* 3.9 13.0 - - - -
31C ILE* 2.9 18.8 + - + +
32C PHE* 3.3 28.0 + - - +
34C TYR* 1.3 83.4 - - - +
36C GLU* 1.3 66.8 + - - +
37C LEU* 3.9 25.2 + - + +
340C LEU* 5.2 2.0 - - + -
352C LEU* 3.9 13.2 - - + -
355C PHE* 3.6 43.5 - - + -
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Residues in contact with GLU 36 (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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3C LYS 5.3 2.9 + - - -
4C LYS* 3.7 40.9 + - + +
5C ILE 2.9 11.0 + - - +
6C SER* 3.7 4.3 + - - -
7C GLY 2.7 29.8 + - - -
8C GLY 4.0 1.0 + - - -
32C PHE* 6.0 0.4 - - - -
35C VAL* 1.3 72.8 - - - +
37C LEU* 1.3 56.8 + - - +
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Residues in contact with LEU 37 (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 GLY* 3.6 25.4 - - - +
8C GLY 3.6 2.9 - - - +
10C VAL* 3.7 26.9 - - + -
31C ILE* 4.1 25.6 - - + -
32C PHE* 4.9 9.4 - - + -
35C VAL* 3.9 8.5 + - + -
36C GLU* 1.3 76.0 - - - +
38C ASP* 1.3 59.3 + - - +
39C LEU* 2.9 40.4 + - + +
336C TRP* 4.2 13.2 - - + -
340C LEU* 3.9 16.2 - - + -
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Residues in contact with ASP 38 (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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8C GLY* 2.5 27.0 + - - +
9C SER* 2.8 16.4 + - - +
10C VAL 3.1 12.7 + - - -
37C LEU* 1.3 67.1 - - - +
39C LEU* 1.3 61.2 + - - +
40C HIS* 2.7 48.1 + - - -
67C HIS* 4.8 0.9 - - - -
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Residues in contact with LEU 39 (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 VAL* 3.4 20.2 - - + +
12C GLU* 3.9 29.6 - - + +
27C LYS* 5.2 2.5 - - + +
32C PHE* 4.0 29.2 - - + -
37C LEU* 2.9 39.6 + - + +
38C ASP* 1.3 77.2 - - - +
40C HIS* 1.3 63.3 + - - +
41C SER* 3.7 19.6 + - - +
336C TRP* 4.8 4.9 - - + -
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Residues in contact with HIS 40 (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 SER* 4.2 0.2 + - - -
10C VAL 2.9 20.9 + - - +
11C VAL* 3.4 12.6 - - + -
12C GLU 2.9 20.9 + - - -
38C ASP* 2.7 54.6 + - - -
39C LEU* 1.3 72.9 + - - +
41C SER* 1.3 59.4 + - - +
42C TYR* 3.4 24.8 + - + +
63C ALA* 5.1 0.6 - - + +
66C LYS* 5.9 0.4 - - - -
67C HIS* 3.1 41.9 + + + -
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Residues in contact with SER 41 (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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12C GLU* 3.1 29.5 + - - -
14C GLN* 4.5 10.1 - - - -
39C LEU* 3.7 21.0 - - - +
40C HIS* 1.3 71.9 - - - +
42C TYR* 1.3 69.3 + - - +
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Residues in contact with TYR 42 (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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11C VAL* 3.9 5.8 - - + -
12C GLU* 3.2 12.1 + - - +
13C MET* 3.3 3.9 - - + -
14C GLN* 2.9 28.6 + - - +
40C HIS* 3.4 29.8 + - + +
41C SER* 1.3 78.9 - - - +
43C ASP* 1.3 58.7 + - - +
44C LEU* 3.4 7.8 + - + -
56C VAL* 4.1 13.9 - - + -
59C ASP* 3.9 23.7 + - + +
60C ALA* 3.7 30.7 - - + -
63C ALA* 3.5 32.9 - - + +
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Residues in contact with ASP 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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14C GLN* 3.8 28.3 - - - +
15C GLY 4.8 1.6 - - - +
20C ARG* 6.0 0.7 - - - -
42C TYR* 1.3 69.1 - - - +
44C LEU* 1.3 59.9 + - - +
45C GLY* 2.8 27.2 + - - -
47C GLU* 5.4 2.4 - - - +
48C ASN* 2.8 52.2 + - - +
56C VAL* 3.4 10.4 - - - +
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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