Contacts of the strand formed by residues 79 - 85 (chain E) in PDB entry 3KZ1
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 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LYS* 5.9 0.9 - - + -
7E LYS 3.4 2.5 + - - +
8E LEU* 3.3 38.9 - - + +
9E VAL 3.2 13.3 + - - -
55E LEU* 6.3 0.2 - - + -
77E THR* 3.1 15.2 - - - +
78E ASP* 1.3 80.8 - - - +
80E ILE* 1.3 71.0 + - - +
81E LEU* 5.5 0.4 - - + -
110E VAL* 4.0 0.9 - - - -
111E PRO* 3.8 11.9 - - + +
113E ILE* 4.0 22.0 - - + -
174E ALA* 3.6 32.5 - - + +
177E ALA* 4.1 5.8 - - + -
178E ALA* 4.0 12.3 - - + -
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Residues in contact with ILE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.6 16.4 - - + +
11E VAL* 4.3 15.3 - - + -
74E TYR* 5.0 5.4 - - + -
77E THR* 4.0 7.6 - - + -
79E VAL* 1.3 81.5 - - - +
81E LEU* 1.3 67.4 + - - +
82E MET* 3.6 6.0 + - + +
103E VAL* 3.3 37.7 - - + -
107E CYS* 3.8 29.6 - - + -
110E VAL* 4.3 10.1 - - + -
111E PRO 3.0 13.8 + - - +
112E ILE* 3.2 9.8 - - + -
113E ILE 2.7 32.6 + - - -
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.5 32.3 - - + +
9E VAL 3.3 6.7 + - - -
10E ILE* 3.4 27.1 - - + +
11E VAL 3.1 26.7 + - - +
21E LEU* 4.7 1.3 - - + -
79E VAL* 4.2 0.6 + - + -
80E ILE* 1.3 72.5 - - - +
82E MET* 1.3 61.1 + - - +
83E CYS* 3.7 0.4 - - - -
113E ILE* 3.6 26.7 - - + +
115E VAL* 4.0 7.0 - - + -
170E VAL* 3.9 24.7 - - + -
171E PHE* 3.7 27.6 - - + -
174E ALA* 4.1 15.0 - - + -
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Residues in contact with MET 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.7 9.4 - - + +
80E ILE* 3.6 4.6 + - + +
81E LEU* 1.3 70.2 - - - +
83E CYS* 1.3 60.5 + - - +
95E ILE* 3.6 29.2 - - + -
99E TRP* 4.0 10.3 - - + +
100E THR* 3.4 36.3 - - + +
103E VAL* 3.5 40.8 - - + -
112E ILE* 3.9 25.8 - - + -
113E ILE 2.9 11.2 + - - +
114E LEU* 3.4 12.3 - - + +
115E VAL 3.0 24.3 + - - -
151E ILE* 4.0 9.4 - - - -
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Residues in contact with CYS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ILE* 3.6 31.9 - - - -
11E VAL 2.9 14.5 + - - +
12E GLY* 3.5 15.9 - - - -
13E ASP 4.3 1.2 + - - -
16E CYS* 3.8 11.2 - - - -
18E LYS* 4.3 3.6 - - + -
21E LEU* 4.2 4.0 - - - -
81E LEU* 4.2 1.6 - - - -
82E MET* 1.3 75.2 - - - +
84E PHE* 1.3 61.3 + - - +
91E SER 5.1 0.2 - - - +
95E ILE* 3.4 16.2 - - - +
99E TRP* 5.0 0.2 - - - -
115E VAL* 3.5 23.6 - - - -
117E ASN* 3.5 27.8 - - - +
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Residues in contact with PHE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E CYS* 4.0 10.1 - - - -
83E CYS* 1.3 73.7 - - - +
85E SER* 1.3 77.5 + - - +
86E ILE* 4.2 3.8 - - + -
91E SER* 3.4 29.4 - - - +
92E LEU* 4.0 26.7 - - + -
95E ILE* 4.2 3.6 - - + -
114E LEU* 3.9 36.8 - - + -
115E VAL 3.1 12.2 + - - +
116E GLY* 3.6 27.1 - - - -
117E ASN* 2.8 27.5 + - - +
139E VAL* 3.9 27.1 - - + -
144E GLY* 4.7 2.7 - - - -
156E TYR* 4.0 16.4 - + - -
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Residues in contact with SER 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA 4.9 0.2 - - - -
16E CYS* 3.7 30.7 - - - +
84E PHE* 1.3 80.2 - - - +
86E ILE* 1.3 64.5 + - - +
87E ASP* 2.4 29.4 + - - -
88E SER* 3.2 15.3 + - - +
91E SER* 2.9 19.8 + - - -
117E ASN 4.0 3.6 - - - -
118E LYS* 3.3 18.3 - - - +
139E VAL* 4.5 0.5 - - - +
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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