Contacts of the strand formed by residues 88 - 94 (chain E) in PDB entry 3JCK
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 LYS 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E LEU* 3.1 3.5 - - - -
39E GLY 2.9 35.1 + - - +
40E ASP* 5.8 1.1 - - - -
41E ALA 6.0 1.1 - - - +
42E ASN* 6.1 2.9 - - - +
81E LYS* 4.0 6.2 - - - +
85E ALA 3.1 21.3 + - - +
86E LYS* 4.1 21.2 - - - +
87E GLU* 1.3 73.7 - - - +
89E LEU* 1.3 69.4 + - - +
90E ILE* 3.3 2.9 + - + +
158F ASP* 2.3 38.4 + - - +
159F LYS* 4.1 7.1 + - - +
160F LYS 4.2 4.2 + - - -
161F ASP* 3.7 28.9 - - + +
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Residues in contact with LEU 89 (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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36E VAL* 3.9 28.3 - - + -
37E ILE 3.6 12.1 - - - +
38E LEU* 4.0 13.2 - - + +
41E ALA* 6.0 0.3 - - - +
52E PHE* 5.5 1.6 - - + -
73E ILE* 4.5 13.0 - - + -
77E ASN* 3.6 22.2 - - - +
81E LYS* 3.9 5.3 - - - +
88E LYS* 1.3 76.4 - - - +
90E ILE* 1.3 70.5 + - - +
91E GLY* 4.4 3.8 - - - +
110E PHE* 5.6 7.0 - - + -
113E TYR* 3.5 39.5 - - + +
114E THR* 3.2 15.9 + - - -
161F ASP* 3.3 21.0 + - - +
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Residues in contact with ILE 90 (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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37E ILE* 2.7 18.3 + - + +
38E LEU 4.0 2.5 - - - -
39E GLY* 3.4 37.9 - - - +
40E ASP 3.6 11.0 - - - +
41E ALA* 4.2 22.0 - - + +
46E ILE* 4.4 13.7 - - + -
47E ARG 4.1 4.9 - - - +
48E VAL* 4.5 9.0 - - + -
88E LYS* 3.4 12.8 - - + +
89E LEU* 1.3 78.6 - - - +
91E GLY* 1.3 59.8 + - - +
110E PHE* 5.4 1.0 - - - +
114E THR* 3.3 31.8 + - - +
117E ASN 5.4 1.1 - - - +
118E PRO* 3.8 6.9 - - + +
119E LEU* 4.2 22.7 - - + +
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Residues in contact with GLY 91 (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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36E VAL* 3.3 5.8 - - - +
37E ILE* 2.5 40.5 + - - +
89E LEU* 4.4 1.3 - - - +
90E ILE* 1.3 84.6 - - - +
92E TRP* 1.3 56.9 + - - -
110E PHE* 5.0 5.6 - - - -
118E PRO* 4.5 5.8 - - - -
119E LEU 3.3 22.2 - - - -
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Residues in contact with TRP 92 (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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32E ARG* 4.5 2.0 - - - -
34E VAL* 4.0 16.2 - - + -
35E GLY 3.2 14.1 - - - +
36E VAL* 3.9 0.7 - - + +
37E ILE* 4.2 4.1 - - - +
91E GLY* 1.3 77.5 - - - -
93E TYR* 1.3 83.9 + - - +
94E HIS* 3.8 21.5 - + + -
103E ASP* 3.8 15.5 - - - -
106E ILE* 3.3 37.7 - - + -
107E ASN* 2.3 39.4 + - - -
110E PHE* 3.2 48.9 - + + -
118E PRO* 5.3 1.8 - - + -
119E LEU 3.2 10.6 + - - +
120E LEU* 3.2 47.9 - - + +
121E LEU* 3.6 2.3 + - - +
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Residues in contact with TYR 93 (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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17E SER 5.2 0.2 - - - -
18E ALA* 3.6 38.7 - - + +
21E HIS* 4.0 18.4 - + - +
33E CYS 4.8 2.2 - - - -
34E VAL* 3.2 25.4 - - - +
35E GLY* 2.8 51.5 + - - +
36E VAL 3.8 4.3 - - - -
37E ILE* 3.5 25.8 - - + -
51E SER* 4.3 9.1 + - - -
52E PHE 4.5 2.4 + - - -
53E ALA* 4.5 5.5 - - - -
92E TRP* 1.3 80.8 - - - +
94E HIS* 1.3 66.6 + - - +
95E SER* 4.4 4.9 - - - -
120E LEU* 3.5 3.1 - - - -
121E LEU* 3.0 34.1 - - + +
123E VAL* 4.7 8.3 - - + -
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Residues in contact with HIS 94 (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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32E ARG* 3.3 36.8 + - - +
33E CYS 2.9 10.5 - - - +
34E VAL* 3.7 7.4 - - + -
92E TRP* 3.8 17.7 - + + -
93E TYR* 1.3 77.0 - - - +
95E SER* 1.3 59.3 + - - +
96E GLY* 3.0 32.2 + - - -
98E LYS 3.5 18.4 - - - -
99E LEU* 3.8 5.7 - - - +
100E ARG* 4.8 0.4 - - - -
103E ASP* 3.6 16.3 + - - -
120E LEU* 4.2 7.4 - - + -
121E LEU 3.8 1.8 + - - -
122E ILE* 3.4 37.4 - - + +
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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