Contacts of the strand formed by residues 81 - 90 (chain E) in PDB entry 4JCQ
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 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E LEU* 5.0 1.3 - - + -
53E ILE* 3.4 12.3 - - + +
55E ILE* 3.6 31.6 - - + -
74E ILE* 3.8 33.7 - - + +
77E ILE* 3.9 21.3 - - + -
79E PRO 3.6 10.9 + - - +
80E THR* 1.3 78.5 - - - +
82E LYS* 1.3 70.1 + - - +
83E VAL* 4.3 6.7 - - + -
100E ALA* 3.5 19.5 - - + +
101E GLU 4.9 0.2 + - - -
104E ASN* 3.6 11.1 + - - +
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Residues in contact with LYS 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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52E PRO* 4.0 29.0 - - + +
53E ILE 2.8 12.3 + - - +
54E THR* 3.4 15.9 - - + +
55E ILE 2.8 32.1 + - - -
80E THR* 4.9 7.8 - - + +
81E VAL* 1.3 76.9 - - - +
83E VAL* 1.3 59.4 + - - +
104E ASN* 3.4 30.7 + - + +
106E PHE* 4.1 23.3 - - + -
189E LEU* 4.4 17.3 - - + +
190E LYS 4.5 16.8 - - - -
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Residues in contact with VAL 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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55E ILE* 3.3 15.9 - - + +
57E ILE* 4.0 18.6 - - + -
74E ILE* 5.2 2.5 - - + -
81E VAL* 4.2 7.6 + - + -
82E LYS* 1.3 77.7 - - - +
84E VAL* 1.3 59.8 + - - +
96E ILE 4.8 3.4 - - - +
97E TYR* 3.5 44.9 - - + +
100E ALA* 3.8 22.4 - - + +
104E ASN 3.0 8.2 + - - +
105E ARG* 3.8 12.8 - - + -
106E PHE* 2.8 35.8 + - - +
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Residues in contact with VAL 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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76D PHE* 5.8 0.2 - - + -
54E THR* 4.0 23.3 - - + -
55E ILE 2.7 9.8 + - - +
56E PHE* 3.3 28.8 - - + -
57E ILE 2.9 25.7 + - - -
83E VAL* 1.3 78.1 - - - +
85E GLY* 1.3 66.3 + - - +
86E THR* 3.7 1.7 + - - +
97E TYR* 4.4 1.8 - - - -
106E PHE* 3.4 6.1 - - + +
107E SER* 4.5 3.1 - - - -
108E LEU* 3.7 35.0 - - + +
183E ILE* 4.6 5.4 - - + -
189E LEU* 4.0 21.1 - - + -
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Residues in contact with GLY 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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57E ILE 3.7 7.4 - - - -
84E VAL* 1.3 72.4 - - - +
86E THR* 1.3 60.4 + - - -
89E VAL* 3.9 10.3 - - - -
97E TYR* 3.6 7.5 - - - -
106E PHE 3.0 12.9 + - - -
107E SER* 3.5 0.9 + - - -
108E LEU* 2.9 27.0 + - - +
111E THR* 3.4 9.2 + - - -
113E TYR* 3.4 16.8 - - - -
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Residues in contact with THR 86 (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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68D ASP 4.7 0.7 + - - -
69D THR* 2.7 45.0 + - + +
72D ASP* 4.9 0.7 + - - +
73D MET* 5.9 0.2 - - - -
27E TYR* 4.2 9.0 - - - +
56E PHE* 4.5 6.1 - - + -
57E ILE 2.9 26.0 + - - +
58E ASN* 3.2 25.4 - - + +
84E VAL 4.1 6.3 - - - +
85E GLY* 1.3 75.5 - - - -
87E GLY* 1.3 60.4 + - - +
88E TRP 3.0 8.6 + - - +
108E LEU* 3.7 25.2 - - + +
111E THR* 3.3 8.7 - - - +
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Residues in contact with GLY 87 (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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65D GLU* 3.5 32.1 - - - +
68D ASP* 4.2 6.7 - - - +
69D THR* 3.7 1.7 - - - +
58E ASN* 3.9 1.6 - - - -
86E THR* 1.3 72.3 + - - +
88E TRP* 1.3 62.6 + - - +
110E ASN 3.3 21.1 + - - +
111E THR* 3.2 6.0 + - - -
112E ARG* 3.2 22.5 + - - +
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Residues in contact with TRP 88 (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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32D GLN* 3.4 13.2 - - - +
65D GLU* 3.5 35.8 - - + +
131D ILE* 4.8 8.7 - - + -
58E ASN* 3.1 30.8 + - - -
59E SER 2.8 34.0 + - - -
60E GLN* 3.6 34.0 - - + +
86E THR 3.0 4.4 + - - -
87E GLY* 1.3 75.6 - - - +
89E VAL* 1.3 68.7 + - - +
111E THR* 4.1 1.3 - - - -
112E ARG* 3.3 45.5 - - + +
167E TRP* 3.6 32.8 - + + -
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Residues in contact with VAL 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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57E ILE* 3.6 25.6 - - + +
59E SER 3.4 3.8 - - - +
85E GLY* 3.9 13.5 - - - -
86E THR 4.3 1.1 - - - +
88E TRP* 1.3 79.8 - - - +
90E ALA* 1.3 59.9 + - - +
93E GLY* 3.5 30.3 - - - +
94E ILE* 3.5 17.4 - - + +
97E TYR* 3.9 13.9 - - + -
111E THR* 4.3 0.7 - - + -
112E ARG 3.0 6.4 + - - -
113E TYR* 3.3 30.8 - - + -
114E MET 3.1 20.3 + - - -
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Residues in contact with ALA 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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59E SER 2.9 7.9 + - - +
60E GLN* 3.7 16.8 - - - +
61E GLY* 3.4 9.0 + - - -
89E VAL* 1.3 77.9 - - - +
91E SER* 1.3 64.6 + - - +
92E ALA 3.2 0.7 + - - -
93E GLY* 2.8 26.2 + - - -
94E ILE* 3.8 3.8 - - - -
114E MET* 3.2 17.9 - - + +
167E TRP* 3.7 27.1 - - + -
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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