Contacts of the strand formed by residues 49 - 56 (chain E) in PDB entry 4JRX
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 GLY 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.6 23.8 - - - -
122D GLY 3.7 5.2 - - - -
123D THR 3.6 10.4 + - - -
43E ARG 3.6 1.4 - - - +
44E GLN* 3.3 5.7 - - - -
45E ASP 3.3 26.8 + - - -
47E GLY 3.6 2.4 - - - +
48E MET* 1.3 82.0 - - - +
50E LEU* 1.4 64.2 + - - -
51E ARG 4.0 0.2 + - - -
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Residues in contact with LEU 50 (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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50D LEU* 3.9 28.7 - - + -
104D PHE* 4.0 21.7 - - + -
121D PHE* 3.8 42.2 + - + +
122D GLY 4.0 5.7 + - - -
42E TYR* 3.9 28.7 - - + -
43E ARG 3.5 2.7 - - - +
44E GLN* 3.8 36.3 - - + +
48E MET 3.7 1.6 + - - +
49E GLY* 1.4 71.8 - - - -
51E ARG* 1.3 61.9 + - - +
52E LEU 4.4 0.3 + - - -
70E GLU* 4.9 1.0 - - - +
103E PHE* 4.3 6.3 - - + -
114E PHE* 3.9 17.7 - - + -
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Residues in contact with ARG 51 (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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42E TYR* 3.2 4.6 - - - -
43E ARG* 2.9 53.5 + - + +
45E ASP* 3.0 29.7 + - - +
48E MET* 3.8 45.6 - - + +
50E LEU* 1.3 75.9 - - - +
52E LEU* 1.4 62.7 + - - +
53E ILE* 3.5 4.2 + - - +
70E GLU* 3.6 29.6 - - - +
71E VAL* 3.6 35.6 - - + +
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Residues in contact with LEU 52 (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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118D LYS* 3.6 40.4 - - + -
119D LEU 4.7 0.7 - - - +
120D ILE* 4.5 6.6 - - + +
302D IOD 4.3 9.6 - - + -
40E TYR* 3.6 29.2 - - + -
41E TRP 3.4 16.8 - - - +
42E TYR* 3.6 21.0 - - + -
50E LEU 4.4 0.2 + - - -
51E ARG* 1.4 70.8 - - - +
53E ILE* 1.3 57.7 + - - +
54E TYR 3.6 14.8 - - - +
55E TYR* 3.9 15.7 - - + -
69E GLY* 4.0 8.1 - - - -
70E GLU* 2.8 35.3 + - - +
71E VAL 3.0 8.8 + - - -
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Residues in contact with ILE 53 (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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41E TRP* 2.8 18.8 + - + +
42E TYR 3.7 21.8 - - - +
43E ARG* 3.8 12.3 - - + -
51E ARG 3.8 10.1 - - - +
52E LEU* 1.3 73.5 - - - +
54E TYR* 1.3 69.6 - - + +
69E GLY* 3.0 19.0 + - - -
71E VAL* 3.4 23.8 - - + +
72E PRO* 3.4 12.6 - - + +
76E TYR* 3.5 32.3 - - + -
89E LEU* 4.1 14.6 - - + -
102E TYR* 3.7 28.7 - - + -
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Residues in contact with TYR 54 (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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41E TRP* 2.9 28.8 + - + +
52E LEU* 3.6 5.0 - - - +
53E ILE* 1.3 91.0 - - + +
55E TYR* 1.3 60.3 + - - +
66E THR* 5.6 2.0 - - - -
67E ASP* 3.3 26.2 - - - -
68E LYS* 3.7 30.0 + - + +
69E GLY 3.9 2.5 - - - +
72E PRO* 3.7 23.9 + - + +
76E TYR* 3.4 33.4 + - + -
77E ASN* 4.1 11.3 + - - -
78E VAL* 3.6 46.9 - - + -
87E PHE* 3.7 3.1 - - - -
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Residues in contact with TYR 55 (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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112D ASN 4.4 3.4 - - - -
113D THR* 3.2 34.9 + - - -
117D ASP 4.4 1.1 - - - -
118D LYS* 3.4 40.5 + - + +
39E MET 3.4 5.6 - - - +
40E TYR* 3.3 40.2 - + + -
52E LEU* 3.9 5.8 - - + -
54E TYR* 1.3 74.7 - - - +
56E SER* 1.3 62.3 + - - +
57E ALA* 4.4 12.6 - - + -
66E THR* 3.6 2.4 - - - -
67E ASP* 2.8 69.5 + - + +
68E LYS 3.5 11.2 - - - -
87E PHE* 3.7 5.4 - - - -
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Residues in contact with SER 56 (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 ASN 3.4 1.2 - - - +
38E SER* 3.2 7.1 - - - -
39E MET 2.8 31.5 + - - +
55E TYR* 1.3 78.0 - - - +
57E ALA* 1.3 57.9 + - - +
58E SER 2.8 15.4 + - - -
65E THR 2.5 26.8 + - - -
66E THR* 4.3 0.9 - - - +
80E ARG* 3.0 20.8 + - - +
87E PHE* 3.7 24.0 - - - -
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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