Contacts of the strand formed by residues 37 - 43 (chain E) in PDB entry 5X6E
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 TYR 37 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ILE 5.3 3.4 - - - -
29E PHE* 4.0 28.2 - + + -
33E ASP* 3.1 28.8 + - + -
35E GLN* 3.1 38.3 + - + +
36E GLU* 1.3 80.4 - - - +
38E CYS* 1.3 67.1 + - - +
39E ILE* 4.6 7.1 - - + +
69E ILE 4.1 0.7 - - - +
70E MET* 3.7 1.0 - - - -
71E SER* 3.0 32.3 + - - +
72E GLY 3.8 3.1 + - - -
96E VAL* 4.1 25.4 - - + -
97E ILE 3.5 11.9 - - - +
98E LYS* 4.3 14.4 - - + -
99E ILE* 3.8 10.1 - - - +
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Residues in contact with CYS 38 (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 TYR* 1.3 75.3 - - - +
39E ILE* 1.3 77.1 + - - +
40E PHE* 4.8 1.6 - - - -
68E VAL* 5.1 8.7 - - - -
69E ILE 3.6 4.3 - - - -
70E MET* 4.3 20.6 - - + +
97E ILE* 2.8 51.2 + - + +
99E ILE* 3.9 5.1 - - + +
102E LEU* 3.9 36.3 - - + -
116E VAL* 6.2 3.6 - - - -
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Residues in contact with ILE 39 (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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28E ILE* 3.5 24.5 - - + -
29E PHE* 3.3 41.3 - - + -
37E TYR* 4.6 9.2 - - + -
38E CYS* 1.3 86.7 - - - +
40E PHE* 1.3 62.6 + - - +
41E LEU* 3.4 14.1 + - + +
68E VAL* 3.1 7.2 - - - +
69E ILE* 2.8 52.2 + - + +
85E LEU* 3.7 9.9 - - + -
94E ALA* 4.2 15.9 - - + -
95E TYR 3.5 8.7 - - - +
96E VAL* 4.9 5.6 - - + -
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Residues in contact with PHE 40 (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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5E ALA* 3.6 26.9 - - + -
8E PHE* 3.8 22.2 - + + -
9E LYS* 3.6 22.7 - - - -
12E LEU* 3.9 15.3 - - + -
38E CYS* 4.4 3.6 - - - -
39E ILE* 1.3 71.4 - - - +
41E LEU* 1.3 63.3 + - - +
42E TYR* 4.0 20.9 - + + -
66E ALA* 4.8 0.2 - - + -
67E PHE 3.8 4.7 - - - -
68E VAL* 3.8 18.6 - - + -
94E ALA* 3.5 0.2 - - - -
95E TYR* 2.7 77.2 + + + +
97E ILE* 5.0 2.6 - - + +
115E TYR* 3.5 23.3 - - - -
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Residues in contact with LEU 41 (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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28E ILE* 4.9 4.7 - - + -
39E ILE* 3.4 6.1 + - + -
40E PHE* 1.3 75.2 - - - +
42E TYR* 1.3 55.7 + - - +
43E ASP 3.8 13.2 - - - +
44E GLY 4.0 8.7 - - - +
46E THR* 3.6 32.8 - - + -
63E TYR* 3.8 26.7 - - + +
64E LYS 4.2 0.4 - - - +
65E GLY 2.7 29.5 - - - +
66E ALA* 3.3 1.6 - - - -
67E PHE* 2.9 30.7 + - + +
69E ILE* 4.1 12.3 - - + -
92E ALA* 4.5 9.9 - - + -
93E THR 3.6 16.6 - - - +
94E ALA* 4.1 13.9 - - + +
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Residues in contact with TYR 42 (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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2E ASN* 5.5 9.3 - - + +
5E ALA* 5.1 0.4 - - + -
6E GLU* 4.6 17.8 + - + +
9E LYS* 3.3 44.6 + - + -
40E PHE* 3.5 22.7 + + + -
41E LEU* 1.3 72.7 - - - +
43E ASP* 1.3 71.5 + - + +
65E GLY* 3.0 23.7 - - - -
66E ALA* 3.2 12.8 + - + +
93E THR* 2.8 23.5 + - + +
95E TYR* 3.9 24.0 - + + -
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Residues in contact with ASP 43 (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 LEU* 3.8 3.8 - - - +
42E TYR* 1.3 90.3 - - + +
44E GLY* 1.3 75.9 + - - +
65E GLY* 4.6 0.9 - - - -
91E GLN* 4.3 7.6 - - - +
92E ALA* 3.2 4.9 - - - +
93E THR* 2.7 50.2 + - - +
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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