Contacts of the strand formed by residues 45 - 51 (chain E) in PDB entry 4LOU
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 LEU 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E VAL* 4.0 2.5 - - + -
38E ARG 3.4 4.5 - - - +
39E GLN* 3.8 30.3 - - + +
44E GLY* 1.3 72.8 - - - -
46E LYS* 1.3 71.5 + - - +
95E TYR* 4.0 20.0 - - + -
111E TRP* 4.0 25.4 - - + -
35F TYR* 5.5 1.3 - - + -
43F PRO* 4.1 10.8 - - + -
86F TYR* 3.6 41.8 - - + -
97F PHE* 3.3 46.1 + - + +
98F GLY 5.1 1.5 + - - +
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Residues in contact with LYS 46 (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 VAL* 3.4 3.9 - - - +
38E ARG* 3.0 45.3 + - + +
43E LYS* 5.9 8.7 - - - +
44E GLY 4.0 12.0 + - - +
45E LEU* 1.3 83.3 + - - +
47E TRP* 1.3 66.6 + - - +
48E ILE* 3.6 5.2 + - + +
97F PHE* 4.5 8.6 + - - +
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Residues in contact with TRP 47 (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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35E SER* 2.6 28.4 + - - -
36E TRP 3.9 4.3 - - - -
37E VAL* 4.1 4.4 - - + +
45E LEU 4.4 0.2 - - - -
46E LYS* 1.3 74.8 - - - +
48E ILE* 1.3 65.8 + - - +
49E GLY* 3.3 11.6 - - - -
50E GLU* 3.1 37.2 - - + -
59E ASN* 4.0 20.6 - - + -
60E TYR 3.7 21.3 - - - -
61E THR* 3.5 32.7 + - - +
108E PHE* 3.6 25.4 - + - -
90F TRP* 4.4 3.4 - + - -
93F HIS* 4.1 8.3 - + - -
94F PRO* 4.0 17.3 - - + -
95F GLN* 2.9 46.6 - - + +
97F PHE* 4.5 10.0 - - + -
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Residues in contact with ILE 48 (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 TRP* 2.7 39.8 + - + +
37E VAL 4.7 0.2 - - - -
38E ARG* 4.0 37.0 - - - +
46E LYS* 4.1 8.5 - - + +
47E TRP* 1.3 83.2 - - - +
49E GLY* 1.3 55.9 + - - +
60E TYR* 3.4 6.1 - - - +
61E THR* 3.0 31.9 + - + +
68E PHE* 3.9 43.5 - - + -
70E ILE* 4.5 3.1 - - + -
81E LEU* 4.2 12.3 - - + -
94E TYR* 4.5 9.2 - - + -
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Residues in contact with GLY 49 (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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35E SER* 2.9 14.7 + - - -
36E TRP 3.1 13.4 + - - -
47E TRP* 3.3 17.7 - - - -
48E ILE* 1.3 82.7 - - - +
50E GLU* 1.3 57.3 + - - -
59E ASN 3.2 14.6 - - - -
70E ILE* 3.1 20.0 - - - +
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Residues in contact with GLU 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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380B PRO 4.3 1.6 - - - +
383B HIS* 2.5 36.0 + - - -
33E TRP* 3.5 17.7 - - + -
34E MET 3.3 12.8 - - - +
35E SER* 4.0 5.8 - - - +
47E TRP* 3.1 11.6 - - + -
49E GLY* 1.3 74.9 - - - -
51E ILE* 1.3 66.7 + - - +
58E ILE* 3.6 6.4 - - - +
59E ASN* 2.6 58.0 + - + +
70E ILE* 4.3 2.6 - - - +
99E LEU* 3.5 3.6 - - + +
90F TRP* 3.1 17.3 - - - -
93F HIS* 3.8 8.5 - - - -
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Residues in contact with ILE 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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33E TRP* 3.5 4.8 - - - -
34E MET* 3.1 19.7 + - + +
50E GLU* 1.3 78.1 - - - +
52E ASN* 1.3 69.9 + - - +
55E SER* 4.0 10.5 - - - +
57E THR 3.6 11.9 - - - +
58E ILE* 4.0 18.4 - - + -
70E ILE* 3.6 23.6 - - + +
71E SER* 3.8 10.8 - - - -
72E ARG* 3.1 57.6 + - + +
79E LEU* 3.8 18.8 - - + -
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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