Contacts of the strand formed by residues 51 - 57 (chain E) in PDB entry 4DOH
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 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E LEU 3.3 5.0 - - - +
47E SER* 3.3 3.6 - - - -
48E ILE* 2.9 34.8 + - + +
49E ASN* 2.9 2.0 + - + +
50E MET* 1.3 73.4 - - - +
52E ASN* 1.3 60.2 + - - +
53E VAL* 4.2 20.5 - - + +
96E ASP* 4.4 9.6 + - - -
98E SER* 3.2 14.4 - - - +
161E TRP* 4.0 24.9 - - + -
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Residues in contact with ASN 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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45E PHE* 4.5 6.1 - - + -
46E LEU 4.0 2.5 - - - -
47E SER* 2.6 33.6 + - - +
50E MET* 3.4 25.7 - - - +
51E LYS* 1.3 74.3 - - - +
53E VAL* 1.3 60.3 + - - +
54E LEU 4.2 0.2 - - - -
96E ASP* 2.9 7.8 - - - +
97E LEU* 2.9 24.9 + - - -
98E SER* 2.9 10.3 + - - +
101E THR* 3.1 38.4 + - - +
129E PHE* 3.5 26.8 - - + -
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Residues in contact with VAL 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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45E PHE* 3.5 3.6 - - - -
46E LEU* 2.8 47.5 + - + +
51E LYS* 4.2 23.3 - - + -
52E ASN* 1.3 77.9 - - - +
54E LEU* 1.3 73.0 + - - +
55E GLN* 3.8 16.0 + - + +
94E TYR* 4.2 16.2 - - + -
95E CYS 3.4 14.4 - - - +
96E ASP* 4.1 17.7 - - + -
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Residues in contact with LEU 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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43E ILE* 3.4 28.3 - - + -
44E THR* 3.3 22.0 - - - +
45E PHE* 4.0 23.5 - - + +
52E ASN 4.2 1.2 + - - -
53E VAL* 1.3 73.8 - - - +
55E GLN* 1.3 70.3 + - - +
56E TRP* 3.6 25.8 - - + -
71E VAL* 4.1 24.0 - - + -
95E CYS* 2.8 34.3 + - + +
97E LEU* 3.9 15.0 - - + +
110E ALA* 4.1 14.8 - - + -
111E ARG 4.9 2.9 - - - +
112E VAL* 4.9 2.5 - - + -
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Residues in contact with GLN 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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42E ASN 3.3 2.6 - - - +
43E ILE* 3.5 2.1 - - - +
44E THR* 3.0 38.8 + - - +
46E LEU* 3.3 33.9 - - + +
53E VAL* 3.9 15.0 - - + +
54E LEU* 1.3 87.2 - - - +
56E TRP* 1.3 67.7 + - - +
93E THR 3.6 7.1 + - - +
94E TYR* 3.6 26.5 - - + +
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Residues in contact with TRP 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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40E PRO* 4.2 21.5 - - + -
41E ALA 3.7 8.7 - - - +
42E ASN 3.5 9.4 - - - +
43E ILE* 4.5 6.7 - - + -
54E LEU* 3.6 30.3 - - + -
55E GLN* 1.3 84.7 - - - +
57E THR* 1.3 69.4 + - - +
58E PRO* 4.1 0.2 - - - +
69E TYR* 3.2 49.9 - + + -
71E VAL* 3.6 22.0 - - + -
90E ILE* 4.3 4.9 - - + -
92E ARG 3.9 1.8 - - - -
93E THR* 3.3 45.4 + - + +
94E TYR* 3.6 16.8 - - - -
95E CYS* 3.8 13.7 - - + -
112E VAL* 3.9 18.6 - - + -
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Residues in contact with THR 57 (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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40E PRO* 4.1 2.9 - - - +
41E ALA* 2.8 38.6 + - - +
42E ASN* 3.9 26.9 + - + +
56E TRP* 1.3 82.5 - - - +
58E PRO* 1.3 81.7 + - - +
59E PRO 3.4 0.3 - - - -
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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