Contacts of the strand formed by residues 66 - 72 (chain E) in PDB entry 5B6N
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 66 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E TRP* 3.3 24.7 - - + +
34E GLY 4.4 0.7 - - - -
35E ILE* 3.5 35.2 - - + +
58E ALA 5.2 0.2 - - - +
61E PHE* 2.6 49.9 + - + +
62E ALA* 3.7 8.3 + - - +
64E ARG* 3.5 12.1 - - + +
65E ASN* 1.3 80.0 - - - +
67E LYS* 1.3 71.5 + - - +
68E LEU 4.2 0.4 + - - -
164E VAL* 4.1 17.3 - - + -
168E GLN* 3.8 7.4 - - - +
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Residues in contact with LYS 67 (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 PHE* 3.4 58.9 + - + +
29E LEU* 5.2 3.3 - - + +
32E SER* 5.1 7.4 - - - +
33E TRP 3.6 6.3 + - - +
34E GLY* 4.0 2.1 - - - -
35E ILE 3.2 21.0 + - - +
62E ALA* 6.0 4.0 - - + -
66E VAL* 1.3 85.6 - - - +
68E LEU* 1.3 62.0 + - - +
69E ILE* 4.8 1.0 - - - +
99E PRO 5.0 11.2 - - - -
100E PHE* 6.0 0.9 - - - +
101E PRO* 5.3 3.1 - - - -
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Residues in contact with LEU 68 (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 PHE* 3.9 3.5 - - - -
35E ILE* 3.4 29.4 - - + -
37E PHE* 3.7 19.5 - - + -
54E ALA* 3.7 15.7 - - + +
58E ALA* 3.6 29.8 - - + +
61E PHE* 4.3 25.4 - - + -
66E VAL 4.3 0.4 + - - +
67E LYS* 1.3 75.8 - - - +
69E ILE* 1.3 66.7 + - - +
100E PHE* 3.5 38.4 - - + +
101E PRO* 3.4 20.1 - - - +
157E PHE* 4.6 4.0 - - + -
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Residues in contact with ILE 69 (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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18E THR* 5.1 1.1 - - + -
23E ILE* 5.1 14.6 - - + -
25E PHE* 5.4 13.7 - - + -
28E PHE* 4.6 19.5 - - + -
29E LEU* 5.9 3.4 - - + -
35E ILE 3.0 15.8 + - - +
36E LEU* 3.4 26.8 - - + +
37E PHE* 2.9 32.3 + - - +
67E LYS 4.8 2.5 - - - +
68E LEU* 1.3 78.2 - - - +
70E ALA* 1.3 71.0 + - - +
100E PHE* 4.6 0.4 - - - -
101E PRO* 3.4 25.1 - - + +
103E ILE* 4.8 21.1 - - + -
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Residues in contact with ALA 70 (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 LEU* 4.3 1.2 - - - +
37E PHE* 3.1 29.2 - - + -
39E HIS* 4.3 2.9 - - - +
51E LEU* 4.3 6.7 - - + -
69E ILE* 1.3 78.6 - - - +
71E LEU* 1.3 67.0 + - - +
100E PHE* 4.0 6.6 - - + -
101E PRO 3.0 8.5 + - - -
102E ILE* 3.5 30.7 - - + -
103E ILE* 3.2 22.9 + - - +
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Residues in contact with LEU 71 (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 LEU* 4.8 15.9 - - + -
37E PHE 3.1 11.2 + - - +
38E SER* 3.2 12.2 - - - +
39E HIS* 3.1 25.1 + - - +
70E ALA* 1.3 80.8 - - - +
72E SER* 1.3 66.2 + - - +
102E ILE* 4.3 0.6 - - - +
103E ILE* 3.5 26.9 - - + -
105E ASP* 4.2 16.6 - - + +
110E LEU* 4.0 29.4 - - + -
111E ALA* 5.5 1.6 - - + +
114E LEU* 6.4 0.9 - - + -
116E MET* 3.5 34.5 - - + -
130E THR* 4.1 6.0 - - + +
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Residues in contact with SER 72 (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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39E HIS* 3.3 31.8 - - - -
40E PRO 4.1 2.9 - - - -
42E ASP* 3.2 17.0 + - - -
71E LEU* 1.3 75.0 - - - +
73E ILE* 1.3 57.9 + - - +
74E ASP* 3.0 22.9 + - - +
79E HIS* 3.2 11.3 - - - -
103E ILE 3.7 5.3 + - - +
105E ASP* 3.0 31.5 + - - +
130E THR* 4.2 4.7 - - - -
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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