Contacts of the strand formed by residues 81 - 86 (chain E) in PDB entry 4FAO
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 81 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.9 31.0 - - + +
85A LEU* 4.6 4.9 - - + -
87A LYS* 5.8 2.2 - - + -
93A PRO* 3.6 31.6 - - + -
44E SER* 4.1 14.8 - - - +
45E TRP 4.0 10.3 - - - +
46E ARG* 4.8 12.6 - - + +
55E VAL* 5.5 2.5 - - + -
76E GLU* 5.9 0.7 - - - +
79E PRO* 3.4 12.8 - - - +
80E GLN* 1.3 94.7 + - + +
82E TYR* 1.3 76.1 + - - +
83E PHE* 3.7 3.4 + - + +
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Residues in contact with TYR 82 (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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44E SER* 3.0 9.4 - - - -
45E TRP* 2.9 76.3 + + + +
47E ASN* 3.4 47.0 + - + +
74E ALA* 4.8 2.7 - - + -
77E GLU 5.1 0.5 + - - -
78E ASN* 3.4 18.6 + - - -
79E PRO* 3.0 41.8 - - + +
80E GLN 4.1 2.5 - - - -
81E VAL* 1.3 73.8 - - - +
83E PHE* 1.3 60.1 + - - +
97E HIS* 3.6 42.2 + + + -
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Residues in contact with PHE 83 (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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27A ILE* 5.5 3.6 - - + +
28A ALA* 3.7 22.0 - - + -
29A PRO* 5.8 1.3 - - + -
85A LEU* 3.6 24.0 - - + -
42E TYR* 3.8 27.6 - + + -
43E ALA 3.6 8.1 - - - -
44E SER* 4.4 1.1 - - - -
45E TRP* 4.4 0.7 - - - -
60E TRP* 3.7 48.5 - + - -
63E ASP* 5.6 0.9 - - - -
74E ALA* 3.1 22.8 - - - +
75E THR 4.5 1.6 + - - -
76E GLU* 5.8 7.7 - - + +
81E VAL* 3.7 5.2 + - + +
82E TYR* 1.3 76.0 - - - +
84E CYS* 1.3 85.7 + - - +
85E CYS* 3.9 15.9 - - + -
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Residues in contact with CYS 84 (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 4.7 - - - +
43E ALA* 3.0 33.8 + - - +
45E TRP* 3.9 20.4 - - + -
72E CYS* 2.0 57.0 - - - -
73E VAL 3.4 27.1 - - - +
74E ALA* 3.6 2.0 - - - +
83E PHE* 1.3 85.4 - - - +
85E CYS* 1.3 61.1 + - - +
95E PHE* 4.1 2.5 - - - -
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Residues in contact with CYS 85 (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 HIS* 4.9 0.2 - - + -
41E CYS 3.0 15.3 - - - +
60E TRP* 4.4 4.9 - - + -
63E ASP* 4.4 5.2 - - - -
65E ASN* 4.3 8.3 - - - -
66E CYS* 2.0 48.5 - - - -
69E ARG* 3.6 20.1 - - - -
71E GLU 4.2 2.3 - - - +
72E CYS* 4.1 4.4 - - - -
73E VAL 4.4 2.6 + - - +
83E PHE* 3.9 22.4 - - + -
84E CYS* 1.3 75.6 - - - +
86E CYS* 1.3 64.4 + - - +
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Residues in contact with CYS 86 (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 HIS* 3.3 12.2 - - - +
41E CYS* 2.9 38.6 + - - -
66E CYS* 3.9 7.1 - - - +
69E ARG 3.6 15.0 - - - +
71E GLU 3.8 14.6 - - - +
72E CYS* 3.9 8.5 - - - -
85E CYS* 1.3 78.7 - - - +
87E GLU* 1.3 59.8 + - - +
91E CYS* 2.0 59.2 - - + -
92E ASN 3.8 2.2 - - - -
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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