Contacts of the strand formed by residues 84 - 89 (chain E) in PDB entry 5IC4
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 GLU 84 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LYS* 5.5 13.1 + - - +
250B PHE* 4.3 11.0 - - + -
252B PHE* 4.6 4.4 - - + -
43E GLU* 3.8 16.6 - - - +
45E GLY 3.0 12.7 + - - +
46E LEU* 3.3 28.3 - - + +
47E CYS 3.0 19.6 + - - -
82E LYS 4.1 0.8 + - - -
83E TYR* 1.3 67.4 - - - +
85E VAL* 1.3 62.0 + - - +
86E ARG* 3.2 30.5 + - + +
111E ARG* 4.1 5.0 + - - -
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 3.6 25.3 - - + -
47E CYS* 3.4 11.4 - - + +
49E ILE* 3.7 21.8 - - + -
75E ARG* 3.8 37.2 + - + +
78E PHE* 3.9 14.6 - - + -
79E ARG 3.8 11.2 - - - +
83E TYR 3.1 13.6 + - - +
84E GLU* 1.3 74.1 - - - +
86E ARG* 1.3 66.3 + - - +
87E ASN* 3.4 21.8 - - - +
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Residues in contact with ARG 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU* 3.4 22.5 - - - +
47E CYS 2.8 8.9 + - - -
48E ILE* 3.8 23.0 - - + +
49E ILE 3.0 26.3 + - - +
75E ARG* 4.7 0.2 - - - +
84E GLU* 3.2 34.8 + - + +
85E VAL* 1.3 79.8 - - - +
87E ASN* 1.3 64.1 + - - +
88E LYS* 3.8 21.1 + - - +
99E LEU* 5.9 1.9 - - - +
103E VAL* 4.3 11.1 - - - +
106E GLU* 2.7 40.4 + - - -
111E ARG* 4.0 3.6 - - - +
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Residues in contact with ASN 87 (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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49E ILE* 3.6 24.1 + - - +
51E ASN* 5.5 2.0 - - - +
71E ALA* 3.7 29.5 + - - +
75E ARG* 2.8 45.2 + - - +
85E VAL* 3.4 10.2 - - - +
86E ARG* 1.3 72.1 - - - +
88E LYS* 1.3 69.4 + - - +
89E ASN* 4.5 15.5 + - - +
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Residues in contact with LYS 88 (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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48E ILE* 5.3 2.1 - - + +
49E ILE 2.8 13.1 + - - +
50E ILE* 3.6 3.7 - - + +
51E ASN* 2.8 35.0 + - - +
86E ARG* 4.0 31.3 - - - +
87E ASN* 1.3 81.1 + - - +
89E ASN* 1.3 58.4 + - - +
91E LEU* 3.7 28.3 - - + -
99E LEU* 3.8 37.8 - - + +
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Residues in contact with ASN 89 (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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51E ASN* 3.4 30.0 + - - +
68E ASP* 4.8 1.9 - - - +
71E ALA* 5.5 1.0 - - - +
87E ASN* 4.5 14.5 + - - +
88E LYS* 1.3 80.5 - - - +
90E ASP* 1.3 77.7 + - + +
91E LEU* 3.5 10.3 + - - +
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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