Contacts of the strand formed by residues 86 - 91 (chain B) in PDB entry 4C58
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 THR 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B SER* 4.5 2.9 - - - -
23B CYS 3.2 22.7 - - - +
24B GLY* 4.0 7.1 - - - +
58B ARG* 3.0 19.4 + - - +
80B GLN* 3.3 0.5 - - - +
81B ASP* 3.0 33.8 + - - +
85B THR* 1.3 89.6 + - - +
87B ALA* 1.3 68.3 + - - +
88B PHE* 3.6 27.6 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 3.4 3.3 - - - -
23B CYS 3.0 30.9 + - - -
39B MET* 3.6 33.9 - - + -
41B TRP* 3.7 15.5 - - + -
56B ILE* 4.6 6.3 - - + -
58B ARG* 4.5 1.1 - - - +
78B ILE* 4.5 7.2 - - + -
79B SER 3.2 11.9 - - - +
80B GLN* 4.2 0.4 - - - +
86B THR* 1.3 77.3 - - - +
88B PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 4.5 21.1 - - + +
21B LEU 3.4 5.8 - - - +
22B SER* 3.5 27.4 - - - -
41B TRP* 3.9 2.9 - - - -
77B THR 3.6 0.9 - - - +
78B ILE* 3.2 9.4 - - - +
79B SER* 2.8 50.6 + - - +
80B GLN 4.3 5.2 - - - -
81B ASP* 4.0 24.5 - - + -
86B THR* 3.6 22.7 - - + -
87B ALA* 1.3 74.6 - - - +
89B LEU* 1.3 60.5 + - - +
90B LEU 4.1 0.9 - - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU 3.8 0.3 - - - +
20B ARG* 3.1 6.7 - - - -
21B LEU* 2.8 45.3 + - + +
41B TRP* 3.7 42.5 - - + -
53B VAL* 4.2 5.6 - - + -
54B ALA* 3.7 27.8 - - + -
76B PHE* 4.0 19.3 - - + -
77B THR 3.6 8.3 - - - +
78B ILE* 3.9 15.7 - - + +
88B PHE* 1.3 72.9 - - - +
90B LEU* 1.3 59.0 + - - +
91B MET* 3.7 30.6 + - + +
102B TYR* 4.5 2.5 - - + -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 4.6 14.8 - - - -
19B LEU 3.8 11.2 - - - +
20B ARG* 4.0 39.8 - - + +
75B ARG 3.9 1.2 - - - +
76B PHE* 3.2 8.7 - - - +
77B THR* 2.9 49.4 + - - +
88B PHE* 4.1 1.0 - - - +
89B LEU* 1.3 70.7 - - - +
91B MET* 1.3 64.1 + - - +
92B SER* 3.9 10.5 - - - +
1129B EDO 4.4 7.4 - - - +
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Residues in contact with MET 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 3.1 6.2 - - - -
19B LEU* 2.8 60.6 + - + +
21B LEU* 3.5 32.1 - - + +
76B PHE* 3.7 31.4 - - + -
89B LEU* 3.9 18.2 - - + +
90B LEU* 1.3 76.0 - - - +
92B SER* 1.3 59.5 + - - +
94B LEU* 3.4 16.2 - - + +
102B TYR* 4.0 29.8 - - - -
124B VAL* 4.0 12.8 - - + -
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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