Contacts of the strand formed by residues 84 - 92 (chain B) 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 ILE 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 5.1 9.6 - - + +
107A ARG* 3.5 23.1 - - + +
110A SER* 4.4 11.2 - - - +
69B GLU* 4.3 1.3 - - - -
70B TYR* 2.8 77.5 + - + +
71B GLN* 4.7 0.9 - - - -
75B GLU* 3.5 37.9 - - + +
82B ILE* 4.5 7.4 - - + +
83B TRP* 1.3 77.8 - - - +
85B PRO* 1.3 72.4 - - + +
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Residues in contact with PRO 85 (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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103A HIS* 4.1 33.7 - - + +
107A ARG* 3.6 9.7 + - - +
68B VAL 4.9 0.4 - - - +
69B GLU* 3.8 25.0 - - + +
83B TRP 3.9 6.5 - - - +
84B ILE* 1.3 96.9 - - + +
86B SER* 1.3 68.8 - - - +
90B SER* 4.5 10.3 - - - +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 4.3 2.1 + - - -
68B VAL* 2.9 34.9 + - - -
69B GLU* 4.1 0.4 - - - +
70B TYR* 4.1 10.1 - - - -
84B ILE 3.5 2.8 + - - -
85B PRO* 1.3 76.9 - - - +
87B SER* 1.3 63.9 + - - +
88B TRP 3.5 0.8 + - - -
89B CYS* 3.1 31.6 + - - +
90B SER* 3.6 13.7 + - - -
97B CYS* 4.8 4.5 - - - -
99B VAL* 5.2 1.8 - - - -
102B ASP* 3.4 15.7 - - - -
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Residues in contact with SER 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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107A ARG* 3.7 34.5 + - - +
86B SER* 1.3 74.7 - - - +
88B TRP* 1.3 97.3 + - - +
90B SER* 5.6 0.4 - - - -
101B ASP* 3.9 11.7 - - - +
102B ASP* 3.2 24.5 + - - -
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Residues in contact with TRP 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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86B SER* 4.3 1.0 - - - -
87B SER* 1.3 109.1 + - - +
89B CYS* 1.3 71.1 + - - +
90B SER* 3.6 3.1 + - - -
92B THR* 3.0 19.8 - - - +
98B ASP* 3.9 24.2 - - + +
101B ASP* 3.1 28.3 + - + +
102B ASP* 4.9 0.4 + - - -
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Residues in contact with CYS 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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66B TYR 4.4 1.8 - - - +
67B SER* 3.5 1.6 - - - -
68B VAL* 2.9 38.9 + - + +
86B SER* 3.1 16.3 + - - +
88B TRP* 1.3 84.3 - - - +
90B SER* 1.3 58.9 + - - +
91B LEU 3.6 2.5 - - - -
92B THR* 3.7 16.8 - - - +
96B GLU 4.3 4.7 - - - +
97B CYS* 2.0 56.1 - - - -
98B ASP 4.3 2.0 - - - -
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Residues in contact with SER 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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67B SER* 4.2 3.4 - - - -
68B VAL 5.3 0.3 + - - -
85B PRO* 4.5 11.6 - - - +
86B SER* 3.6 16.6 + - - -
87B SER 5.6 0.2 - - - -
88B TRP 3.6 4.2 + - - -
89B CYS* 1.3 74.9 + - - +
91B LEU* 1.3 84.0 + - - +
92B THR* 4.5 2.0 - - - +
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Residues in contact with LEU 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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65B TYR* 4.3 19.5 - - + -
66B TYR 2.7 21.4 + - - +
67B SER* 3.1 14.8 + - - +
90B SER* 1.3 89.2 - - - +
92B THR* 1.3 60.9 + - - +
116B THR* 3.4 33.7 - - + -
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Residues in contact with THR 92 (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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54B TRP* 5.8 0.5 - - - -
65B TYR* 3.6 5.2 - - - -
66B TYR* 3.0 32.2 + - - +
88B TRP 3.0 28.5 - - - +
89B CYS* 3.7 20.9 - - - +
90B SER 4.2 3.1 - - - +
91B LEU* 1.3 79.5 - - - +
93B GLU* 1.3 65.3 + - - +
94B GLY 4.3 3.7 + - - -
96B GLU 4.2 12.1 + - - -
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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