Contacts of the strand formed by residues 65 - 72 (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 TYR 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 5.6 2.2 - - + -
63B THR* 3.2 45.7 + - - -
64B VAL* 1.3 74.9 - - - +
66B TYR* 1.3 60.8 + - - +
91B LEU* 4.3 29.4 - - + -
92B THR 3.6 10.8 - - - +
93B GLU* 3.3 40.8 + - + -
115B ALA* 3.4 2.1 - - - -
116B THR* 2.6 49.7 + - - +
118B GLY 5.8 2.7 - - - -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 4.1 7.6 - - + -
54B TRP* 3.2 43.7 - + + -
56B PRO* 3.4 8.5 - - - +
57B VAL* 2.8 31.3 + - - -
64B VAL* 3.7 18.2 - - + +
65B TYR* 1.3 75.8 - - - +
67B SER* 1.3 56.2 + - - +
68B VAL* 4.3 1.8 - - + -
89B CYS* 4.0 2.8 - - + +
91B LEU* 2.7 31.8 + - - -
92B THR* 3.0 18.3 + - - +
93B GLU 3.2 27.8 - - - -
94B GLY 3.5 12.3 - - - -
95B PRO* 3.9 5.2 - - + -
113B VAL* 4.2 3.6 - - + -
114B ARG 3.3 4.5 - - - +
115B ALA* 3.5 33.7 - - + -
116B THR* 5.0 0.4 - - - -
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 1.3 72.0 + - - +
68B VAL* 1.3 62.5 + - - +
69B GLU* 5.8 0.9 - - - -
89B CYS 3.5 5.6 - - - -
90B SER* 4.7 1.6 - - - -
91B LEU* 3.1 38.0 + - - +
113B VAL* 3.3 1.0 - - - -
114B ARG* 2.7 55.4 + - - -
116B THR* 4.8 1.1 - - - +
124B TRP* 3.0 18.6 - - - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.3 24.0 - - + -
54B TRP* 3.7 29.8 - - + -
66B TYR* 5.2 1.1 - - + -
67B SER* 1.3 75.1 - - - +
69B GLU* 1.3 74.2 + - - +
85B PRO* 4.2 0.9 - - - +
86B SER* 2.9 30.3 + - - +
89B CYS* 2.9 33.1 + - + +
90B SER* 5.3 0.5 + - - -
97B CYS* 4.0 10.8 - - + -
99B VAL* 4.6 6.5 - - + -
111B LEU* 4.9 3.6 - - + -
112B ARG 3.2 8.5 - - - +
113B VAL* 3.7 9.2 - - + -
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Residues in contact with GLU 69 (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 1.1 + - - -
68B VAL* 1.3 82.0 - - - +
70B TYR* 1.3 64.7 + - - +
83B TRP* 3.6 18.3 - - + +
84B ILE 3.6 8.5 - - - +
85B PRO* 3.8 23.5 - - + +
86B SER 4.1 1.6 - - - +
111B LEU* 3.4 5.9 - - - +
112B ARG* 2.7 72.7 + - + +
124B TRP* 3.3 25.0 - - + -
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Residues in contact with TYR 70 (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* 3.3 24.0 + - + +
110A SER* 4.3 14.3 - - - -
69B GLU* 1.3 73.3 - - - +
71B GLN* 1.3 67.8 + - - +
72B GLY 4.8 0.4 - - - -
83B TRP* 3.6 5.8 - - - -
84B ILE* 2.8 88.5 + - + +
85B PRO 4.0 5.2 - - - -
86B SER* 4.1 8.1 - - - -
99B VAL* 6.4 0.2 - - + -
102B ASP* 3.5 44.6 + - + -
109B TYR* 3.9 29.2 - + + -
110B ASN 3.1 6.1 - - - +
111B LEU* 3.2 28.0 - - + -
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Residues in contact with GLN 71 (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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70B TYR* 1.3 79.8 - - - +
72B GLY* 1.3 60.5 + - - +
75B GLU* 3.6 18.4 - - + +
76B SER* 3.2 32.7 + - - +
80B SER* 3.4 20.8 + - - +
82B ILE 2.9 22.6 - - - +
83B TRP* 3.7 25.7 - - + -
84B ILE* 4.7 0.4 - - - -
109B TYR* 3.5 4.0 - - - -
110B ASN* 2.7 60.6 + - + +
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Residues in contact with GLY 72 (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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114A ASN* 3.5 8.9 - - - +
70B TYR* 4.3 1.8 - - - -
71B GLN* 1.3 76.1 - - - +
73B GLU* 1.3 57.1 + - - -
74B TYR 3.1 3.1 - - - -
75B GLU* 2.8 38.6 + - - -
76B SER* 2.9 11.0 + - - -
108B PRO 4.1 2.0 - - - -
109B TYR* 3.8 25.5 - - - -
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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