Contacts of the helix formed by residues 74 - 84 (chain B) in PDB entry 6OW3
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 ASP 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B SER 4.1 9.9 - - - +
67B THR* 4.9 14.1 - - - +
68B ILE* 5.2 0.9 - - - +
72B LYS 3.6 2.5 + - - +
73B GLU* 1.3 76.2 - - - +
75B VAL* 1.3 67.5 + - - +
76B VAL* 3.3 11.1 + - + +
77B GLU* 2.9 21.1 + - - +
78B ILE* 3.1 22.5 + - - +
872D ARG* 2.8 39.2 + - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.5 9.6 - - + -
61B VAL* 3.7 24.7 - - + -
63B HIS 4.3 0.4 - - - +
64B GLU* 3.3 20.2 - - - +
66B SER* 3.2 19.0 + - - +
68B ILE* 3.9 22.9 - - + -
74B ASP* 1.3 75.2 - - - +
76B VAL* 1.3 64.6 + - - +
78B ILE* 3.1 10.2 + - - +
79B ILE* 2.9 30.6 + - + +
165B ILE* 3.9 27.4 - - + -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 3.6 23.8 - - + +
65B PHE* 3.9 25.4 - - + -
66B SER 6.0 0.2 - - - +
74B ASP* 3.3 11.3 + - + +
75B VAL* 1.3 77.0 - - - +
77B GLU* 1.3 57.9 + - - +
79B ILE* 3.1 10.2 + - + +
80B LEU* 2.8 31.0 + - + +
842D VAL* 3.6 34.8 - - + -
872D ARG* 3.9 17.0 - - - +
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Residues in contact with GLU 77 (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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73B GLU* 3.9 25.5 - - + +
74B ASP* 2.9 23.5 + - - +
75B VAL 3.2 0.4 - - - -
76B VAL* 1.3 76.5 - - - +
78B ILE* 1.3 62.5 + - - +
80B LEU* 3.4 6.7 + - - +
81B ASN* 3.1 33.7 + - - +
867D ARG* 3.2 40.4 + - - -
872D ARG* 3.1 30.4 + - - +
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Residues in contact with ILE 78 (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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58B ILE* 4.5 9.2 - - + -
68B ILE* 3.8 29.2 - - + -
71B VAL* 4.4 3.1 - - + -
73B GLU* 4.0 17.3 - - + +
74B ASP 3.1 17.2 + - - +
75B VAL* 3.1 8.2 + - - +
77B GLU* 1.3 73.4 - - - +
79B ILE* 1.3 65.4 + - - +
81B ASN* 3.2 4.0 + - - +
82B LEU* 2.9 35.1 + - + +
129B ILE* 4.2 19.7 - - + +
130B ALA* 4.2 18.4 - - + -
138B LEU* 4.6 5.2 - - + -
140B MET* 3.5 26.2 - - + -
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Residues in contact with ILE 79 (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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56B VAL* 4.2 17.9 - - + -
58B ILE* 5.9 1.1 - - + -
64B GLU* 3.4 39.7 - - + +
75B VAL* 2.9 27.9 + - + +
76B VAL* 3.6 8.7 - - + +
78B ILE* 1.3 75.9 - - + +
80B LEU* 1.3 58.4 + - + +
82B LEU* 2.9 12.6 + - + +
83B LYS* 2.9 36.1 + - - +
165B ILE* 4.1 14.8 - - + -
167B VAL* 3.7 31.6 - - + -
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Residues in contact with LEU 80 (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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76B VAL* 2.8 22.5 + - + +
77B GLU* 3.4 15.0 - - - +
79B ILE* 1.3 76.3 - - + +
81B ASN* 1.3 63.0 + - - +
83B LYS* 3.0 25.6 + - + +
84B GLU* 3.3 13.5 + - - +
842D VAL* 3.5 39.0 - - + +
843D PHE 3.6 6.5 - - - +
844D ALA* 3.3 30.2 - - + +
865D THR* 6.1 0.4 - - + -
867D ARG* 3.5 37.2 - - + +
872D ARG* 4.9 7.6 - - + +
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Residues in contact with ASN 81 (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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73B GLU* 5.0 3.6 - - - +
77B GLU* 3.1 14.4 + - - +
78B ILE 3.5 7.2 - - - +
80B LEU* 1.3 74.5 - - - +
82B LEU* 1.3 58.2 + - - +
84B GLU* 3.0 25.3 + - - +
127B LEU* 3.5 15.5 - - + +
128B HIS* 3.3 35.2 + - - +
129B ILE* 2.8 32.6 + - + +
867D ARG* 2.6 40.4 + - - +
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Residues in contact with LEU 82 (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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53B VAL* 3.6 25.7 - - + +
56B VAL* 3.8 32.8 - - + -
78B ILE* 2.9 34.2 + - + +
79B ILE* 2.9 20.1 + - + +
81B ASN* 1.3 74.1 - - + +
83B LYS* 1.3 63.7 + - - +
85B LEU* 3.1 28.4 + - + +
114B PHE* 4.3 18.8 - - + -
129B ILE* 4.8 13.0 - - + -
140B MET* 4.4 4.9 - - - -
142B VAL* 4.0 20.6 - - + -
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Residues in contact with LYS 83 (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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53B VAL* 5.2 5.2 - - - +
79B ILE* 2.9 20.6 + - - +
80B LEU* 3.0 20.5 + - + +
82B LEU* 1.3 75.8 - - - +
84B GLU* 1.3 57.1 + - - +
85B LEU 3.1 9.2 + - - +
150B TYR* 4.8 0.2 + - - -
167B VAL* 3.8 20.4 - - + -
168B ASP* 3.1 43.4 + - - +
170B VAL* 4.7 18.1 - - + +
842D VAL 2.8 29.3 + - - -
844D ALA* 4.2 6.5 - - + -
848D GLU* 3.0 33.2 + - - +
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Residues in contact with GLU 84 (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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80B LEU 3.5 13.7 - - - +
81B ASN 3.0 11.1 + - - +
83B LYS* 1.3 74.5 - - - +
85B LEU* 1.3 57.6 + - - +
86B VAL* 3.8 5.9 + - - +
124B ASN* 3.1 18.5 + - - -
127B LEU* 3.2 19.0 - - + +
175B ARG* 5.1 14.7 + - - +
844D ALA* 3.6 16.5 - - + +
845D ASN* 3.1 29.6 + - - +
867D ARG* 3.0 24.3 + - - +
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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