Contacts of the strand formed by residues 76 - 83 (chain B) in PDB entry 3SBW
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 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 4.2 20.6 - - + +
69B ARG 3.4 3.8 - - - -
70B LEU* 3.7 20.4 - - + -
74B ASN 4.0 0.8 + - - -
75B GLN* 1.3 85.0 + - - +
77B GLU* 1.3 62.0 + - - +
78B LYS 4.2 0.4 - - - -
122B LEU* 4.7 2.0 - - + -
136B GLU* 3.6 24.0 - - - +
123C TYR* 3.7 27.6 + - + +
124C LYS* 3.3 25.5 + - - -
125C ARG* 3.7 14.7 - - - +
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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
----------------------------------------------------------
68B ASN* 3.6 2.5 - - - -
69B ARG* 2.8 43.2 + - - +
71B SER* 4.0 24.9 + - - -
75B GLN* 4.5 8.5 - - + +
76B THR* 1.3 79.8 - - - +
78B LYS* 1.3 62.9 + - - +
79B GLN* 2.9 27.7 + - - +
124C LYS* 4.5 9.0 - - - +
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Residues in contact with LYS 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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64B MET* 5.5 1.4 - - - +
66B ASN* 3.7 14.6 - - - +
68B ASN* 3.0 18.1 + - - +
76B THR 4.2 0.4 - - - -
77B GLU* 1.3 72.7 - - - +
79B GLN* 1.3 65.4 + - - +
80B ALA 3.8 12.6 - - - +
81B ALA* 3.6 24.2 - - - +
90B VAL* 3.5 34.8 - - + +
18C MET* 3.4 19.1 - - - +
19C PHE* 3.6 17.6 + - - +
20C THR* 5.2 4.0 + - - +
121C ALA 2.5 34.1 + - - +
122C ASP* 3.9 25.7 + - - +
124C LYS* 5.0 1.0 - - - +
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Residues in contact with GLN 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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67B TRP* 2.7 23.8 + - + +
68B ASN 4.3 1.6 - - - -
69B ARG* 3.4 34.2 + - + +
77B GLU* 2.9 32.4 + - - +
78B LYS* 1.3 82.2 + - - +
80B ALA* 1.3 59.9 + - - +
89B PRO* 3.6 2.9 - - - +
90B VAL* 3.0 25.5 + - - +
91B GLN 4.6 1.6 + - - -
92B ASP 4.6 1.4 + - - +
95B PHE* 3.6 55.0 - - + +
121B TYR* 4.3 4.9 - - + -
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Residues in contact with ALA 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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66B ASN* 3.7 2.1 - - - -
67B TRP* 2.8 29.2 + - + +
78B LYS* 3.8 7.9 - - - +
79B GLN* 1.3 80.2 - - - +
81B ALA* 1.3 63.0 + - - +
87B SER* 4.4 2.2 - - - +
88B GLN 3.3 15.0 - - - +
89B PRO* 3.9 2.9 - - + -
90B VAL* 4.3 2.9 - - - +
95B PHE* 3.6 28.0 - - + +
97B ILE* 4.1 17.5 - - + -
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Residues in contact with ALA 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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64B MET* 4.8 10.3 - - + -
65B LEU 3.3 4.7 - - - -
66B ASN* 3.4 19.7 - - - +
78B LYS* 3.6 6.3 - - - +
80B ALA* 1.3 74.9 - - - +
82B PHE* 1.3 62.0 + - - +
83B SER* 4.0 3.1 + - - +
86B LEU 3.8 1.4 - - - +
87B SER* 3.5 0.7 - - - -
88B GLN* 2.8 36.5 + - - +
97B ILE* 3.9 4.3 - - - -
18C MET* 3.5 27.6 - - + -
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Residues in contact with PHE 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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59B TRP* 4.2 21.5 - + - -
61B GLU* 4.7 1.6 - - - -
63B LEU 4.2 0.7 - - - +
64B MET* 3.4 2.8 - - - +
65B LEU* 2.7 47.5 + - + +
81B ALA* 1.3 73.1 - - - +
83B SER* 1.3 66.7 + - - +
85B GLY* 3.4 42.8 - - - -
86B LEU* 3.4 15.9 - - - -
87B SER* 3.8 11.0 - - - +
97B ILE* 3.7 28.4 - - + +
99B GLN* 3.6 41.1 - - + -
106B PHE* 4.0 16.2 - + + -
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Residues in contact with SER 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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59B TRP* 6.0 0.2 - - - -
63B LEU 4.4 6.3 - - - -
64B MET* 3.8 34.5 - - - +
81B ALA* 4.0 4.4 + - - +
82B PHE* 1.3 80.0 - - - +
84B ASN* 1.3 75.2 + - - +
85B GLY 3.3 2.2 - - - -
86B LEU* 3.0 17.7 + - - +
88B GLN* 4.8 8.8 + - - +
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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