Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 2JBO
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 GLY 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLY 4.0 0.2 - - - +
72A LEU* 3.8 13.9 - - - -
73A GLY* 3.0 27.4 + - - -
74A ILE 3.1 7.9 + - - -
75A ASN* 1.3 80.7 - - - +
77A LYS* 1.3 64.3 + - - +
78A VAL* 3.8 2.6 + - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER 5.7 0.4 - - - +
69A VAL* 3.8 35.2 - - + -
71A GLY 3.5 4.9 - - - -
72A LEU* 4.2 11.2 - - + -
75A ASN 3.7 5.2 + - - +
76A GLY* 1.3 75.6 - - - +
78A VAL* 1.3 61.6 + - - +
79A LEU* 4.0 24.0 + - + +
92A LEU 4.3 3.6 - - - +
93A LYS* 4.8 1.4 - - - +
94A MET* 4.6 12.5 + - - +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.3 4.2 - - - -
70A LEU* 2.5 40.0 + - + -
71A GLY 2.6 27.4 + - - +
76A GLY 4.8 1.8 - - - +
77A LYS* 1.3 77.2 - - - +
79A LEU* 1.3 66.5 + - - +
91A ALA* 4.0 20.9 - - + -
92A LEU 3.5 14.1 - - - +
93A LYS* 4.4 15.5 - - + +
138A MET* 6.0 0.2 - - - -
1348A P4O 3.9 44.9 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 4.2 13.7 - - + -
66A THR 3.8 22.2 - - - +
67A SER* 3.9 13.0 - - - +
68A GLN 3.3 14.1 - - - +
69A VAL* 4.6 0.9 - - - -
70A LEU* 3.7 4.0 - - - +
77A LYS* 4.1 29.2 - - + +
78A VAL* 1.3 76.8 - - - +
80A GLN* 1.3 64.0 + - - +
81A ILE* 4.5 1.8 - - + -
91A ALA* 3.4 5.5 - - - -
92A LEU* 2.8 50.9 + - + +
94A MET* 5.7 7.2 - - + -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 2.7 42.5 + - - +
68A GLN* 3.0 38.6 + - + +
70A LEU* 3.7 25.2 - - + +
79A LEU* 1.3 72.4 - - - +
81A ILE* 1.3 69.4 + - - +
82A PHE* 3.9 13.7 - - + -
89A LYS* 3.3 50.4 - - + +
90A PHE 3.6 6.3 - - - +
140A CYS* 4.3 6.9 - - - -
1348A P4O 5.3 1.6 + - - -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 4.6 4.9 - - + -
63A TYR* 3.2 37.7 - - + -
64A LYS 3.2 11.2 - - - +
65A VAL* 3.8 28.0 - - + -
79A LEU 4.4 1.3 - - - +
80A GLN* 1.3 80.0 - - - +
82A PHE* 1.3 65.7 + - - +
89A LYS* 3.4 7.3 - - - +
90A PHE* 2.8 47.8 + - + +
92A LEU* 3.9 27.1 - - + -
137A VAL* 4.1 22.4 - - + -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.1 8.6 - - - -
64A LYS* 2.8 65.2 + - + +
66A THR* 3.9 23.6 - - + -
80A GLN* 3.9 9.9 - - - -
81A ILE* 1.3 79.7 - - - +
83A ASN* 1.3 65.6 + - - +
84A LYS* 3.2 0.4 + - - -
87A GLN* 3.8 32.5 - - + +
88A GLU 3.3 5.2 - - - +
89A LYS* 3.4 35.7 - - + -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 3.6 10.7 + - - +
63A TYR* 3.6 31.2 + - + -
82A PHE* 1.3 71.2 - - - +
84A LYS* 1.3 58.8 + - - +
85A ARG* 3.1 13.9 + - - +
86A THR* 2.9 35.7 + - - -
87A GLN* 2.6 36.5 + - - +
88A GLU 2.8 17.3 + - - +
90A PHE* 4.0 18.5 - - + -
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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