Contacts of the strand formed by residues 81 - 89 (chain A) in PDB entry 5LJC
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 LYS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.3 30.9 + - + +
72A GLU 3.2 9.9 - - - +
73A ASP* 4.0 26.1 + - - +
75A THR* 5.8 1.0 - - - +
79A ASP 5.5 1.1 - - - +
80A ARG* 1.3 81.2 - - - +
82A CYS* 1.3 66.6 + - - +
98A LYS 4.4 1.4 - - - +
99A GLY* 4.7 5.9 - - - -
100A GLU 5.4 0.9 + - - -
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Residues in contact with CYS 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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70A PHE 3.6 0.3 - - - +
71A GLU* 3.5 6.6 - - - +
72A GLU* 2.8 33.3 + - - +
74A LEU* 3.6 25.3 - - + +
80A ARG* 5.2 2.2 - - - -
81A LYS* 1.3 79.4 - - - +
83A MET* 1.3 62.5 + - - +
84A THR* 3.4 17.0 - - - +
97A GLN* 4.0 20.9 - - + -
98A LYS 3.1 16.2 - - - +
99A GLY* 4.6 4.0 - - - -
100A GLU 5.5 1.3 - - - -
104A ARG* 4.0 18.2 - - - -
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Residues in contact with MET 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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69A GLU* 3.3 42.2 - - + +
70A PHE 3.7 4.9 - - - +
71A GLU* 5.6 4.5 - - + -
82A CYS* 1.3 71.4 - - - +
84A THR* 1.3 59.3 + - - +
85A THR* 4.2 0.3 + - - -
96A VAL 3.7 1.4 - - - +
98A LYS* 2.8 49.4 + - + +
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Residues in contact with THR 84 (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 MET* 4.7 0.4 - - + -
69A GLU* 3.2 2.4 - - - +
70A PHE* 2.8 65.9 + - + -
72A GLU* 2.7 35.0 + - - +
82A CYS* 3.4 17.2 - - - +
83A MET* 1.3 70.5 - - - +
85A THR* 1.3 66.9 + - - +
86A VAL* 4.6 0.4 - - + -
95A CYS* 3.5 28.3 - - - -
96A VAL 3.3 4.5 - - - +
97A GLN* 3.6 4.8 - - + +
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Residues in contact with THR 85 (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 GLY 4.1 22.4 - - - +
68A LYS 4.4 1.3 - - - -
69A GLU* 3.3 31.0 + - - +
83A MET 4.2 0.7 + - - -
84A THR* 1.3 76.0 - - - +
86A VAL* 1.3 68.5 + - - +
87A SER* 3.9 18.5 + - - +
94A GLN 3.6 1.9 - - - +
95A CYS* 3.3 1.4 - - - -
96A VAL* 2.9 37.4 + - - +
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Residues in contact with VAL 86 (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 MET* 4.4 2.0 - - + -
64A PHE* 3.7 46.0 - - + -
65A GLN 5.5 0.4 + - - -
66A VAL* 3.5 2.7 - - + +
67A GLY* 2.7 33.6 + - - +
68A LYS 5.2 1.6 + - - -
70A PHE* 4.4 11.6 - - + -
85A THR* 1.3 76.4 - - - +
87A SER* 1.3 59.5 + - - +
93A LEU* 4.0 30.5 - - + -
94A GLN 3.3 8.7 - - - +
95A CYS* 3.9 19.1 - - + +
106A TRP* 4.0 16.2 - - + -
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Residues in contact with SER 87 (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 VAL* 3.9 7.0 - - - -
67A GLY* 4.5 5.5 - - - +
85A THR* 3.9 15.8 + - - +
86A VAL* 1.3 76.2 + - - +
88A TRP* 1.3 67.5 + - - +
93A LEU* 3.6 4.4 - - - -
94A GLN* 2.8 41.2 + - - +
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Residues in contact with TRP 88 (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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1A PRO* 3.6 37.6 - - + +
2A VAL 4.1 1.6 - - - -
4A PHE* 3.9 21.1 - + - -
44A GLN* 4.0 21.5 - - - -
46A GLY 4.5 1.3 - - - -
47A ASP* 2.8 30.5 + - - -
49A MET* 5.4 0.2 - - - -
66A VAL* 3.4 26.9 - - + +
87A SER* 1.3 78.2 - - - +
89A ASP* 1.3 61.3 + - - +
90A GLY 3.5 18.2 - - - +
91A ASP 4.0 9.6 - - - -
92A LYS 3.5 15.7 - - - -
93A LEU* 3.4 30.3 - - + -
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Residues in contact with ASP 89 (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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87A SER 3.6 0.2 + - - -
88A TRP* 1.3 74.4 - - - +
90A GLY* 1.3 63.2 + - - +
91A ASP 3.2 0.7 + - - -
92A LYS* 2.8 37.8 + - + +
94A GLN* 3.1 42.6 + - + +
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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