Contacts of the strand formed by residues 82 - 90 (chain B) in PDB entry 1LGQ
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 4.6 0.6 - - - +
90A VAL* 2.6 45.7 + - - +
103A ILE* 4.0 19.3 - - + -
104A TYR 3.8 11.4 - - - +
105A LEU* 5.0 0.9 - - - -
60B HIS* 3.1 20.4 + - + -
61B CYS* 4.0 9.6 - - - +
74B LEU* 4.2 19.3 - - + -
76B ASP* 2.8 24.2 + - - -
81B GLY* 1.3 71.2 - - - -
83B VAL* 1.3 71.8 + - - +
84B ILE* 4.4 3.1 - - + -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.8 28.9 - - + -
88A LYS 3.2 11.7 - - - +
89A VAL* 4.4 20.6 - - + -
104A TYR* 2.8 56.5 + - + +
107A TYR* 3.8 28.3 - - + -
81B GLY 5.7 0.9 - - - -
82B THR* 1.3 76.9 - - - +
84B ILE* 1.3 68.6 + - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS 3.5 0.9 - - - +
88A LYS* 2.8 41.8 + - + +
90A VAL* 3.6 27.6 - - + -
95A CYS* 4.5 13.0 - - + -
96A PRO 5.2 1.6 - - - +
97A LEU* 4.6 4.5 - - + -
101A ASP* 4.2 17.9 - - + +
102A VAL 3.3 10.3 - - - +
103A ILE* 3.5 26.7 - - + -
74B LEU* 4.3 20.0 - - + -
82B THR* 4.4 4.7 - - + -
83B VAL* 1.3 84.0 - - - +
85B ASN* 1.3 71.0 + - - +
86B LYS* 3.6 11.2 + - + +
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Residues in contact with ASN 85 (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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85A ASN* 3.0 38.7 + - - -
86A LYS 3.2 4.4 - - - +
87A LEU* 3.2 19.8 - - + +
100A GLY 4.6 1.6 + - - +
101A ASP* 3.4 8.7 - - - +
102A VAL* 2.9 40.9 + - + +
104A TYR* 4.0 24.2 - - + +
83B VAL 4.4 0.2 - - - -
84B ILE* 1.3 72.4 - - - +
86B LYS* 1.3 61.0 + - - +
87B LEU* 4.1 9.5 - - - +
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE 3.5 2.1 - - - +
85A ASN* 3.4 1.3 - - - -
86A LYS* 2.6 51.4 + - + +
88A LYS* 5.0 11.4 - - + +
95A CYS* 4.7 12.8 - - - -
96A PRO* 3.2 27.3 + - - +
98A GLN* 3.7 18.5 + - + +
101A ASP* 2.5 37.4 + - - +
84B ILE* 3.6 12.7 + - + +
85B ASN* 1.3 77.3 - - - +
87B LEU* 1.3 76.3 + - - +
88B LYS* 3.8 9.3 + - + +
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Residues in contact with LEU 87 (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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83A VAL* 4.4 14.1 - - + -
84A ILE 3.5 4.5 - - - -
85A ASN* 3.2 26.2 - - + +
100A GLY* 5.3 13.7 - - - +
101A ASP* 4.3 4.8 + - - +
85B ASN* 4.1 9.2 - - - +
86B LYS* 1.3 80.5 - - - +
88B LYS* 1.3 60.9 + - - +
89B VAL* 4.2 5.1 + - + +
104B TYR* 6.2 2.2 - - + -
107B TYR* 3.3 40.4 - - + +
109B LYS* 5.9 1.6 - - - -
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Residues in contact with LYS 88 (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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82A THR 3.8 0.5 - - - +
83A VAL* 3.3 6.1 - - - +
84A ILE* 2.8 46.1 + - + +
86A LYS* 5.5 11.2 - - + +
86B LYS* 3.8 12.3 + - + +
87B LEU* 1.3 74.6 - - - +
89B VAL* 1.3 70.1 + - - +
90B VAL* 4.0 3.8 - - + +
93B GLN* 4.8 15.3 - - - +
94B THR 5.3 1.2 + - - -
95B CYS* 3.1 36.6 - - - +
96B PRO* 4.5 8.1 - - - +
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Residues in contact with VAL 89 (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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80A SER 5.2 0.9 - - - +
81A GLY* 5.2 1.1 - - - -
82A THR 3.7 8.3 - - - +
83A VAL* 4.5 17.0 - - + +
87B LEU* 4.9 4.3 - - + +
88B LYS* 1.3 83.3 - - - +
90B VAL* 1.3 63.7 + - - +
91B LYS* 3.5 39.4 + - + +
93B GLN* 4.4 9.0 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.3 4.9 - - + +
76A ASP* 3.1 18.6 - - + +
82A THR* 2.7 45.9 + - - +
84A ILE* 3.8 29.2 - - + -
88B LYS* 4.6 8.5 - - + +
89B VAL* 1.3 74.5 - - - +
91B LYS* 1.3 60.7 + - - +
93B GLN* 3.2 42.2 - - + +
95B CYS* 3.9 24.9 - - + -
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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