Contacts of the strand formed by residues 116 - 122 (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 VAL 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.9 25.4 - - - +
50A PHE* 4.2 9.6 - - + -
53A ASN* 3.8 25.4 - - - +
56A VAL* 5.5 1.3 - - + -
103B ILE 3.7 0.5 - - - +
104B TYR* 3.3 1.7 - - - -
105B LEU* 2.9 41.6 + - + +
106B VAL* 3.0 26.6 + - + +
114B HIS 4.0 4.3 - - - +
115B ASN* 1.3 78.1 - - - +
117B ALA* 1.3 59.6 + - - +
118B TYR* 3.9 23.6 - - + -
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Residues in contact with ALA 117 (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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21A ARG* 3.4 11.6 - - - +
22A LEU* 3.0 39.5 + - + +
102B VAL* 3.7 14.8 - - + -
103B ILE 3.1 4.0 - - - -
104B TYR* 3.6 29.8 - - + +
115B ASN* 3.9 3.4 + - + -
116B VAL* 1.3 75.4 - - - +
118B TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 118 (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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19A LEU* 4.0 21.5 - - + -
20A LEU 3.3 11.0 - - - -
21A ARG* 3.4 54.5 + - + +
28A GLU* 5.3 1.0 + - - -
31A VAL* 4.7 14.9 - - + +
40A ILE* 6.5 0.4 - - + -
48A LEU* 4.0 21.5 - - + +
50A PHE* 3.2 38.6 - + - -
102B VAL* 3.3 3.8 - - - -
103B ILE* 2.6 51.8 + - + +
105B LEU* 4.1 14.4 - - + -
116B VAL* 3.9 8.7 - - + -
117B ALA* 1.3 78.2 - - - +
119B LEU* 1.3 61.7 + - - +
120B TYR 3.6 1.4 + - - -
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Residues in contact with LEU 119 (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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18A ARG 3.6 0.5 - - - +
19A LEU* 3.2 7.2 - - - -
20A LEU* 2.9 40.8 + - + +
22A LEU* 3.9 28.2 - - + +
30A HIS* 6.3 0.7 - - + -
100B GLY* 3.3 37.0 - - - +
101B ASP 3.6 7.0 - - - +
102B VAL* 3.8 12.6 - - + -
118B TYR* 1.3 72.0 - - - +
120B TYR* 1.3 62.3 + - - +
121B GLU* 4.0 25.0 - - + +
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Residues in contact with TYR 120 (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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16A TRP* 3.8 20.9 - + - -
17A GLY* 4.4 1.3 - - - -
18A ARG 3.5 8.7 - - - -
19A LEU* 3.6 17.7 - - + -
33A LEU* 4.1 9.4 - - + -
63A ILE* 5.3 0.7 - - + -
72A VAL* 3.4 30.6 - - + +
97B LEU* 3.9 37.9 - - + -
98B GLN 3.5 28.7 - - - -
99B THR* 3.9 2.5 - - - -
100B GLY* 2.9 27.0 + - - -
101B ASP 2.9 14.2 + - - +
103B ILE* 4.8 3.6 - - + -
118B TYR 3.6 1.0 + - - -
119B LEU* 1.3 71.7 - - - +
121B GLU* 1.3 77.2 + - - +
122B SER* 3.4 32.4 - - - -
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Residues in contact with GLU 121 (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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17A GLY* 3.2 0.3 - - - -
18A ARG* 2.7 81.4 + - + +
30A HIS* 4.6 5.2 - - - -
99B THR* 4.0 21.9 - - + +
100B GLY* 4.6 1.5 + - - +
119B LEU* 4.0 27.5 - - + +
120B TYR* 1.3 86.2 - - - +
122B SER* 1.3 65.3 + - - +
123B LEU* 6.0 0.2 - - + -
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Residues in contact with SER 122 (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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16A TRP* 3.5 9.9 - - - -
72A VAL* 5.6 2.5 - - - -
99B THR* 2.9 22.5 + - - +
120B TYR* 3.4 21.4 - - - -
121B GLU* 1.3 78.0 - - - +
123B LEU* 1.3 65.2 + - - +
124B SER* 4.2 16.8 + - - +
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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