Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 5LPN
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 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS 3.1 5.1 + - - +
12A LEU* 3.1 21.4 - - - +
13A LEU* 2.9 24.1 + - - +
82A ALA* 3.5 0.9 - - - +
83A MET* 1.3 80.2 - - - +
85A ILE* 1.3 65.1 + - - +
115A VAL* 3.8 0.4 - - - -
116A GLU 3.4 8.3 - - - -
166A LEU* 4.0 9.4 - - - +
170A ILE* 3.6 6.3 - - - +
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Residues in contact with ILE 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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13A LEU* 3.1 27.4 - - + +
15A ILE* 3.8 36.1 - - + -
79A TYR* 4.5 4.7 - - + -
82A ALA* 4.2 12.3 - - + -
84A GLY* 1.3 77.8 - - - +
86A MET* 1.3 65.4 + - - +
87A LEU* 3.8 1.2 + - - +
107A ILE* 3.8 31.6 - - + -
111A ALA* 4.2 19.5 - - + -
115A VAL* 4.0 14.4 - - + -
116A GLU 2.9 9.8 + - - +
117A ARG* 3.4 4.1 - - - -
118A MET* 2.9 26.3 + - - +
166A LEU* 4.2 2.7 - - - +
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Residues in contact with MET 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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12A LEU* 6.2 0.4 - - + -
13A LEU 2.9 9.0 + - - +
14A LEU* 3.5 27.5 - - + -
15A ILE 2.9 27.7 + - - +
85A ILE* 1.3 73.0 - - - +
87A LEU* 1.3 59.8 + - - +
88A VAL* 3.6 4.8 - - + +
118A MET* 3.2 34.3 - - - +
120A LEU* 3.9 23.6 - - + -
162A ALA* 3.9 11.2 - - + +
163A PHE* 3.5 55.2 - - + +
166A LEU* 3.7 20.9 - - + -
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Residues in contact with LEU 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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15A ILE* 3.5 12.1 - - + +
85A ILE 4.2 3.1 - - - +
86A MET* 1.3 73.2 - - - +
88A VAL* 1.3 60.8 + - - +
100A ILE* 4.1 18.4 - - + +
103A TRP* 3.8 13.7 - - + -
104A LEU* 3.5 50.0 - - + +
107A ILE* 3.6 25.4 - - + -
117A ARG* 3.8 22.4 - - + -
118A MET 2.9 14.9 + - - +
119A LEU* 3.5 9.0 - - + +
120A LEU* 2.8 27.0 + - - +
146A ILE* 5.0 2.7 - - + -
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Residues in contact with VAL 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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14A LEU* 4.8 4.7 - - + -
15A ILE 2.9 16.4 + - - +
16A GLY* 3.4 19.4 - - - -
17A ASP 4.2 2.1 + - - -
20A VAL* 3.6 25.3 - - + +
22A LYS* 4.0 17.0 - - + +
25A VAL* 5.1 7.6 - - + -
86A MET* 3.6 18.2 - - + +
87A LEU* 1.3 79.6 - - - +
89A TYR* 1.3 69.4 + - - +
96A SER* 5.1 1.2 - - - +
100A ILE* 4.3 5.8 - - - +
103A TRP* 5.2 0.7 - - - -
120A LEU* 3.3 24.7 - - + +
122A ASN* 4.1 14.6 - - + -
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Residues in contact with TYR 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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20A VAL* 3.7 6.0 - - - +
88A VAL* 1.3 74.8 - - - +
90A ASP* 1.3 68.4 + - - +
91A ILE* 4.4 9.7 - - + +
96A SER* 3.7 31.2 - - - +
97A PHE* 3.4 40.3 - + + +
100A ILE* 4.1 4.0 - - + -
119A LEU* 3.9 30.3 - - + -
120A LEU 2.9 15.2 + - - +
121A GLY* 3.6 22.6 - - - -
122A ASN* 2.9 30.3 + - - +
132A VAL* 4.2 15.0 - - + +
133A PRO 5.0 1.4 + - - -
134A LYS* 5.5 0.5 - - - -
137A GLY* 3.6 11.1 + - - -
148A PHE* 3.2 26.2 - + - -
150A GLU* 5.2 1.0 + - - +
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Residues in contact with ASP 90 (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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19A GLY 4.1 2.3 - - - +
20A VAL* 3.9 15.3 - - + -
89A TYR* 1.3 81.6 - - - +
91A ILE* 1.3 66.5 + - - +
92A THR* 3.0 28.2 + - - +
93A ASN* 2.8 39.3 + - + +
96A SER* 3.0 12.9 + - - +
122A ASN 3.8 4.1 - - - +
123A LYS* 2.6 47.8 + - - +
132A VAL* 4.3 0.7 - - - +
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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