Contacts of the strand formed by residues 116 - 122 (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 GLU 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A MET 3.5 8.2 + - - +
85A ILE* 2.9 26.3 + - - -
114A ASP 3.7 0.2 + - - -
115A VAL* 1.3 82.5 - - - +
117A ARG* 1.3 63.1 + - - +
147A ARG* 6.1 0.5 - - - +
166A LEU* 3.8 20.6 - - + -
169A ASP* 4.0 24.7 - - + +
170A ILE* 4.3 11.9 - - + -
173A LYS* 2.8 40.9 + - - +
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Residues in contact with ARG 117 (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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85A ILE* 3.4 5.4 - - + -
87A LEU* 3.8 16.4 - - + -
104A LEU* 3.8 30.1 + - - +
107A ILE* 3.3 42.9 - - + +
108A ASP* 3.1 30.9 + - - +
112A ASN 5.2 1.6 + - - -
113A GLU* 4.8 13.3 + - - +
115A VAL* 4.0 15.1 + - + +
116A GLU* 1.3 80.7 - - - +
118A MET* 1.3 61.3 + - - +
144A HIS* 6.2 2.1 - - - -
146A ILE* 3.1 43.2 - - + +
147A ARG* 4.1 3.1 + - - +
166A LEU* 5.1 0.7 - - - -
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Residues in contact with MET 118 (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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85A ILE 2.9 7.7 + - - +
86A MET* 3.2 31.7 - - - +
87A LEU* 2.9 27.8 + - - +
117A ARG* 1.3 74.3 - - - +
119A LEU* 1.3 63.4 + - - +
120A LEU* 4.0 8.7 - - + -
146A ILE* 4.6 0.4 - - - -
147A ARG* 3.7 31.0 - - + +
149A PHE* 3.9 16.6 - - + -
162A ALA* 3.3 20.9 - - - +
165A THR* 3.6 31.6 - - + -
166A LEU* 3.6 24.4 - - + +
169A ASP* 4.4 2.2 - - - +
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Residues in contact with LEU 119 (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 LEU* 3.5 11.0 - - + +
89A TYR* 3.9 19.1 - - + -
100A ILE* 3.7 40.8 - - + -
104A LEU* 6.5 0.2 - - + -
118A MET* 1.3 73.0 - - - +
120A LEU* 1.3 65.9 + - - +
137A GLY 3.6 17.0 - - - +
140A ILE* 3.7 17.5 - - + -
141A ALA* 4.4 4.7 - - + -
146A ILE* 4.1 14.0 - - + +
147A ARG 2.9 14.8 + - - +
148A PHE* 3.4 26.2 - - + -
149A PHE 2.9 24.9 + - - -
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Residues in contact with LEU 120 (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* 5.8 0.4 - - + -
25A VAL* 4.6 20.6 - - + -
86A MET* 3.9 34.8 - - + -
87A LEU 2.8 15.3 + - - +
88A VAL* 3.3 17.5 - - + +
89A TYR* 2.9 32.9 + - - +
118A MET* 4.0 15.3 - - + -
119A LEU* 1.3 85.6 - - - +
121A GLY* 1.3 60.0 + - - +
122A ASN 3.7 0.2 - - - -
149A PHE* 3.4 23.8 - - + +
151A THR* 4.1 19.3 - - + +
162A ALA* 4.0 12.6 - - + -
163A PHE* 5.5 0.4 - - + -
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Residues in contact with GLY 121 (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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89A TYR* 3.6 33.7 - - - -
91A ILE* 3.7 10.6 - - - +
120A LEU* 1.3 69.4 - - - +
122A ASN* 1.3 65.3 + - - +
124A CYS 4.5 0.3 + - - -
148A PHE* 3.9 2.1 - - - -
149A PHE 2.9 13.0 + - - -
150A GLU* 3.3 7.4 - - - +
151A THR 2.9 23.4 + - - +
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Residues in contact with ASN 122 (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 2.9 29.1 + - - +
21A GLY* 3.5 7.9 - - - -
25A VAL* 3.7 17.4 - - - +
88A VAL* 4.1 9.2 - - + -
89A TYR 2.9 14.1 + - - +
90A ASP* 3.8 0.7 - - - +
91A ILE* 3.2 25.5 + - - +
120A LEU 3.7 1.2 + - - -
121A GLY* 1.3 71.1 - - - +
123A LYS* 1.3 77.7 + - - +
151A THR* 3.1 24.0 + - - +
153A ALA 3.4 9.2 + - - -
202A GNP 3.2 31.7 + - - +
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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