Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 5LK5
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 ILE 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASN* 5.6 0.2 - - - +
91A LEU* 3.9 27.8 - - + -
93A VAL* 5.7 0.9 - - + -
111A LYS* 3.4 2.6 - - - -
112A LEU* 2.8 46.0 + - + +
128A TYR* 3.7 5.7 - - - -
129A ASN* 1.3 87.0 - - + +
131A MET* 1.3 71.0 + - - +
132A PHE* 4.4 2.5 - - + +
146A VAL* 5.5 0.4 - - + -
147A ILE 3.3 11.2 - - - +
148A PHE* 4.0 26.7 - - + -
174A LEU* 4.1 22.0 - - + -
176A VAL* 5.1 5.2 - - + -
306A TYR 5.3 1.1 - - - +
308A TYR* 3.8 12.8 - - + -
311A PHE* 3.9 14.8 - - + -
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Residues in contact with MET 131 (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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109A TYR* 3.6 39.0 - - + -
110A VAL 3.4 12.6 - - - +
111A LYS* 4.1 20.9 - - + +
128A TYR* 3.8 19.6 - - + -
130A ILE* 1.3 75.6 - - - +
132A PHE* 1.3 67.6 + - - +
145A HIS* 3.5 41.1 - - + +
146A VAL* 3.5 3.6 + - - -
147A ILE* 2.9 55.5 + - + +
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Residues in contact with PHE 132 (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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93A VAL* 3.9 13.5 - - + -
95A PHE* 3.6 16.1 - + - -
109A TYR* 3.4 4.8 - - - -
110A VAL* 2.9 38.3 + - + +
130A ILE* 4.7 2.9 - - + -
131A MET* 1.3 78.2 - - - +
133A GLY* 1.3 64.0 + - - +
144A VAL* 3.7 21.8 - - + -
145A HIS 3.3 10.8 - - - -
146A VAL* 4.0 11.2 - - + -
172A TYR* 3.9 20.9 - + + -
173A THR 3.5 32.5 - - - -
174A LEU* 3.5 45.1 - - + -
184A VAL* 4.0 13.7 - - + -
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Residues in contact with GLY 133 (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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95A PHE* 4.3 3.8 - - - -
109A TYR* 3.6 8.7 - - - +
132A PHE* 1.3 82.4 - - - +
134A PRO* 1.3 76.1 - - - +
144A VAL* 4.0 10.8 - - - -
145A HIS* 2.9 37.8 + - - +
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.5 1.8 - - + -
97A VAL* 4.2 9.6 - - + -
99A HIS* 4.7 9.9 - - + +
106A GLY 5.2 0.2 - - - -
108A GLY* 2.8 55.7 + - - +
109A TYR* 3.5 4.9 - - - -
133A GLY* 1.3 84.9 - - - +
135A ASP* 1.3 56.6 + - - +
136A ILE* 5.2 1.1 - - + -
143A LYS 3.4 6.7 - - - +
144A VAL* 4.4 1.3 - - + -
163A CYS* 3.8 14.8 - - + -
164A LYS 5.2 0.7 - - - +
172A TYR* 3.7 50.7 - - + +
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Residues in contact with ASP 135 (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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106A GLY 3.6 5.4 - - - +
107A GLY* 3.6 16.6 + - - -
109A TYR* 4.0 12.8 + - + -
134A PRO* 1.3 74.5 - - - +
136A ILE* 1.3 73.0 + - - +
137A CYS* 5.4 2.0 - - - +
141A THR* 3.7 12.7 - - + +
142A LYS* 3.7 2.3 - - - -
143A LYS* 2.8 37.0 + - + +
145A HIS* 3.1 38.3 + - + +
163A CYS* 4.4 0.4 - - - -
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Residues in contact with ILE 136 (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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99A HIS* 4.0 13.9 - - + +
103A ILE* 3.8 33.4 - - + +
104A ASP 3.8 14.6 - - - +
105A CYS* 3.8 0.2 - - - -
106A GLY 2.7 41.2 + - - +
134A PRO 5.2 0.4 - - - -
135A ASP* 1.3 85.0 + - - +
137A CYS* 1.3 65.1 + - - +
138A GLY 4.5 0.4 - - - +
141A THR* 3.3 10.1 - - - +
142A LYS* 3.9 15.9 - - + -
163A CYS* 3.8 12.3 - - - -
164A LYS 3.6 24.0 - - - +
165A ASP* 4.0 17.0 - - + -
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Residues in contact with CYS 137 (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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104A ASP 3.7 2.5 - - - -
105A CYS* 2.2 41.1 - - - -
135A ASP* 5.4 2.9 - - - +
136A ILE* 1.3 75.1 - - - +
138A GLY* 1.3 66.2 + - - +
139A PRO* 4.4 0.5 - - - +
140A GLY* 4.2 1.4 + - - -
141A THR* 3.0 36.4 + - + +
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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