Contacts of the strand formed by residues 130 - 137 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ASN* 5.5 0.2 - - - +
91F LEU* 3.9 17.0 - - + -
93F VAL* 5.8 0.9 - - + -
111F LYS* 3.4 2.8 - - - -
112F LEU* 2.8 43.1 + - + +
128F TYR* 3.7 5.7 - - - -
129F ASN* 1.3 85.8 - - + +
131F MET* 1.3 72.0 + - - +
132F PHE* 4.7 2.2 - - + -
146F VAL* 5.6 0.2 - - + -
147F ILE 3.3 11.2 - - - +
148F PHE* 3.9 27.1 - - + -
174F LEU* 4.1 21.8 - - + -
176F VAL* 5.1 4.7 - - + -
306F TYR 5.3 1.3 - - - +
308F TYR* 3.9 12.6 - - + -
311F PHE* 3.9 24.2 - - + -
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Residues in contact with MET 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F TYR* 3.6 40.4 - - + +
110F VAL 3.4 11.7 - - - +
111F LYS* 4.2 20.2 - - + -
128F TYR* 3.8 20.1 - - + -
130F ILE* 1.3 75.0 - - - +
132F PHE* 1.3 67.2 + - - +
145F HIS* 3.5 39.5 - - + +
146F VAL* 3.5 3.1 - - - -
147F ILE* 2.9 56.1 + - + +
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Residues in contact with PHE 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F VAL* 4.0 12.1 - - + -
95F PHE* 3.7 16.4 - + - -
109F TYR* 3.5 5.8 - - - -
110F VAL* 2.9 36.4 + - + +
112F LEU* 6.5 0.2 - - + -
130F ILE* 4.7 2.9 - - + -
131F MET* 1.3 78.0 - - - +
133F GLY* 1.3 64.4 + - - +
144F VAL* 3.8 21.3 - - + -
145F HIS 3.3 10.8 - - - -
146F VAL* 4.0 10.5 - - + -
172F TYR* 3.9 20.2 - + + -
173F THR 3.5 32.8 - - - -
174F LEU* 3.5 45.3 - - + -
184F VAL* 4.1 13.5 - - + -
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Residues in contact with GLY 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F PHE* 4.3 3.8 - - - -
109F TYR* 3.6 8.9 - - - +
132F PHE* 1.3 85.2 - - - +
134F PRO* 1.3 76.1 - - - +
144F VAL* 4.0 6.5 - - - -
145F HIS* 2.9 38.2 + - - +
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Residues in contact with PRO 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F PHE* 4.5 2.0 - - + -
97F VAL* 4.2 9.9 - - + -
99F HIS* 4.7 9.9 - - + +
106F GLY 5.3 0.2 - - - -
108F GLY* 2.8 55.4 + - - +
109F TYR* 3.5 4.7 - - - -
133F GLY* 1.3 85.0 - - - +
135F ASP* 1.3 55.2 + - - +
136F ILE* 5.2 1.3 - - + -
143F LYS 3.4 7.2 - - - +
144F VAL* 4.4 1.9 - - + -
163F CYS* 3.8 16.2 - - + -
164F LYS 5.2 0.9 - - - +
172F TYR* 3.7 50.0 - - + +
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Residues in contact with ASP 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F GLY* 3.5 13.7 - - - +
107F GLY* 3.6 7.4 + - - -
109F TYR* 4.0 12.5 + - + -
134F PRO* 1.3 74.6 - - - +
136F ILE* 1.3 74.4 + - - +
137F CYS* 5.4 2.5 - - - +
141F THR* 3.7 14.3 - - + +
142F LYS* 3.7 2.3 - - - -
143F LYS* 2.8 36.3 + - + +
145F HIS* 3.1 37.6 + - + +
163F CYS* 4.4 0.2 - - - -
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F HIS* 4.0 13.7 - - + +
103F ILE* 3.8 33.7 - - + +
104F ASP 3.8 15.0 - - - +
105F CYS* 3.8 0.3 - - - -
106F GLY* 2.7 40.7 + - - +
134F PRO 5.2 0.2 - - - -
135F ASP* 1.3 85.6 + - - +
137F CYS* 1.3 65.5 + - - +
138F GLY 4.4 5.4 - - - +
141F THR 3.4 10.5 - - - +
142F LYS* 4.8 6.5 - - + -
163F CYS* 3.8 12.3 - - - -
164F LYS 3.6 23.3 - - - +
165F ASP* 4.0 18.4 - - + -
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Residues in contact with CYS 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ASP 3.7 2.2 - - - -
105F CYS* 2.2 40.4 - - - -
135F ASP* 5.4 2.9 - - - +
136F ILE* 1.3 74.1 - - - +
138F GLY* 1.3 66.8 + - - +
139F PRO* 4.4 0.5 - - - +
140F GLY* 4.2 1.4 + - - -
141F THR* 3.1 35.4 + - + +
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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