Contacts of the strand formed by residues 130 - 137 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.9 28.0 - - + -
93C VAL* 5.8 1.1 - - + -
111C LYS* 3.4 2.8 - - - -
112C LEU* 2.8 45.4 + - + +
128C TYR* 3.7 6.1 - - - -
129C ASN* 1.3 86.2 - - + +
131C MET* 1.3 72.6 + - - +
132C PHE* 4.6 2.0 - - + +
146C VAL* 5.5 0.4 - - + -
147C ILE 3.3 11.0 - - - +
148C PHE* 3.9 26.9 - - + -
174C LEU* 4.1 21.8 - - + -
176C VAL* 5.0 4.5 - - + -
306C TYR 5.3 1.6 - - - +
308C TYR* 3.9 12.3 - - + -
311C PHE* 3.9 13.9 - - + -
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Residues in contact with MET 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TYR* 3.6 39.3 - - + -
110C VAL 3.4 12.3 - - - +
111C LYS* 4.1 20.6 - - + +
128C TYR* 3.8 19.7 - - + -
130C ILE* 1.3 76.9 - - - +
132C PHE* 1.3 66.1 + - - +
145C HIS* 3.5 41.5 - - + +
146C VAL* 3.5 3.6 - - - -
147C ILE* 2.8 56.7 + - + +
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C VAL* 3.9 11.9 - - + -
95C PHE* 3.6 16.2 - + - -
109C TYR* 3.4 5.1 - - - -
110C VAL* 2.9 39.4 + - + +
130C ILE* 4.7 2.9 - - + -
131C MET* 1.3 77.1 - - - +
133C GLY* 1.3 61.2 + - - +
144C VAL* 3.7 22.2 - - + -
145C HIS 3.3 10.8 - - - -
146C VAL* 4.1 10.8 - - + -
172C TYR* 3.9 19.7 - + + -
173C THR 3.5 32.8 - - - -
174C LEU* 3.4 46.9 - - + -
184C VAL* 4.0 14.4 - - + -
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Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PHE* 4.2 4.3 - - - -
109C TYR* 3.6 9.2 - - - +
132C PHE* 1.3 80.9 - - - +
134C PRO* 1.3 76.7 - - - +
144C VAL* 4.0 9.9 - - - -
145C HIS* 2.9 37.5 + - - +
172C TYR* 5.1 0.2 - - - -
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Residues in contact with PRO 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PHE* 4.4 2.2 - - + -
97C VAL* 4.2 10.1 - - + -
99C HIS* 4.7 9.6 - - + +
108C GLY* 2.8 55.1 + - - +
109C TYR* 3.5 4.9 - - - -
133C GLY* 1.3 84.8 - - - +
135C ASP* 1.3 54.6 + - - +
136C ILE* 5.2 1.6 - - + -
143C LYS 3.4 7.4 - - - +
144C VAL* 4.4 1.8 - - + -
163C CYS* 3.8 15.7 - - + -
164C LYS 5.2 0.7 - - - +
172C TYR* 3.7 50.7 - - + +
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Residues in contact with ASP 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLY 3.6 5.3 - - - +
107C GLY* 3.5 15.9 + - - -
109C TYR* 4.0 12.5 + - + -
134C PRO* 1.3 74.2 - - - +
136C ILE* 1.3 75.4 + - - +
137C CYS* 5.4 2.1 - - - +
141C THR* 3.7 12.8 - - + +
142C LYS* 3.7 2.1 - - - -
143C LYS* 2.8 37.1 + - + +
145C HIS* 3.1 36.1 + - + +
163C CYS* 4.4 0.4 - - - -
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 4.2 12.6 - - + +
103C ILE* 3.9 32.5 - - + +
104C ASP 3.8 14.8 - - - +
105C CYS* 3.8 0.5 - - - -
106C GLY* 2.7 41.1 + - - +
134C PRO 5.2 0.7 - - - -
135C ASP* 1.3 83.3 + - - +
137C CYS* 1.3 64.8 + - - +
138C GLY 4.4 6.1 - - - +
141C THR* 3.3 10.1 - - - +
142C LYS* 4.2 9.4 - - + -
163C CYS* 3.5 26.9 - - - -
164C LYS 3.6 13.7 - - - +
165C ASP* 4.0 18.6 - - + -
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Residues in contact with CYS 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ASP 3.7 2.7 - - - -
105C CYS* 2.2 39.7 - - - -
135C ASP* 5.4 2.5 - - - +
136C ILE* 1.3 74.1 - - - +
138C GLY* 1.3 65.2 + - - +
140C GLY* 4.2 1.2 + - - -
141C THR* 3.1 35.9 + - + +
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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