Contacts of the strand formed by residues 141 - 150 (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 THR 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ASP* 3.8 20.4 - - - +
136C ILE* 3.3 5.1 - - - +
137C CYS* 3.1 46.5 + - + +
138C GLY 3.5 4.0 - - - +
139C PRO 3.5 0.2 - - - -
140C GLY* 1.3 76.9 + - - +
142C LYS* 1.3 67.9 + - - +
143C LYS* 4.2 19.1 - - + -
145C HIS* 6.3 0.2 - - - +
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Residues in contact with LYS 142 (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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135C ASP 3.7 1.1 - - - -
136C ILE* 4.2 13.0 - - + +
138C GLY 3.5 20.2 - - - -
139C PRO* 3.4 27.9 + - - +
140C GLY 4.1 2.0 + - - -
141C THR* 1.3 73.6 - - - +
143C LYS* 1.3 59.5 + - - +
162C ARG* 3.2 27.0 - - + +
163C CYS* 3.1 35.0 + - - +
165C ASP* 2.9 43.1 + - + +
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Residues in contact with LYS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PRO* 3.4 2.6 - - - +
135C ASP 2.8 37.9 + - - +
141C THR* 4.2 17.0 - - + -
142C LYS* 1.3 75.9 - - - +
144C VAL* 1.3 71.5 + - - +
145C HIS* 3.3 41.3 + - + +
146C VAL 5.7 0.2 - - - +
156C LEU* 4.6 11.5 - - - +
157C ILE* 4.0 27.7 + - - +
159C LYS 4.8 4.8 + - - -
160C ASP* 5.8 5.8 - - - +
161C ILE 3.2 8.5 - - - +
162C ARG* 6.3 0.2 - - - +
163C CYS* 3.5 2.9 - - - +
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C PHE* 3.7 30.5 - - + -
133C GLY* 3.6 12.8 - - - +
134C PRO* 4.5 0.7 - - + -
143C LYS* 1.3 80.4 - - - +
145C HIS* 1.3 66.4 + - - +
146C VAL* 3.6 4.3 + - + +
157C ILE* 4.3 4.9 - - - +
159C LYS 5.3 0.3 - - - +
161C ILE* 2.8 51.0 + - + +
162C ARG 3.9 0.9 - - - +
163C CYS* 3.7 27.6 - - + -
172C TYR* 4.0 15.7 - - + -
184C VAL* 4.5 8.3 - - + -
186C ILE* 4.2 3.1 - - + -
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Residues in contact with HIS 145 (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* 4.2 3.6 - + - -
131C MET* 3.5 35.2 - - + +
132C PHE* 3.3 6.4 - - - -
133C GLY 2.9 32.7 + - - +
135C ASP* 3.1 43.1 + - + +
143C LYS* 3.3 32.3 + - + +
144C VAL* 1.3 73.2 - - - +
146C VAL* 1.3 66.2 + - - +
147C ILE* 4.1 15.3 - - + +
156C LEU* 4.4 15.0 - - + +
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Residues in contact with VAL 146 (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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130C ILE* 5.5 0.4 - - + -
131C MET 3.5 3.6 - - - +
132C PHE* 4.1 7.6 - - + -
144C VAL* 3.6 9.4 + - + +
145C HIS* 1.3 79.2 - - - +
147C ILE* 1.3 62.3 + - - +
148C PHE* 4.0 10.1 - - + -
157C ILE* 3.1 41.9 + - + +
161C ILE* 4.4 3.4 - - + -
174C LEU* 3.9 28.5 - - + -
182C TYR* 5.4 0.2 - - + -
184C VAL* 4.1 24.0 - - + -
200C TRP* 3.1 33.1 + - + -
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Residues in contact with ILE 147 (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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128C TYR* 3.5 22.4 - - + +
130C ILE* 3.3 11.4 - - - +
131C MET* 2.8 72.8 + - + +
145C HIS* 4.1 10.5 - - + +
146C VAL* 1.3 82.7 - - - +
148C PHE* 1.3 64.8 + - - +
154C ASN* 3.8 9.2 - - + +
155C VAL 3.3 24.7 - - - +
156C LEU* 4.0 26.7 - - + -
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Residues in contact with PHE 148 (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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129C ASN 3.8 1.1 - - - -
130C ILE* 3.9 27.6 - - + -
146C VAL* 4.0 11.0 - - + -
147C ILE* 1.3 79.8 - - - +
149C ASN* 1.3 57.8 + - - +
153C LYS 3.6 0.3 - - - +
155C VAL* 2.8 41.9 + - - +
174C LEU* 5.1 0.4 - - + -
176C VAL* 3.9 30.5 - - + -
182C TYR* 5.8 0.4 - - + -
196C LEU* 3.9 24.2 - - + -
200C TRP* 3.6 41.1 - + - -
202C PHE* 3.9 26.7 - + + -
305C ILE* 4.7 3.6 - - + -
306C TYR 4.6 2.9 - - - -
308C TYR* 3.6 23.3 - + - +
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Residues in contact with ASN 149 (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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127C GLU* 4.3 21.6 - - - +
128C TYR* 3.1 27.7 - - + +
129C ASN* 2.9 17.6 + - - +
147C ILE* 5.0 0.2 - - - +
148C PHE* 1.3 72.5 - - - +
150C TYR* 1.3 62.7 + - - +
151C LYS 5.2 0.2 + - - -
152C GLY* 4.0 10.2 + - - -
153C LYS 3.0 27.4 + - - +
154C ASN* 3.1 19.3 + - - +
308C TYR* 2.6 30.1 + - - -
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Residues in contact with TYR 150 (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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148C PHE 3.7 0.6 + - - -
149C ASN* 1.3 78.2 - - - +
151C LYS* 1.3 109.7 + - + +
152C GLY 3.2 1.6 - - - -
153C LYS* 2.8 26.3 + - - +
155C VAL* 4.5 5.2 - - + +
202C PHE* 3.7 57.9 - + + -
203C LEU* 4.1 15.6 - - + +
302C ASP* 2.6 36.4 + - - +
304C SER* 5.8 0.2 - - - -
305C ILE* 4.0 27.8 - - + -
308C TYR* 5.2 0.2 - - - +
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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