Contacts of the strand formed by residues 141 - 150 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135G ASP* 3.8 21.1 - - - +
136G ILE* 3.3 4.7 - - - -
137G CYS* 3.0 45.9 + - + +
138G GLY 3.6 6.6 - - - +
139G PRO 3.5 0.2 - - - -
140G GLY* 1.3 76.9 + - - +
142G LYS* 1.3 66.5 + - - +
143G LYS* 4.1 22.2 - - + -
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Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 4.3 3.4 - - - +
165E ASP* 3.3 18.4 + - - -
135G ASP 3.7 0.9 - - - -
136G ILE* 4.2 12.8 - - + -
138G GLY 3.6 18.6 - - - +
139G PRO* 3.8 19.1 + - - +
140G GLY 4.1 2.0 + - - -
141G THR* 1.3 79.4 - - - +
143G LYS* 1.3 59.7 + - - +
160G ASP* 5.4 1.4 - - - +
161G ILE 3.7 0.2 - - - +
162G ARG* 3.2 49.4 + - - +
163G CYS* 3.1 34.2 + - - +
165G ASP* 3.0 42.6 + - + -
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Residues in contact with LYS 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E ARG* 5.7 7.1 - - - +
134G PRO* 3.4 2.6 - - - +
135G ASP* 2.8 36.2 + - + +
141G THR* 4.1 19.3 - - + -
142G LYS* 1.3 76.1 - - - +
144G VAL* 1.3 72.8 + - - +
145G HIS* 3.5 40.7 + - + +
156G LEU* 5.0 9.4 - - - +
157G ILE* 4.4 18.8 + - - +
159G LYS 4.8 7.7 + - - -
160G ASP* 4.9 13.2 + - - +
161G ILE 3.2 7.4 - - - +
163G CYS* 3.5 3.5 - - - +
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Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G PHE* 3.8 30.7 - - + -
133G GLY* 3.6 12.3 - - - +
134G PRO* 4.5 0.4 - - + -
143G LYS* 1.3 77.9 - - - +
145G HIS* 1.3 67.4 + - - +
146G VAL* 3.7 4.5 + - + +
157G ILE* 4.3 6.8 - - - +
159G LYS 5.3 0.5 - - - +
161G ILE* 2.8 51.2 + - + +
162G ARG 3.9 1.1 - - - +
163G CYS* 3.7 27.6 - - + -
172G TYR* 4.0 15.9 - - + -
184G VAL* 4.5 8.5 - - + -
186G ILE* 4.2 3.1 - - + -
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Residues in contact with HIS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TYR* 4.2 3.4 - + - -
131G MET* 3.5 35.3 - - + +
132G PHE* 3.3 7.1 - - - -
133G GLY 2.9 32.5 + - - +
135G ASP* 3.1 43.6 + - + +
143G LYS* 3.5 29.5 + - + +
144G VAL* 1.3 72.0 - - - +
146G VAL* 1.3 65.2 + - - +
147G ILE* 4.1 15.5 - - + +
156G LEU* 4.4 16.9 - - + +
157G ILE* 5.2 0.4 - - - -
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Residues in contact with VAL 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ILE* 5.5 0.4 - - + -
131G MET 3.5 3.8 - - - +
132G PHE* 4.0 7.6 - - + -
144G VAL* 3.7 8.1 + - + +
145G HIS* 1.3 79.6 + - - +
147G ILE* 1.3 63.0 - - - +
148G PHE* 4.1 10.3 - - + -
157G ILE* 3.1 41.6 + - + +
161G ILE* 4.4 3.4 - - + -
174G LEU* 3.9 29.2 - - + -
182G TYR* 5.4 0.2 - - + -
184G VAL* 4.0 24.5 - - + -
200G TRP* 3.1 32.6 + - + -
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Residues in contact with ILE 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G TYR* 3.5 22.6 - - + +
130G ILE* 3.3 11.6 - - - +
131G MET* 2.9 74.1 + - + +
145G HIS* 4.1 10.8 - - + +
146G VAL* 1.3 82.1 - - - +
148G PHE* 1.3 65.4 + - - +
154G ASN* 3.8 9.9 - - + +
155G VAL 3.3 24.2 - - - +
156G LEU* 4.0 25.8 - - + -
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Residues in contact with PHE 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G ASN 3.8 1.1 - - - -
130G ILE* 3.9 28.5 - - + -
146G VAL* 4.1 11.4 - - + -
147G ILE* 1.3 79.8 - - - +
149G ASN* 1.3 60.2 + - - +
150G TYR* 3.6 0.7 + - + -
153G LYS 3.6 0.2 - - - +
155G VAL* 2.7 41.2 + - - +
174G LEU* 5.2 0.4 - - + -
176G VAL* 3.9 29.8 - - + -
182G TYR* 5.7 0.7 - - + -
196G LEU* 3.9 25.1 - - + -
200G TRP* 3.6 40.2 - + - -
202G PHE* 3.9 26.2 - + + -
305G ILE* 4.7 3.6 - - + -
306G TYR 4.6 3.6 - - - -
308G TYR* 3.5 22.7 - + - +
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Residues in contact with ASN 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G GLU* 3.9 22.5 - - - +
128G TYR* 3.1 27.9 - - + +
129G ASN* 2.9 17.6 + - - +
147G ILE* 5.0 0.2 - - - +
148G PHE* 1.3 73.0 - - - +
150G TYR* 1.3 61.0 + - - +
151G LYS 5.2 0.2 + - - -
152G GLY* 4.0 9.8 + - - -
153G LYS 3.1 26.5 + - - +
154G ASN* 3.1 18.9 + - - +
308G TYR* 2.6 31.5 + - + -
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Residues in contact with TYR 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G PHE 3.6 0.6 + - - -
149G ASN* 1.3 78.0 - - - +
151G LYS* 1.3 110.3 + - + +
152G GLY 3.2 1.8 - - - -
153G LYS* 2.8 26.0 + - - +
155G VAL* 4.5 3.6 - - + +
202G PHE* 3.7 58.3 - + + -
203G LEU* 4.1 16.4 - - + +
302G ASP* 2.6 35.9 + - - +
304G SER* 5.8 0.4 - - - -
305G ILE* 4.0 28.5 - - + -
308G TYR* 5.2 0.9 - - - +
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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