Contacts of the strand formed by residues 141 - 150 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135J ASP* 3.8 21.5 - - - +
136J ILE* 3.4 4.9 - - - +
137J CYS* 3.1 47.0 + - + +
138J GLY 3.6 4.0 - - - +
139J PRO 3.6 1.8 - - - -
140J GLY* 1.3 76.0 - - - +
142J LYS* 1.3 67.7 + - - +
143J LYS* 4.2 16.6 - - + -
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Residues in contact with LYS 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ASP 3.7 1.6 - - - -
136J ILE* 4.8 7.4 - - + +
138J GLY 4.5 4.6 + - - -
139J PRO* 3.6 25.4 + - - +
140J GLY 4.0 2.2 + - - -
141J THR* 1.3 78.7 - - - +
143J LYS* 1.3 57.9 + - - +
162J ARG* 3.2 26.4 - - + +
163J CYS* 3.1 39.7 + - - +
165J ASP* 2.6 44.2 - - + +
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Residues in contact with LYS 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J PRO* 3.4 2.9 - - - +
135J ASP* 2.8 33.9 + - + +
141J THR* 4.2 19.1 - - + -
142J LYS* 1.3 76.2 - - - +
144J VAL* 1.3 73.5 + - - +
145J HIS* 3.9 33.5 + - + +
156J LEU* 5.3 7.3 - - - +
157J ILE* 3.9 25.1 + - - +
158J ASN 5.9 0.2 - - - -
159J LYS 4.1 12.7 + - - -
160J ASP* 4.5 15.7 + - - +
161J ILE 3.2 7.4 - - - +
163J CYS* 3.5 2.8 - - - +
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Residues in contact with VAL 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J PHE* 3.8 31.0 - - + -
133J GLY* 3.7 13.0 - - - +
134J PRO* 4.8 0.4 - - + -
143J LYS* 1.3 79.4 - - - +
145J HIS* 1.3 65.1 + - - +
146J VAL* 3.6 4.0 + - + -
157J ILE* 4.3 7.4 - - - +
161J ILE* 2.9 49.6 + - + +
162J ARG 3.9 1.3 - - - +
163J CYS* 3.7 28.0 - - + -
172J TYR* 4.0 15.9 - - + -
184J VAL* 4.5 8.3 - - + -
186J ILE* 4.2 3.6 - - + -
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Residues in contact with HIS 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J TYR* 4.3 2.9 - + - -
131J MET* 3.5 35.0 - - + +
132J PHE* 3.3 5.9 - - - -
133J GLY 3.0 33.2 + - - +
135J ASP* 3.2 43.2 + - + +
143J LYS* 4.0 25.7 - - + +
144J VAL* 1.3 73.5 - - - +
146J VAL* 1.3 65.3 + - - +
147J ILE* 4.1 14.6 - - + +
156J LEU* 4.4 17.7 - - + +
157J ILE* 5.2 0.2 - - - -
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Residues in contact with VAL 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ILE* 5.5 0.2 - - + -
131J MET 3.5 3.8 - - - +
132J PHE* 4.0 13.0 - - + -
144J VAL* 3.6 8.5 + - + +
145J HIS* 1.3 78.8 - - - +
147J ILE* 1.3 61.1 + - - +
148J PHE* 4.1 10.5 - - + -
157J ILE* 3.1 41.3 + - + +
161J ILE* 4.5 3.6 - - + -
174J LEU* 3.9 29.6 - - + -
182J TYR* 5.5 0.2 - - + -
184J VAL* 4.0 19.7 - - + -
200J TRP* 3.2 31.8 + - + -
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Residues in contact with ILE 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J TYR* 3.5 23.2 - - + +
130J ILE* 3.3 10.9 - - - +
131J MET* 2.9 73.6 + - + +
145J HIS* 4.1 9.4 - - + +
146J VAL* 1.3 82.7 - - - +
148J PHE* 1.3 66.1 + - - +
154J ASN* 3.8 9.9 - - + +
155J VAL 3.3 24.2 - - - +
156J LEU* 4.0 26.9 - - + -
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Residues in contact with PHE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J ASN 3.8 1.3 - - - -
130J ILE* 3.9 24.0 - - + -
146J VAL* 4.1 11.2 - - + -
147J ILE* 1.3 78.6 - - - +
149J ASN* 1.3 60.7 + - - +
150J TYR* 3.7 0.6 + - + -
153J LYS 3.6 0.9 - - - +
155J VAL* 2.8 39.5 + - - +
174J LEU* 5.2 0.9 - - + -
176J VAL* 3.9 26.5 - - + -
182J TYR* 5.7 0.9 - - + -
196J LEU* 3.9 26.2 - - + -
200J TRP* 3.6 40.8 - + - -
202J PHE* 3.9 25.1 - + + -
305J ILE* 4.6 4.3 - - + -
306J TYR 4.5 7.4 - - - -
308J TYR* 3.5 24.9 - + - +
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Residues in contact with ASN 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLU* 3.9 22.5 + - - +
128J TYR* 3.2 28.0 - - + +
129J ASN* 2.9 17.7 + - - +
148J PHE* 1.3 70.9 - - - +
150J TYR* 1.3 63.3 + - - +
151J LYS 5.3 0.2 + - - -
152J GLY* 4.1 9.8 + - - -
153J LYS 3.0 26.9 + - - +
154J ASN* 3.1 19.7 + - - +
308J TYR* 2.6 31.6 + - + -
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Residues in contact with TYR 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J PHE 3.7 0.2 + - - -
149J ASN* 1.3 76.4 - - - +
151J LYS* 1.3 108.3 + - + +
152J GLY 3.2 1.1 - - - -
153J LYS* 2.8 25.8 + - - +
155J VAL* 4.5 5.3 - - + +
202J PHE* 3.7 59.0 - + + -
203J LEU* 4.1 14.7 - - + +
302J ASP* 2.6 35.1 + - - +
305J ILE* 4.0 27.8 - - + +
308J TYR* 5.2 0.7 - - - +
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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