Contacts of the strand formed by residues 130 - 137 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ASN* 5.6 0.2 - - - +
91D LEU* 3.9 27.8 - - + -
93D VAL* 5.7 0.9 - - + -
111D LYS* 3.4 2.3 - - - -
112D LEU* 2.8 45.0 + - + +
128D TYR* 3.8 5.4 - - - -
129D ASN* 1.3 86.8 - - + +
131D MET* 1.3 71.2 + - - +
132D PHE* 4.3 2.5 - - + +
146D VAL* 5.5 0.2 - - + -
147D ILE 3.3 10.8 - - - +
148D PHE* 4.0 26.0 - - + -
174D LEU* 4.1 21.5 - - + -
176D VAL* 5.0 4.9 - - + -
306D TYR 5.3 1.6 - - - +
308D TYR* 3.9 12.6 - - + -
311D PHE* 3.9 14.6 - - + -
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Residues in contact with MET 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TYR* 3.6 39.5 - - + -
110D VAL 3.4 12.8 - - - +
111D LYS* 4.1 21.1 - - + -
128D TYR* 3.8 19.7 - - + -
130D ILE* 1.3 76.0 - - - +
132D PHE* 1.3 66.9 + - - +
145D HIS* 3.5 39.6 - - + +
146D VAL* 3.5 3.1 - - - -
147D ILE* 2.8 56.2 + - + +
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 4.0 11.9 - - + -
95D PHE* 3.6 16.0 - + - -
109D TYR* 3.4 5.3 - - - -
110D VAL* 2.9 37.4 + - + +
130D ILE* 4.3 3.1 - - + -
131D MET* 1.3 77.3 - - - +
133D GLY* 1.3 63.2 + - - +
144D VAL* 3.8 21.1 - - + -
145D HIS 3.3 11.4 - - - -
146D VAL* 4.0 11.4 - - + -
172D TYR* 3.9 20.2 - + + -
173D THR 3.5 32.1 - - - -
174D LEU* 3.5 46.0 - - + -
184D VAL* 4.0 14.6 - - + -
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 4.3 4.0 - - - -
109D TYR* 3.6 8.3 - - - +
132D PHE* 1.3 82.2 - - - +
134D PRO* 1.3 77.1 - - - +
135D ASP 3.7 0.2 + - - -
144D VAL* 4.0 10.8 - - - -
145D HIS* 3.0 37.8 + - - +
172D TYR* 5.1 0.2 - - - -
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Residues in contact with PRO 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 4.4 1.8 - - + -
97D VAL* 4.2 10.3 - - + -
99D HIS* 4.7 9.6 - - + +
108D GLY* 2.8 54.6 + - - +
109D TYR* 3.5 4.7 - - - -
133D GLY* 1.3 85.4 - - - +
135D ASP* 1.3 56.8 + - - +
136D ILE* 5.2 1.3 - - + -
143D LYS 3.4 6.7 - - - +
144D VAL* 4.4 1.6 - - + -
163D CYS* 3.8 15.5 - - + -
164D LYS 5.2 0.7 - - - +
172D TYR* 3.7 50.3 - - + +
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Residues in contact with ASP 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLY 3.6 5.4 - - - +
107D GLY* 3.5 16.3 + - - -
109D TYR* 4.0 13.4 + - + -
134D PRO* 1.3 74.5 - - - +
136D ILE* 1.3 73.6 + - - +
137D CYS* 5.4 2.2 - - - +
141D THR* 3.7 14.3 - - + +
142D LYS* 3.7 2.6 - - - -
143D LYS* 2.8 35.9 + - + +
145D HIS* 3.1 37.3 + - + +
163D CYS* 4.4 0.4 - - - -
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 4.1 13.0 - - + +
103D ILE* 3.8 34.1 - - + +
104D ASP 3.9 14.4 - - - +
105D CYS* 3.8 0.3 - - - -
106D GLY* 2.7 40.6 + - - +
134D PRO 5.2 0.4 - - - -
135D ASP* 1.3 86.1 + - - +
137D CYS* 1.3 66.0 + - - +
138D GLY 4.5 5.4 - - - +
141D THR* 3.3 10.1 - - - +
142D LYS* 4.8 7.9 - - + -
163D CYS* 3.8 12.3 - - - -
164D LYS 3.6 23.8 - - - +
165D ASP* 4.0 17.0 - - + -
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Residues in contact with CYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ASP 3.7 2.2 - - - -
105D CYS* 2.2 40.6 - - - -
135D ASP* 5.4 2.5 - - - +
136D ILE* 1.3 75.6 - - - +
138D GLY* 1.3 68.1 + - - +
139D PRO* 4.5 0.3 - - - +
140D GLY* 4.2 1.6 + - - -
141D THR* 3.1 36.2 + - + +
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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