Contacts of the strand formed by residues 130 - 137 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E ASN* 5.6 0.2 - - - +
91E LEU* 3.9 28.5 - - + -
93E VAL* 5.8 0.7 - - + -
111E LYS* 3.4 2.1 - - - -
112E LEU* 2.8 44.2 + - + +
128E TYR* 3.7 5.2 - - - -
129E ASN* 1.3 85.4 - - + +
131E MET* 1.3 72.5 + - - +
132E PHE* 4.7 2.0 - - + -
146E VAL* 5.5 0.2 - - + -
147E ILE 3.3 11.0 - - - +
148E PHE* 3.9 27.1 - - + -
174E LEU* 4.1 21.3 - - + -
176E VAL* 5.0 4.9 - - + -
306E TYR 5.3 1.3 - - - +
308E TYR* 3.9 13.0 - - + -
311E PHE* 3.9 14.4 - - + -
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Residues in contact with MET 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TYR* 3.6 39.9 - - + -
110E VAL 3.4 12.6 - - - +
111E LYS* 4.1 20.9 - - + -
128E TYR* 3.8 20.5 - - + -
130E ILE* 1.3 76.5 - - - +
132E PHE* 1.3 66.3 + - - +
145E HIS* 3.6 39.1 - - + +
146E VAL* 3.5 2.9 - - - -
147E ILE* 2.8 54.4 + - + +
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Residues in contact with PHE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E VAL* 4.0 13.0 - - + -
95E PHE* 3.7 16.0 - + - -
109E TYR* 3.4 5.1 - - - -
110E VAL* 2.9 35.5 + - + +
130E ILE* 4.7 2.5 - - + -
131E MET* 1.3 77.5 - - - +
133E GLY* 1.3 64.4 + - - +
144E VAL* 3.7 21.3 - - + -
145E HIS 3.3 10.3 - - - -
146E VAL* 4.0 10.8 - - + -
172E TYR* 3.8 20.4 - + + -
173E THR 3.5 32.3 - - - -
174E LEU* 3.5 47.1 - - + -
184E VAL* 4.0 13.9 - - + -
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Residues in contact with GLY 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E PHE* 4.3 3.8 - - - -
109E TYR* 3.6 8.8 - - - +
132E PHE* 1.3 83.2 - - - +
134E PRO* 1.3 75.8 - - - +
144E VAL* 4.0 10.1 - - - -
145E HIS* 2.9 37.2 + - - +
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Residues in contact with PRO 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E PHE* 4.5 2.2 - - + -
97E VAL* 4.3 9.9 - - + -
99E HIS* 4.7 10.5 - - + +
106E GLY 5.3 0.2 - - - -
108E GLY* 2.7 54.2 + - - +
109E TYR* 3.5 4.7 - - - -
133E GLY* 1.3 85.4 - - - +
135E ASP* 1.3 56.0 + - - +
136E ILE* 5.2 1.1 - - + -
143E LYS 3.4 7.0 - - - +
144E VAL* 4.4 0.9 - - - -
163E CYS* 3.8 15.5 - - + -
164E LYS 5.2 0.7 - - - +
172E TYR* 3.7 51.4 - - + +
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Residues in contact with ASP 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E GLY 3.6 4.6 - - - +
107E GLY* 3.6 16.1 + - - -
109E TYR* 4.0 12.6 + - + -
134E PRO* 1.3 74.5 - - - +
136E ILE* 1.3 73.0 + - - +
137E CYS* 5.4 2.7 - - - +
141E THR* 3.7 4.0 - - - +
142E LYS* 3.7 1.9 - - - -
143E LYS* 2.8 39.6 + - + +
145E HIS* 3.1 37.0 + - + +
163E CYS* 4.4 0.2 - - - -
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Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E HIS* 4.0 12.6 - - + +
103E ILE* 3.8 32.8 - - + +
104E ASP 3.9 15.5 - - - +
105E CYS* 3.8 0.3 - - - -
106E GLY* 2.7 41.7 + - - +
134E PRO* 5.2 0.7 - - + -
135E ASP* 1.3 86.6 + - - +
137E CYS* 1.3 66.0 + - - +
138E GLY 4.4 6.3 - - - +
141E THR 3.3 9.4 - - - +
142E LYS* 4.5 7.6 - - + -
163E CYS* 3.8 11.2 - - - -
164E LYS 3.6 24.0 - - - +
165E ASP* 4.0 18.8 - - + -
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Residues in contact with CYS 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ASP 3.7 2.7 - - - -
105E CYS* 2.2 41.5 - - - -
135E ASP* 5.4 2.5 - - - +
136E ILE* 1.3 74.9 - - - +
138E GLY* 1.3 62.3 + - - +
140E GLY* 4.3 1.2 + - - -
141E THR* 2.2 42.7 + - - +
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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