Contacts of the strand formed by residues 132 - 140 (chain E) in PDB entry 5LS6
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 132 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D GLN* 2.9 20.7 + - - -
86E ASN* 3.7 21.0 + - - +
87E SER* 6.0 0.2 - - - -
88E LEU* 3.6 24.8 - - + +
113E PHE* 4.0 12.3 - - + -
124E TYR* 3.5 39.1 - - + -
125E GLU 3.5 7.0 - - - +
126E CYS* 4.3 6.1 - - - -
130E GLY 3.5 5.3 + - - +
131E GLU* 1.3 80.4 - - - +
133E ARG* 1.3 58.8 + - - +
134E LEU 3.8 0.3 + - - -
426E ILE* 4.5 9.0 - - + -
434E ILE* 5.2 3.8 - - + -
436E ARG* 3.7 38.6 - - + +
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Residues in contact with ARG 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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70D ILE* 5.8 3.6 - - - -
94D GLN* 3.4 11.4 - - - +
124E TYR* 3.3 4.7 - - - -
125E GLU* 2.7 40.7 + - - +
127E HIS* 3.1 42.1 + - + +
131E GLU* 3.1 32.8 + - - +
132E ILE* 1.3 72.5 - - - +
134E LEU* 1.3 67.6 + - - +
135E LEU* 3.3 17.5 + - + +
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Residues in contact with LEU 134 (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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70D ILE* 4.8 1.9 - - - +
83D CYS* 3.4 27.6 - - + +
85D VAL* 3.5 20.4 - - + -
94D GLN* 2.7 38.5 + - + +
96D ILE* 3.5 34.2 - - + +
122E THR* 3.5 31.9 - - + -
123E LEU 3.9 4.9 - - - +
124E TYR* 3.6 20.4 - - + -
132E ILE 3.8 0.6 + - - -
133E ARG* 1.3 72.9 - - - +
135E LEU* 1.3 62.0 + - - +
136E GLN 4.6 4.0 - - - +
137E SER* 5.0 1.8 - - - -
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Residues in contact with LEU 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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68D VAL* 3.6 32.3 - - + +
69D HIS 4.9 1.6 - - - +
70D ILE* 3.3 48.2 - - + +
71D LEU 4.7 0.7 - - - +
96D ILE* 3.2 22.5 - - - +
112E VAL* 4.1 10.8 - - + -
123E LEU* 3.1 20.2 + - + +
124E TYR* 3.9 2.7 - - - -
125E GLU* 3.4 28.7 - - + +
133E ARG* 3.3 24.5 - - + +
134E LEU* 1.3 74.6 - - - +
136E GLN* 1.3 72.9 + - + +
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Residues in contact with GLN 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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69D HIS 3.4 18.4 + - - +
70D ILE* 4.7 3.1 - - - -
71D LEU 4.5 4.9 - - - +
96D ILE* 4.3 7.4 - - - +
122E THR* 3.3 3.6 - - - +
123E LEU* 2.6 48.4 + - + +
134E LEU* 3.9 1.5 - - - +
135E LEU* 1.3 86.3 - - + +
137E SER* 1.3 58.7 + - - +
138E TYR* 3.1 28.9 + - + -
177E PRO* 3.1 38.8 + - - +
180E MET* 3.3 31.0 - - - +
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Residues in contact with SER 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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83D CYS* 3.5 19.5 - - - -
96D ILE* 4.0 9.0 - - - +
97D PRO 4.0 2.1 + - - +
98D LEU* 3.1 33.4 - - - +
99D LYS* 3.2 15.9 + - - +
120E ARG* 3.7 5.4 - - - -
121E VAL 3.4 5.2 + - - -
122E THR* 2.6 31.7 + - - +
134E LEU* 5.0 1.1 - - - -
136E GLN* 1.3 75.5 - - - +
138E TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 138 (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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99D LYS* 3.0 34.8 - - + +
101D LEU* 3.6 28.2 - - + +
120E ARG* 2.9 22.0 - - - +
121E VAL* 2.9 33.5 + - + +
123E LEU* 3.8 22.9 - - + -
136E GLN* 3.1 33.8 + - + -
137E SER* 1.3 76.2 - - - +
139E VAL* 1.3 62.2 + - - +
175E ILE* 3.3 27.4 - - + -
177E PRO* 3.3 19.9 - - - +
180E MET* 3.5 30.3 - - + -
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Residues in contact with VAL 139 (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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98D LEU* 3.5 39.0 - - + -
99D LYS 2.9 8.7 + - - +
100D THR* 3.3 10.4 - - + +
101D LEU* 2.5 38.3 + - - -
119E ASN* 3.3 20.0 - - - +
120E ARG* 3.7 20.2 - - + +
138E TYR* 1.3 77.0 - - - +
140E ASP* 1.3 72.9 + - - +
141E ALA* 5.1 1.3 - - - -
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Residues in contact with ASP 140 (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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101D LEU* 3.8 9.3 - - - +
119E ASN* 2.9 23.5 + - + +
139E VAL* 1.3 85.3 - - - +
141E ALA* 1.3 76.0 + - - +
142E ASP* 3.2 18.0 + - - +
145E GLU* 3.5 35.8 - - + +
147E PHE* 3.8 16.8 - - + -
169E ARG* 4.1 6.1 + - - -
173E ARG* 2.5 41.5 + - - +
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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