Contacts of the strand formed by residues 140 - 146 (chain E) in PDB entry 5BOU
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 GLY 140 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E ASN 4.9 3.6 - - - -
136E TYR* 3.5 26.5 - - - -
137E ASP 3.1 22.0 + - - -
138E LYS 3.5 1.6 + - - -
139E SER* 1.3 78.5 - - - +
141E ALA* 1.3 61.5 + - - -
142E HIS* 3.1 16.8 - - - -
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Residues in contact with ALA 141 (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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38E ARG* 3.5 22.2 + - - +
39E SER 3.6 23.6 - - - +
40E ASN* 4.3 6.1 + - - +
42E HIS 3.6 26.5 - - - +
43E ALA* 4.3 3.1 - - + +
135E GLY 3.5 5.4 - - - -
136E TYR* 3.5 15.8 - - + -
139E SER 4.2 1.2 + - - +
140E GLY* 1.3 73.4 - - - -
142E HIS* 1.3 70.4 + - - +
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Residues in contact with HIS 142 (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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38E ARG* 3.7 8.3 + - - +
43E ALA* 3.9 4.0 - - - +
104E VAL* 3.7 28.0 - - + -
105E GLU* 5.6 5.9 + - + -
133E ILE 4.5 0.4 - - - -
134E ILE* 3.4 5.9 - - - +
135E GLY 2.9 31.0 + - - +
137E ASP* 2.9 24.6 + - - -
139E SER* 2.7 36.5 + - - -
140E GLY 3.1 24.3 + - - -
141E ALA* 1.3 78.2 + - - +
143E LEU* 1.3 61.6 + - - +
144E LEU* 4.8 1.8 - - + -
154E GLU* 2.7 28.8 + - - +
59F LYS* 4.9 11.4 - - + -
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Residues in contact with LEU 143 (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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36E GLY* 3.4 40.4 - - - +
37E LEU 3.8 0.4 - - - +
38E ARG* 4.0 8.8 - - + +
132E LEU* 4.5 9.2 - - + -
133E ILE 3.4 5.2 - - - +
134E ILE* 3.6 24.9 - - + -
142E HIS* 1.3 76.0 - - - +
144E LEU* 1.3 83.1 - - - +
154E GLU* 3.4 2.7 + - - +
155E LEU* 2.9 41.6 + - + +
156E TYR 3.6 8.1 - - - +
157E GLY* 3.4 27.4 - - - +
158E THR* 3.8 8.5 - - + +
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Residues in contact with LEU 144 (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 VAL* 3.2 44.4 - - + +
105E GLU* 4.6 5.4 - - + -
108E GLY* 3.6 24.7 - - - +
132E LEU* 3.3 6.1 - - - +
133E ILE* 2.7 54.8 + - + +
142E HIS* 4.8 0.4 - - + -
143E LEU* 1.3 89.4 - - - +
145E GLU* 1.3 59.4 + - - +
146E PHE 4.2 0.2 - - - -
152E VAL* 3.9 14.6 - - + -
153E THR 3.3 6.3 - - - +
154E GLU* 3.9 27.4 - - + +
155E LEU* 5.1 0.4 - - - -
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Residues in contact with GLU 145 (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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131E LEU 3.6 2.7 - - - +
132E LEU* 3.8 18.4 - - + -
144E LEU* 1.3 74.0 - - - +
146E PHE* 1.3 66.4 + - - +
147E GLN* 4.0 22.0 - - + +
151E ASN 3.7 2.4 - - - +
152E VAL* 3.3 6.7 - - - -
153E THR* 2.8 36.5 + - - +
155E LEU* 3.6 23.1 - - + +
158E THR* 2.9 22.3 + - - -
159E ALA 4.8 0.4 - - - +
160E ILE* 3.7 22.6 - - + +
168E LYS* 4.5 9.9 + - - -
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Residues in contact with PHE 146 (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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83E LEU* 3.8 27.1 - - + -
111E LEU* 3.6 34.5 - - + -
112E CYS* 4.5 1.6 - - - -
115E ALA* 3.8 19.1 - - + -
127E TYR* 5.2 0.7 - - + -
129E VAL 3.6 18.8 - - - -
130E GLY* 3.5 6.2 - - - -
131E LEU* 2.8 59.3 + - + +
133E ILE* 4.0 12.3 - - + -
144E LEU 4.2 0.4 - - - -
145E GLU* 1.3 75.9 - - - +
147E GLN* 1.3 84.9 + - - +
148E PRO* 3.8 6.5 - - + -
150E GLY* 4.9 0.4 - - - -
151E ASN 3.9 2.0 - - - -
152E VAL* 3.8 21.5 - - + -
160E ILE* 5.3 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