Contacts of the strand formed by residues 132 - 139 (chain E) in PDB entry 1RBO
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 ALA 132 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ARG 4.6 0.2 - - - -
42E VAL* 4.0 0.3 - - - -
43E SER* 3.1 40.0 + - - +
125E PHE 5.9 0.4 - - - -
130E LEU* 3.5 8.3 - - - +
131E ARG* 1.3 84.1 - - + +
133E LEU* 1.3 65.1 + - - +
306E ASN* 3.4 35.7 - - + +
307E HIS* 3.6 13.7 - - - +
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Residues in contact with LEU 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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40E PHE* 3.8 21.8 - - + -
41E ARG 3.4 9.0 - - - +
42E VAL* 3.7 33.7 - - + -
57E VAL* 4.3 9.4 - - + -
124E VAL* 3.6 44.2 - - + +
125E PHE* 3.0 38.1 - - + +
130E LEU* 4.1 12.6 - - + -
132E ALA* 1.3 77.7 - - - +
134E ARG* 1.3 61.9 + - - +
306E ASN 3.6 2.6 + - - -
307E HIS* 3.2 7.8 + - - -
308E GLY 3.0 18.2 + - - -
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Residues in contact with ARG 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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40E PHE* 3.4 6.5 - - - -
41E ARG* 2.7 45.3 + - + +
125E PHE* 4.4 0.4 - - - -
133E LEU* 1.3 76.0 - - - +
135E LEU* 1.3 62.9 + - - +
136E GLU* 3.0 36.6 + - - -
302E ASP 3.1 26.3 + - - -
304E GLN 3.3 17.8 + - - -
305E LYS* 3.3 26.2 + - - +
306E ASN 3.9 11.9 - - - +
307E HIS 4.0 1.1 - - - -
308E GLY 3.2 24.0 - - - +
309E MET 4.0 2.6 - - - +
310E HIS* 3.4 24.8 - - - +
473E ASP* 3.0 29.9 + - - -
474E THR 5.3 0.8 + - - -
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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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38E ALA* 3.9 20.4 - - + -
39E ALA 3.7 10.1 - - - +
40E PHE* 4.0 21.8 - - + -
117E PHE* 5.2 2.2 - - + -
120E ILE* 4.1 12.1 - - + -
121E VAL* 3.9 19.3 - - + -
125E PHE* 4.0 9.5 - - + -
134E ARG* 1.3 72.5 - - - +
136E GLU* 1.3 60.0 + - - +
137E ASP 3.6 19.3 - - - +
138E LEU* 4.1 8.5 - - + -
308E GLY 3.0 10.0 + - - +
309E MET* 3.4 8.2 - - + -
310E HIS 2.8 27.4 + - - -
313E VAL* 3.9 32.2 - - + +
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Residues in contact with GLU 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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39E ALA* 2.9 16.6 + - + +
41E ARG* 2.8 54.4 + - + +
98E ILE* 4.9 2.2 - - + -
134E ARG* 3.0 31.0 + - - +
135E LEU* 1.3 74.6 - - - +
137E ASP* 1.3 61.5 + - - +
310E HIS* 3.7 5.5 - - - +
312E ARG* 2.7 53.6 + - - +
313E VAL* 3.6 3.9 - - - +
363E TYR* 3.8 29.9 - - + +
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Residues in contact with ASP 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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38E ALA* 3.6 2.8 - - - -
39E ALA* 3.1 24.2 + - + -
135E LEU* 3.6 7.5 - - - +
136E GLU* 1.3 80.7 - - - +
138E LEU* 1.3 76.9 + - - +
312E ARG* 3.9 13.9 - - - +
313E VAL* 3.6 8.8 - - - +
316E LYS* 3.0 28.3 + - - +
348E LEU* 5.4 0.7 - - - +
362E ILE* 3.9 7.4 - - - +
363E TYR* 3.0 44.6 + - + -
364E PHE* 3.4 20.1 + - + +
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Residues in contact with LEU 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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36E ILE* 4.1 5.8 - - + -
37E LEU 3.1 16.8 - - - +
38E ALA* 3.7 21.1 - - + -
116E MET* 4.1 31.4 - - + -
117E PHE* 4.3 6.1 - - + -
120E ILE* 3.7 28.9 - - + -
135E LEU* 4.1 10.8 - - + -
137E ASP* 1.3 81.7 + - - +
139E ARG* 1.3 55.1 + - - +
140E ILE* 3.6 13.6 + - + -
313E VAL* 4.0 24.0 - - + +
316E LYS* 2.6 39.4 + - + +
364E PHE* 3.9 3.1 - - - -
366E GLN* 3.5 1.9 - - - +
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Residues in contact with ARG 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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31E THR* 5.1 2.2 + - - -
32E LEU 3.0 25.3 + - - -
33E ASP* 4.0 18.9 + - - +
35E ASP 2.7 32.5 + - - +
36E ILE* 3.4 8.3 - - - +
37E LEU* 2.8 60.8 + - + +
138E LEU* 1.3 71.5 - - - +
140E ILE* 1.3 70.5 + - - +
141E PRO* 3.9 6.5 - - - -
364E PHE* 3.6 24.8 - - + -
365E THR 3.5 25.1 + - - +
366E GLN* 3.7 4.5 - - - +
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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