Contacts of the strand formed by residues 142 - 150 (chain E) in PDB entry 3RBQ
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 GLN 142 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ASP* 3.7 6.2 + - - +
96E MET* 3.0 54.9 + - + +
97E ASP* 4.6 2.8 + - - +
140E LEU* 3.6 1.2 - - - +
141E ARG* 1.3 115.0 + - - +
143E VAL* 1.3 68.9 + - - +
193E ILE* 3.5 21.7 - - + +
194E TYR 3.3 11.7 - - - +
195E ASP* 2.8 24.0 + - - +
196E PHE* 4.5 0.9 - - - -
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Residues in contact with VAL 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ILE* 4.5 11.2 - - + -
94E ARG 3.3 13.2 - - - +
95E ASP* 4.6 0.4 - - - -
96E MET* 3.7 4.7 - - - -
102E LEU* 4.0 9.0 - - + -
137E PHE* 4.7 2.0 - - + -
140E LEU* 3.7 26.7 - - + -
142E GLN* 1.3 80.8 - - - +
144E GLY* 1.3 59.9 + - - +
192E HIS 3.6 0.7 - - - +
193E ILE* 3.6 3.1 - - - +
194E TYR* 2.8 58.3 + - + +
196E PHE* 3.5 20.8 - - + -
500K DAO 4.0 22.0 - - + -
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Residues in contact with GLY 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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92E LYS 3.5 1.6 - - - +
93E ILE* 3.2 5.2 - - - -
94E ARG* 2.8 42.1 + - - +
96E MET* 3.5 20.4 - - - +
143E VAL* 1.3 72.8 - - - +
145E ALA* 1.3 62.0 + - - -
146E THR 4.0 0.2 + - - -
191E GLU* 4.0 3.1 - - - -
192E HIS 3.3 7.2 - - - -
193E ILE* 4.0 6.7 - - - -
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Residues in contact with ALA 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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91E PHE* 3.8 19.3 - - + -
92E LYS 3.2 5.4 - - - -
93E ILE* 3.3 19.7 - - + -
143E VAL 4.1 0.6 + - - -
144E GLY* 1.3 73.6 - - - -
146E THR* 1.3 59.7 + - - +
147E VAL* 4.1 4.2 + - + +
190E CYS 3.8 0.3 - - - +
191E GLU* 3.2 6.5 - - - +
192E HIS* 2.7 41.6 + - + +
194E TYR* 3.8 21.7 - - + +
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Residues in contact with THR 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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90E ARG* 3.8 25.0 - - - +
91E PHE* 3.3 4.7 - - - -
92E LYS* 2.6 58.3 + - - +
94E ARG* 3.6 20.6 + - - -
145E ALA* 1.3 71.5 - - - +
147E VAL* 1.3 64.0 + - - +
148E GLU* 4.8 1.8 - - + +
189E THR* 4.3 16.6 - - + -
190E CYS 3.6 8.3 - - - +
191E GLU* 3.8 9.8 - - + +
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Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E PHE* 3.4 39.5 - - + -
90E ARG 3.4 5.6 - - - +
91E PHE* 3.8 20.0 - - + +
145E ALA* 4.3 5.6 - - + +
146E THR* 1.3 80.3 - - - +
148E GLU* 1.3 61.9 + - - +
149E PHE* 4.4 5.0 - - + -
179E PHE* 4.8 4.7 - - + -
189E THR* 3.4 4.3 - - - +
190E CYS* 2.9 41.6 + - + +
192E HIS* 4.0 27.1 - - + +
502K ALA* 3.9 11.9 - - + -
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Residues in contact with GLU 148 (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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88E PHE* 3.6 3.5 - - - -
89E VAL* 2.8 26.7 + - - +
90E ARG* 2.4 68.6 + - + +
146E THR* 4.9 1.1 - - + -
147E VAL* 1.3 79.3 - - - +
149E PHE* 1.3 62.8 + - - +
187E LYS* 2.9 36.0 + - + +
188E ASN 3.1 8.5 - - - +
189E THR* 3.7 23.1 - - + +
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Residues in contact with PHE 149 (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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86E ILE* 4.0 13.5 - - + -
87E ASP 3.1 17.0 - - - +
88E PHE* 3.7 21.3 - + + -
89E VAL* 4.3 1.1 - - - +
147E VAL* 4.4 3.4 - - + -
148E GLU* 1.3 80.2 - - - +
150E THR* 1.3 62.3 + - - +
151E VAL* 3.7 24.5 - - + -
159E PHE* 3.8 12.8 - + - -
179E PHE* 3.8 37.5 - + + -
182E CYS* 4.0 17.5 - - - -
187E LYS* 4.1 2.4 - - - +
188E ASN* 2.5 74.0 + - + +
189E THR 4.1 10.1 - - - -
190E CYS* 4.6 0.9 - - + -
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Residues in contact with THR 150 (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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85E LYS 3.4 4.0 + - - +
86E ILE* 3.4 3.6 - - - -
87E ASP* 2.9 51.2 + - - +
89E VAL* 4.4 13.4 - - + +
149E PHE* 1.3 78.6 - - - +
151E VAL* 1.3 65.2 + - - +
186E SER 3.3 7.2 - - - +
187E LYS* 4.0 24.7 - - + +
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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