Contacts of the strand formed by residues 87 - 95 (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 ASP 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E LYS 4.2 5.2 - - - +
86E ILE* 1.3 78.1 - - - +
88E PHE* 1.3 66.8 + - - +
89E VAL* 3.6 10.5 + - - +
107E LYS* 3.0 30.7 + - - -
125E ALA 5.6 1.7 - - - +
149E PHE* 3.1 5.9 - - - -
150E THR* 2.9 45.3 + - - +
228E MET* 5.7 0.2 - - - -
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Residues in contact with PHE 88 (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* 4.1 10.8 - - + -
87E ASP* 1.3 77.3 + - - +
89E VAL* 1.3 63.1 + - - +
90E ARG 3.7 2.7 - - - +
107E LYS* 3.6 13.2 - - - +
147E VAL* 3.4 33.7 - - + -
148E GLU 3.6 2.2 - - - +
149E PHE* 3.7 22.7 - + + -
159E PHE* 4.3 2.9 - + - -
179E PHE* 4.5 7.6 - + - -
220E TYR* 3.3 41.3 - + - -
228E MET* 3.6 32.3 - - + +
230E ASN* 4.3 9.6 - - - -
502K ALA* 3.9 24.0 - - + +
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Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ASP* 3.6 23.8 + - - +
88E PHE* 1.3 79.0 - - - +
90E ARG* 1.3 64.5 + - + +
105E ILE* 6.3 0.2 - - - -
106E LYS* 3.6 2.0 - - - +
107E LYS* 3.0 55.5 + - + +
148E GLU* 2.8 11.8 + - - +
149E PHE* 5.0 1.3 - - - -
150E THR* 4.4 17.0 - - + -
187E LYS* 5.1 13.2 - - + -
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Residues in contact with ARG 90 (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* 3.7 1.1 - - - +
89E VAL* 1.3 81.6 + - - +
91E PHE* 1.3 69.2 + - - +
92E LYS* 3.5 29.8 - - - +
104E GLU* 3.3 25.7 + - - +
105E ILE* 3.4 12.8 - - - +
106E LYS* 4.1 19.7 - - + +
146E THR* 4.1 20.6 - - - +
147E VAL* 3.4 6.1 - - - +
148E GLU* 2.4 80.4 + - + +
189E THR* 5.8 0.2 - - - +
502K ALA 5.0 1.0 - - - +
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Residues in contact with PHE 91 (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* 1.3 75.5 - - - +
92E LYS* 1.3 61.9 + - - +
93E ILE* 3.7 35.2 - - + -
103E PHE* 3.8 14.6 - + - -
104E GLU* 3.3 2.6 - - - +
105E ILE* 2.9 42.4 + - + +
131E TYR* 3.5 17.0 - - - -
145E ALA* 3.8 19.3 - - + -
146E THR 3.3 2.0 - - - -
147E VAL* 3.8 13.9 - - + -
192E HIS* 6.0 0.4 - - - -
194E TYR* 5.3 2.0 - - - -
500K DAO 3.8 25.1 - - + -
502K ALA* 3.3 44.2 - - + +
503K GLY* 3.5 14.8 - - - -
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Residues in contact with LYS 92 (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* 3.5 29.4 - - - +
91E PHE* 1.3 76.0 - - - +
93E ILE* 1.3 65.4 + - - +
94E ARG* 4.6 17.7 + - - +
101E VAL* 3.4 34.3 - - + +
103E PHE 3.4 12.1 - - - +
104E GLU* 3.9 22.1 + - + +
144E GLY 3.5 1.4 - - - +
145E ALA* 3.2 2.3 - - - -
146E THR* 2.6 56.6 + - - +
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Residues in contact with ILE 93 (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* 3.7 21.3 - - + -
92E LYS* 1.3 73.9 - - - +
94E ARG* 1.3 63.2 + - - +
101E VAL* 3.7 2.8 - - - +
102E LEU* 2.8 29.8 + - + -
103E PHE* 3.0 28.4 + - + +
131E TYR* 5.1 0.7 - - + -
133E PHE* 3.9 28.0 - - + -
137E PHE* 4.7 5.4 - - + -
143E VAL* 4.5 13.2 - - + -
144E GLY 3.2 3.6 - - - +
145E ALA* 3.3 33.4 - - + +
500K DAO 4.0 24.0 - - + -
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Residues in contact with ARG 94 (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* 4.6 15.0 - - - +
93E ILE* 1.3 75.6 - - - +
95E ASP* 1.3 65.9 + - - +
96E MET* 3.6 30.6 - - - +
99E GLY* 3.9 17.6 - - - +
100E THR 3.4 11.9 - - - +
101E VAL* 4.2 9.6 - - + -
102E LEU* 3.8 6.1 - - - -
143E VAL* 3.3 6.1 - - - +
144E GLY 2.8 39.5 + - - +
146E THR* 3.6 16.8 + - - -
191E GLU* 2.5 39.9 + - - -
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Residues in contact with ASP 95 (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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94E ARG* 1.3 73.0 - - - +
96E MET* 1.3 62.2 + - - +
97E ASP* 3.0 17.0 + - - +
98E SER* 2.8 33.3 + - - +
99E GLY* 2.8 32.1 + - - -
100E THR* 2.9 12.8 + - - +
102E LEU* 3.7 18.2 - - + +
140E LEU* 3.7 27.9 - - + +
141E ARG 5.4 0.9 + - - -
142E GLN 3.7 10.9 + - - +
143E VAL* 4.6 1.1 - - - -
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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