Contacts of the strand formed by residues 117 - 122 (chain E) in PDB entry 2BWJ
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 LEU 117 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E ILE 3.6 1.9 + - - +
14E ILE* 3.4 24.0 - - + -
15E PHE 3.0 22.3 + - - -
115E PRO* 3.2 2.8 - - - +
116E GLN* 1.3 80.0 - - - +
118E VAL* 1.3 72.0 + - - +
119E ILE* 4.0 17.0 - - + -
172E GLN* 3.3 17.5 - - + +
174E HIS* 3.3 38.4 - - + +
192E ALA 3.8 20.9 - - - +
193E ILE* 3.9 26.0 - - + -
196E ILE* 4.2 13.2 - - + -
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Residues in contact with VAL 118 (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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15E PHE* 3.3 18.8 - - + +
17E ILE* 3.9 28.3 - - + -
115E PRO* 4.2 7.6 - - + -
117E LEU* 1.3 78.6 - - - +
119E ILE* 1.3 62.8 + - - +
120E CYS* 4.4 4.9 - - - -
167E TYR* 3.8 21.1 - - + -
171E THR* 3.7 20.9 - - + -
172E GLN 2.8 9.9 + - - +
173E LEU* 3.3 27.6 - - + +
174E HIS 2.9 25.5 + - - -
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Residues in contact with ILE 119 (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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14E ILE* 3.6 26.5 - - + -
15E PHE 2.7 11.6 + - - +
16E ILE* 3.3 18.4 - - + -
17E ILE* 2.8 33.8 + - - +
31E LEU* 5.1 0.7 - - + -
94E LEU* 5.1 1.8 - - + -
117E LEU* 4.0 14.8 - - + -
118E VAL* 1.3 74.4 - - - +
120E CYS* 1.3 63.1 - - - +
121E MET* 4.7 1.6 - - + +
174E HIS* 3.5 3.8 - - + +
176E ILE* 3.8 16.6 - - + -
189E LEU* 3.3 33.4 - - + +
192E ALA* 5.0 3.6 - - + -
193E ILE* 3.9 27.4 - - + -
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Residues in contact with CYS 120 (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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17E ILE* 3.4 7.0 - - + +
118E VAL* 4.4 4.3 - - - -
119E ILE* 1.3 77.9 - - - +
121E MET* 1.3 61.1 + - - +
122E ASP* 3.1 6.1 + - + +
156E TYR* 5.8 1.1 - - - +
164E ILE* 3.7 38.8 - - + -
173E LEU* 3.8 30.1 - - - -
174E HIS 2.9 11.9 + - - +
175E LYS* 3.5 13.6 - - + -
176E ILE* 2.7 32.6 + - - +
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Residues in contact with MET 121 (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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16E ILE* 4.3 22.4 - - + -
17E ILE 2.7 24.2 + - - +
18E GLY* 3.8 18.7 - - - -
19E GLY 4.5 1.0 + - - -
22E SER* 4.0 7.5 - - - +
23E GLY 4.7 1.8 - - - -
24E LYS* 4.1 26.5 - - + -
27E GLN* 4.5 11.0 - - - -
119E ILE* 4.8 0.4 - - + -
120E CYS* 1.3 69.3 - - - +
122E ASP* 1.3 64.1 + - - +
123E CYS* 3.5 7.6 + - - +
156E TYR* 4.4 6.6 + - - -
176E ILE* 3.3 36.3 - - + -
178E ALA* 4.0 16.2 - - + -
185E VAL* 3.7 17.3 - - + -
189E LEU* 4.1 9.2 - - + -
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Residues in contact with ASP 122 (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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142A VAL* 5.6 6.1 - - - +
120E CYS* 3.1 8.2 + - + +
121E MET* 1.3 70.7 - - - +
123E CYS* 1.3 61.5 + - - +
175E LYS* 4.4 24.7 - - + +
176E ILE 2.6 21.2 + - - +
177E ASN* 3.6 6.9 - - - +
178E ALA* 2.7 27.7 + - - -
179E GLU* 4.0 2.1 + - - +
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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