Contacts of the strand formed by residues 156 - 163 (chain E) in PDB entry 3PB1
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 LYS 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.1 32.8 + - + +
18E GLY* 2.8 32.0 + - - +
19E GLY 4.6 2.6 + - - -
20E GLU 3.3 17.3 - - - +
21E PHE* 3.8 19.7 - - + +
22E THR* 3.8 3.1 - - - -
139E THR* 3.2 7.8 - - - +
140E GLY 3.1 36.3 + - - +
142E GLY 5.1 0.7 - - - +
144E GLU* 3.1 41.8 + - + +
152E PRO* 4.2 8.5 - - + -
154E GLN 3.8 9.6 - - - +
155E LEU* 1.3 79.2 - - - +
157E MET* 1.3 61.4 + - - +
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Residues in contact with MET 157 (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 3.8 - - - -
19E GLY* 3.3 0.9 - - - -
20E GLU* 2.8 37.5 + - + +
22E THR* 4.0 12.5 - - + +
27E GLN* 3.9 15.7 - - - +
137E GLU* 3.0 55.2 - - + +
138E ILE 3.1 10.8 - - - +
139E THR* 3.4 17.3 - - - +
156E LYS* 1.3 74.7 - - - +
158E THR* 1.3 80.4 + - - +
159E VAL* 4.5 3.4 - - - -
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Residues in contact with THR 158 (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* 3.6 16.1 - - + +
17E ILE 4.1 1.8 - - - +
19E GLY* 3.2 19.4 + - - -
137E GLU* 3.4 0.3 - - - -
138E ILE* 2.9 57.3 + - + +
157E MET* 1.3 89.0 - - - +
159E VAL* 1.3 66.0 + - - +
188E THR* 2.6 37.6 + - + +
189E ASP 4.4 0.9 - - - +
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Residues in contact with VAL 159 (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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135E SER* 3.9 28.9 - - - +
136E CYS 3.3 8.3 - - - +
137E GLU* 3.9 28.3 - - + +
157E MET* 4.8 3.4 - - - -
158E THR* 1.3 78.7 + - - +
160E VAL* 1.3 65.5 + - - +
161E LYS* 5.6 1.6 - - + -
185E ASP* 4.6 3.3 - - - +
188E THR* 3.0 23.0 - - - +
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Residues in contact with VAL 160 (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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134E THR 3.7 0.3 - - - +
135E SER* 3.6 1.0 - - - -
136E CYS* 2.8 38.5 + - - +
138E ILE* 4.0 29.2 - - + -
159E VAL* 1.3 79.5 - - - +
161E LYS* 1.3 60.7 + - - +
183E ALA* 3.6 21.3 - - + +
184E ALA* 3.9 20.2 - - - +
185E ASP* 5.2 1.3 - - - +
188E THR* 3.8 25.8 - - + +
189E ASP* 4.6 2.5 - - - +
199E LEU* 3.8 21.3 - - + -
228E TYR* 4.6 2.5 - - - +
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Residues in contact with LYS 161 (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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133E GLY* 3.7 24.4 + - - +
134E THR 3.3 4.5 - - - +
135E SER* 3.9 19.7 - - - +
159E VAL* 5.6 1.3 - - + -
160E VAL* 1.3 74.0 - - - +
162E LEU* 1.3 67.8 + - - +
163E ILE* 3.7 5.0 - - + +
183E ALA* 3.2 5.6 - - - -
184E ALA 2.9 37.8 + - - +
185E PRO* 4.0 28.7 - - - +
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Residues in contact with LEU 162 (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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129E ASP* 5.9 0.4 - - + -
130E PRO* 3.8 47.3 - - + +
131E GLN 4.0 5.2 - - - +
132E PHE* 4.1 5.1 - - + +
133E GLY* 2.9 32.0 + - - +
134E THR* 3.0 14.1 + - - +
136E CYS* 3.7 27.1 - - + -
161E LYS* 1.3 74.0 - - - +
163E ILE* 1.3 61.8 + - - +
181E LEU* 3.9 21.3 - - + -
182E CYS 3.8 1.8 - - - -
183E ALA* 4.2 9.0 - - + -
199E LEU* 4.0 23.3 - - + -
201E CYS* 4.3 1.3 - - - -
210E THR* 4.7 3.6 - - + -
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Residues in contact with ILE 163 (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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132E PHE* 4.4 4.3 - - - -
161E LYS* 3.7 4.5 - - + +
162E LEU* 1.3 80.7 - - - +
164E SER* 1.3 75.1 + - - +
165E HIS* 3.8 2.4 + - - -
167E GLU* 3.5 35.7 - - + +
168E CYS* 4.3 10.3 - - + +
171E TYR* 5.0 1.1 - - + -
181E LEU* 4.4 7.1 - - - +
182E CYS* 2.9 28.7 + - + +
183E ALA 4.1 1.8 - - - -
184E ALA* 3.6 42.4 - - + +
185E ASP 5.8 0.9 - - - +
186E TRP* 5.1 5.4 - - + -
225E PRO* 4.3 12.8 - - + -
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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