Contacts of the strand formed by residues 134 - 140 (chain E) in PDB entry 1ACB
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 THR 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E PHE* 4.5 5.2 - - + -
131E ALA* 2.8 35.9 + - - +
132E ALA 3.1 2.2 + - - -
133E GLY* 1.3 75.5 - - - +
135E THR* 1.4 68.6 + - - +
136E CYS* 3.4 25.7 + - - -
161E PRO* 3.5 0.3 - - - +
162E LEU* 3.0 31.0 + - + -
201E CYS* 4.6 6.7 - - + -
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Residues in contact with THR 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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12E GLY* 5.4 3.8 - - - +
13E LEU* 3.8 33.3 - - + +
133E GLY 3.5 4.9 + - - -
134E THR* 1.4 77.7 - - - +
136E CYS* 1.3 76.4 + - - +
159E SER* 3.7 21.3 - - - -
160E LEU 3.6 11.2 - - - +
161E PRO* 4.4 4.1 - - + +
201E CYS* 5.1 2.3 - - - +
202E LYS 5.5 1.0 + - - -
207E TRP* 6.1 0.2 - - - -
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Residues in contact with CYS 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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13E LEU* 5.4 0.2 - - - -
134E THR* 3.5 14.6 - - - -
135E THR* 1.3 81.5 - - - +
137E VAL* 1.3 66.6 + - - +
159E SER* 3.3 5.5 - - - -
160E LEU* 2.7 33.9 + - - +
162E LEU* 3.8 15.7 - - + -
199E LEU* 4.2 14.6 - - + -
200E VAL 3.4 6.5 - - - +
201E CYS* 2.1 50.3 - - - +
207E TRP* 5.7 0.4 - - - -
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Residues in contact with VAL 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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10E LEU* 4.2 11.7 - - + -
13E LEU* 3.6 26.9 - - + -
27E TRP* 4.0 24.7 - - + -
136E CYS* 1.3 79.8 - - - +
138E THR* 1.3 75.4 + - - +
139E THR* 4.2 6.3 - - + -
157E GLN* 4.4 4.5 - - + -
158E ALA 3.3 15.3 - - - +
159E SER* 4.4 2.0 - - - -
160E LEU* 3.6 4.0 - - - -
199E LEU* 3.3 4.0 - - - +
200E VAL* 2.9 44.3 + - + +
207E TRP* 3.9 13.5 - - + -
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Residues in contact with THR 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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16E ILE* 3.5 16.6 - - + +
137E VAL* 1.3 75.0 - - - +
139E THR* 1.3 65.0 + - - +
157E GLN* 3.3 3.1 - - - -
158E ALA* 2.9 35.7 + - + +
160E LEU* 3.5 30.1 - - + -
189E SER 6.1 0.2 - - - -
190E SER* 4.7 7.6 + - - +
198E PRO* 2.7 21.2 + - - -
199E LEU* 4.3 6.7 - - - -
200E VAL* 5.8 0.2 - - - -
213E VAL* 3.8 17.5 - - - +
228E TYR* 4.3 7.5 - - - +
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Residues in contact with THR 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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16E ILE* 3.7 8.2 - - - +
27E TRP* 3.7 44.4 - - + +
29E TRP* 5.3 0.5 + - - -
30E GLN* 2.6 29.3 + - - +
137E VAL* 4.2 4.3 - - + -
138E THR* 1.3 85.9 + - - +
140E GLY* 1.4 60.6 + - - +
155E LEU* 4.4 6.3 - - - -
156E GLN 3.3 7.6 - - - +
157E GLN* 3.8 10.1 - - + -
194E ASP* 4.5 6.4 - - - +
197E GLY* 4.8 3.1 - - - -
198E PRO* 3.2 25.7 + - - +
200E VAL* 6.3 1.1 - - + -
213E VAL* 5.2 0.9 - - - +
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Residues in contact with GLY 140 (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* 3.8 3.8 - - - +
30E GLN* 4.0 9.4 - - - -
139E THR* 1.4 77.3 - - - +
141E TRP* 1.3 59.2 + - - -
142E GLY 3.3 6.6 + - - -
155E LEU* 3.5 14.6 - - - +
156E GLN* 2.9 37.7 + - - +
194E ASP* 3.4 13.5 - - - -
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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