Contacts of the strand formed by residues 197 - 203 (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 GLY 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E GLN* 4.5 2.5 - - - -
43E GLY* 3.8 4.2 - - - -
44E GLY* 4.0 10.3 - - - -
45E SER* 4.3 0.9 - - - -
139E THR 4.8 1.8 - - - -
194E ASP 3.0 11.6 + - - -
195E SER 3.0 7.3 + - - -
196E GLY* 1.3 83.0 - - - +
198E PRO* 1.3 70.1 - - - +
212E ILE* 3.4 5.9 - - - -
213E VAL* 2.9 29.0 + - - -
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Residues in contact with PRO 198 (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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29E TRP* 4.2 15.9 - - + +
30E GLN* 3.2 23.1 - - - +
44E GLY 4.6 0.2 - - - +
45E SER* 3.3 22.1 - - - +
138E THR* 2.7 34.3 + - - -
139E THR* 3.2 25.1 - - - +
197E GLY* 1.3 86.4 - - - +
199E LEU* 1.3 56.9 + - - +
200E VAL* 3.9 15.3 - - + -
209E LEU* 3.7 18.6 - - + -
211E GLY 4.1 0.2 - - - +
213E VAL* 4.7 0.2 - - - -
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Residues in contact with LEU 199 (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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136E CYS* 4.2 9.2 - - + -
137E VAL 3.3 15.0 - - - +
138E THR* 4.3 2.2 - - - +
160E LEU* 3.9 30.5 - - + -
162E LEU* 3.9 13.9 - - + -
181E ILE* 5.0 4.0 - - + -
183E ALA* 4.3 12.6 - - + -
198E PRO* 1.3 74.4 - - - +
200E VAL* 1.3 61.4 + - - +
201E CYS* 4.9 0.9 - - - -
209E LEU* 3.9 0.7 - - - +
210E VAL* 2.9 42.9 + - + -
211E GLY* 3.1 32.0 + - - +
228E TYR* 3.8 25.6 - - + -
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Residues in contact with VAL 200 (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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27E TRP* 4.4 11.2 - - + -
29E TRP* 4.1 8.7 - - + +
121E VAL* 4.0 16.6 - - + -
136E CYS* 3.4 1.6 - - - +
137E VAL* 2.9 48.0 + - + +
139E THR* 6.3 0.9 - - + -
198E PRO* 3.9 13.7 - - + -
199E LEU* 1.3 80.4 - - - +
201E CYS* 1.3 61.4 + - - +
207E TRP* 3.5 29.4 - - + -
208E THR 3.3 13.7 - - - +
209E LEU* 3.9 19.5 - - + -
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Residues in contact with CYS 201 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E PHE* 4.1 14.6 - - + -
134E THR* 4.6 4.9 - - + -
135E THR 5.1 0.4 - - - -
136E CYS* 2.1 51.1 - - - +
162E LEU* 4.4 5.2 - - - -
199E LEU* 4.9 0.7 - - - -
200E VAL* 1.3 72.3 - - - +
202E LYS* 1.3 63.3 + - - +
203E LYS 3.5 1.0 + - - -
207E TRP* 3.5 8.2 - - - -
208E THR* 2.8 31.8 + - - +
210E VAL* 3.5 34.5 - - + -
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Residues in contact with LYS 202 (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* 6.6 1.1 - - + -
130E PHE* 5.2 1.8 - - - -
135E THR 5.5 2.0 + - - -
201E CYS* 1.3 74.6 - - - +
203E LYS* 1.3 57.6 + - - +
204E ASN 4.0 2.1 + - - -
205E GLY* 3.7 30.7 + - - +
206E ALA 3.4 8.5 - - - +
207E TRP* 3.5 53.6 - - + +
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Residues in contact with LYS 203 (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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128E ASP* 3.6 32.5 - - - +
129E ASP 3.5 22.3 + - - +
130E PHE* 3.5 29.6 - - + -
201E CYS 3.5 1.2 + - - -
202E LYS* 1.3 69.1 - - - +
204E ASN* 1.3 91.6 + - - +
205E GLY 3.4 0.2 - - - -
206E ALA* 2.8 23.7 + - - +
208E THR* 3.4 19.2 + - + +
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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