Contacts of the strand formed by residues 212 - 220 (chain E) in PDB entry 1A81
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 212 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E LEU* 3.6 4.1 - - - +
209E HIS* 2.7 43.4 + - + +
210E GLU 2.9 5.7 + - - +
211E GLY* 1.3 78.9 - - - +
213E VAL* 1.3 71.9 + - - +
214E LEU* 4.0 25.9 - - + +
171F GLU* 5.1 5.5 + - - -
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Residues in contact with VAL 213 (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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179E GLU* 3.2 49.4 - - + +
182E VAL* 4.1 23.8 - - + -
183E LEU* 4.8 10.0 - - + +
206E CYS* 4.6 8.7 - - + -
207E LEU 3.7 6.3 - - - +
208E LEU* 4.8 2.0 - - - +
211E GLY 4.0 1.6 + - - -
212E LYS* 1.3 82.3 - - + +
214E LEU* 1.3 74.9 + - - +
215E HIS* 3.4 22.6 + - + +
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Residues in contact with LEU 214 (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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205E LEU 2.8 1.7 - - - +
206E CYS* 2.8 35.5 - - - -
207E LEU* 2.8 40.4 + - + +
209E HIS* 4.7 17.0 - - + -
212E LYS* 4.0 24.0 - - + +
213E VAL* 1.3 84.3 - - - +
215E HIS* 1.3 61.6 + - - +
216E TYR* 4.5 5.6 - - + +
252E LEU* 4.4 22.0 - - + -
171F GLU* 3.9 42.6 - - + +
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Residues in contact with HIS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ARG* 3.5 39.7 + - + +
178E SER* 4.5 2.2 - - - -
179E GLU* 2.8 41.7 + - + +
195E ARG* 3.9 15.8 + - - +
204E ALA* 5.8 0.4 - - + -
205E LEU 2.9 4.7 - - - +
206E CYS* 3.7 17.2 - - + +
213E VAL* 3.4 24.3 - - + +
214E LEU* 1.3 77.4 - - + +
216E TYR* 1.3 57.2 + - - +
169F ASP 4.3 6.2 - - - +
170F PTR 3.5 20.2 - - + +
171F GLU* 2.7 34.9 + - - +
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Residues in contact with TYR 216 (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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204E ALA* 3.5 2.4 - - - -
205E LEU* 2.6 59.3 + - + +
207E LEU* 4.6 14.1 - - + -
214E LEU* 4.6 9.2 - - + -
215E HIS* 1.3 72.3 - - - +
217E ARG* 1.3 66.1 + - - +
218E ILE* 3.9 1.6 - - + +
228E ILE* 4.8 16.2 - - + -
250E GLY 3.9 1.0 + - - -
251E LEU* 3.2 42.6 - - + -
252E LEU* 3.2 28.2 + - - +
170F PTR 3.8 2.7 - - - -
171F GLU* 2.9 59.6 - - + +
172F PRO 3.5 13.1 + - - -
173F ILE* 4.9 2.7 - - + -
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Residues in contact with ARG 217 (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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197E ARG* 3.9 19.3 - - - +
202E SER* 3.8 22.0 + - - -
203E TYR 4.6 2.6 + - - -
216E TYR* 1.3 73.9 - - - +
218E ILE* 1.3 68.6 + - - +
219E ASP* 3.3 26.9 + - - +
228E ILE* 3.5 9.1 - - - +
229E PRO* 2.8 42.3 - - + +
170F PTR 3.3 49.5 - - + +
171F GLU 4.7 2.3 + - - +
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Residues in contact with ILE 218 (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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194E ILE* 3.8 29.2 - - + -
202E SER* 3.8 5.9 + - - -
203E TYR* 3.1 50.6 + - + +
204E ALA* 4.2 5.8 - - - +
205E LEU* 4.3 10.1 - - + +
216E TYR 3.5 8.3 + - - +
217E ARG* 1.3 79.2 + - - +
219E ASP* 1.3 67.6 + - - +
226E LEU* 4.5 12.6 - - + -
227E SER 4.3 16.8 - - - +
228E ILE* 4.9 10.3 - - + -
237E LEU* 4.5 6.1 - - + -
240E LEU* 3.9 26.0 - - + -
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Residues in contact with ASP 219 (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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201E GLY 4.4 3.8 - - - +
202E SER* 5.2 1.6 - - - +
203E TYR* 6.3 0.4 - - - -
217E ARG* 3.3 36.8 + - - +
218E ILE* 1.3 79.9 - - - +
220E LYS* 1.3 63.2 + - - +
221E ASP* 3.5 7.1 + - - +
225E LYS 3.6 0.3 - - - +
226E LEU* 3.5 3.0 - - - -
227E SER* 3.0 45.2 + - - +
229E PRO* 3.4 18.2 - - - +
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Residues in contact with LYS 220 (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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160E THR* 5.8 7.9 + - - +
200E ASN 4.4 9.8 + - - +
201E GLY* 3.2 37.0 + - - +
203E TYR* 5.2 9.4 + - + -
219E ASP* 1.3 72.5 - - - +
221E ASP* 1.3 68.7 + - - +
224E GLY* 3.4 38.9 + - - -
225E LYS 3.8 6.1 - - - -
226E LEU* 4.4 18.0 - - + +
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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