Contacts of the strand formed by residues 227 - 235 (chain E) in PDB entry 1II4
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 227 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193E LYS* 5.5 0.7 - - - -
194E ASN* 3.6 11.9 - - - -
225E ASP 3.3 1.7 + - - -
226E LYS* 1.3 80.8 - - - +
228E ASN* 1.3 66.3 + - - -
229E TYR* 3.6 9.9 - - - -
245E HIS* 3.6 1.8 - - - -
246E LEU 2.9 31.7 + - - -
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Residues in contact with ASN 228 (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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192E LEU 3.4 0.3 - - - +
193E LYS* 3.2 5.5 - - - +
194E ASN* 2.6 51.5 + - - +
195E GLY 5.6 0.4 - - - +
227E GLY* 1.3 74.7 - - - -
229E TYR* 1.3 62.8 + - - +
230E THR* 4.1 2.4 + - - +
243E THR* 3.7 19.4 - - + +
244E TYR 3.3 2.8 - - - +
245E HIS* 3.7 22.2 - - - +
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Residues in contact with TYR 229 (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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177E PHE* 3.9 29.6 - + + -
191E TRP* 4.6 4.3 - - + -
192E LEU 3.1 11.9 - - - +
193E LYS* 3.7 27.2 - - + +
198E PHE* 3.7 36.8 - + - -
216E LEU* 4.0 14.1 - - + -
218E MET* 3.5 19.2 - - + +
225E ASP* 2.5 33.6 + - - -
227E GLY 3.6 17.5 - - - -
228E ASN* 1.3 74.1 - - - +
230E THR* 1.3 60.1 + - - +
242E HIS 3.9 0.9 - - - +
243E THR* 3.4 0.7 - - - -
244E TYR* 2.7 46.8 + - + +
246E LEU* 3.6 15.0 - - + -
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Residues in contact with THR 230 (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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190E ARG 3.6 0.3 - - - +
191E TRP* 3.1 8.5 - - - -
192E LEU* 2.6 55.1 + - + +
195E GLY* 5.2 5.5 + - - -
228E ASN* 4.1 2.8 + - - +
229E TYR* 1.3 73.4 + - - +
231E CYS* 1.3 72.5 + - - +
232E VAL* 3.9 8.0 + - + -
241E ASN* 3.9 18.8 - - + +
242E HIS 3.3 11.9 - - - +
243E THR* 2.7 29.2 + - - +
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Residues in contact with CYS 231 (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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156E TRP* 3.6 9.2 - - - -
179E CYS* 2.5 45.1 - - - -
189E MET* 3.7 13.2 - - + -
190E ARG 3.3 6.1 - - - -
191E TRP* 3.6 19.4 - - + -
230E THR* 1.3 74.1 - - - +
232E VAL* 1.3 59.7 + - - +
233E VAL 4.0 0.2 - - - -
240E ILE 4.0 0.2 - - - +
241E ASN* 3.1 21.0 - - - +
242E HIS* 3.0 26.3 + - - -
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Residues in contact with VAL 232 (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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188E THR 3.6 1.0 - - - +
189E MET* 3.4 3.1 - - - +
190E ARG* 2.8 59.6 + - + +
192E LEU* 4.1 23.8 - - + -
230E THR* 4.1 10.3 - - + -
231E CYS* 1.3 76.5 - - - +
233E VAL* 1.3 61.6 + - - +
234E GLU* 3.4 25.4 - - - +
239E SER* 3.9 9.9 - - - +
240E ILE 3.7 4.9 - - - +
241E ASN* 4.1 13.0 - - + -
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Residues in contact with VAL 233 (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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154E PRO* 3.9 8.7 - - + +
156E TRP* 3.4 34.5 - - + -
181E ALA* 3.9 14.8 - - + -
187E PRO* 3.4 29.8 - - + -
188E THR 3.1 9.6 - - - +
189E MET* 3.6 25.6 - - + -
214E TRP* 4.2 3.8 - - + -
232E VAL* 1.3 73.8 - - - +
234E GLU* 1.3 67.0 + - - +
239E SER* 3.3 1.6 + - - -
240E ILE* 2.9 38.8 + - + +
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Residues in contact with GLU 234 (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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154E PRO* 3.8 4.0 - - - -
187E PRO* 2.9 6.5 - - - +
188E THR* 2.8 50.3 + - - +
190E ARG* 3.2 31.3 + - - -
232E VAL* 3.4 9.3 - - + +
233E VAL* 1.3 80.0 - - - +
235E ASN* 1.3 62.8 + - - +
238E GLY 3.2 14.8 - - - +
239E SER* 3.1 23.2 + - - +
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Residues in contact with ASN 235 (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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152E ARG 2.8 26.4 + - - -
153E ALA 3.7 0.2 - - - -
154E PRO* 3.2 25.4 - - - +
183E GLY* 4.1 2.0 - - - -
184E ASN 4.0 2.6 - - - +
185E PRO* 3.3 37.9 + - + +
186E MET 4.8 1.1 - - - +
187E PRO* 4.1 4.9 - - + +
234E GLU* 1.3 77.1 - - - +
236E GLU* 1.3 59.7 + - - +
237E TYR* 2.6 38.2 + - - +
238E GLY 3.0 16.4 + - - +
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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