Contacts of the strand formed by residues 238 - 249 (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 238 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153E ALA* 4.1 2.0 - - - -
154E PRO* 3.4 12.1 - - - +
234E GLU* 3.2 3.8 - - - +
235E ASN* 3.0 33.1 + - - +
236E GLU 3.5 1.4 - - - -
237E TYR* 1.3 81.2 - - - +
239E SER* 1.3 60.2 + - - -
240E ILE* 6.0 0.4 - - - -
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Residues in contact with SER 239 (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* 4.1 0.8 - - - +
232E VAL* 3.9 8.5 - - - +
233E VAL 3.3 6.7 + - - -
234E GLU* 3.1 30.0 + - - +
238E GLY* 1.3 75.6 - - - -
240E ILE* 1.3 69.4 + - - +
241E ASN* 5.5 0.3 - - - +
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Residues in contact with ILE 240 (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* 3.4 40.6 - - + +
155E TYR* 3.7 11.4 - - - +
156E TRP* 3.6 40.0 - - + +
231E CYS 4.0 0.2 - - - +
232E VAL* 3.7 2.0 - - - +
233E VAL* 2.9 39.5 + - + +
238E GLY* 6.0 0.2 - - - -
239E SER* 1.3 83.8 + - - +
241E ASN* 1.3 63.8 + - - +
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Residues in contact with ASN 241 (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* 3.9 10.9 + - - -
230E THR* 3.9 18.1 - - + +
231E CYS 3.1 15.0 - - - +
232E VAL* 4.1 11.9 - - + -
239E SER 5.5 0.3 - - - +
240E ILE* 1.3 77.8 - - - +
242E HIS* 1.3 66.0 + - - +
243E THR* 4.4 6.3 + - - +
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Residues in contact with HIS 242 (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* 4.0 4.4 + - + +
162E MET* 3.3 61.9 + - + +
165E ARG* 3.4 34.0 + - + +
179E CYS* 4.2 0.4 - - - -
229E TYR 3.9 0.9 - - - +
230E THR* 3.3 2.9 - - - +
231E CYS* 3.0 36.2 + - - -
241E ASN* 1.3 77.8 - - - +
243E THR* 1.3 71.7 + - - +
244E TYR* 3.3 39.1 - + - -
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Residues in contact with THR 243 (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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165E ARG* 4.3 12.7 + - - +
228E ASN* 3.7 22.0 - - + -
229E TYR 3.4 4.3 - - - +
230E THR* 2.7 29.1 + - - +
241E ASN* 4.4 6.1 + - - +
242E HIS* 1.3 92.0 + - - +
244E TYR* 1.3 77.5 + - - +
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Residues in contact with TYR 244 (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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161E LYS 3.6 5.1 + - - -
162E MET* 3.4 24.0 - - - +
164E LYS 3.4 26.9 - - - -
165E ARG* 3.3 8.7 - - - +
167E HIS* 3.9 13.0 - + - -
177E PHE* 3.5 46.4 - + + -
178E ARG 2.5 33.4 + - - -
179E CYS* 3.9 7.9 - - - -
191E TRP* 4.5 4.9 - + - -
228E ASN* 3.3 3.6 - - - -
229E TYR* 2.7 39.8 + - + +
242E HIS* 3.3 31.9 - + - -
243E THR* 1.3 77.2 - - - +
245E HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 245 (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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165E ARG* 2.9 9.1 + - - +
166E LEU* 3.5 20.8 - - + +
167E HIS* 2.8 31.6 + - - +
177E PHE* 4.9 0.2 - - - -
227E GLY 3.6 5.4 - - - +
228E ASN* 3.7 15.3 - - - +
244E TYR* 1.3 75.5 - - - +
246E LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 246 (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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166E LEU* 5.0 0.4 - - - -
167E HIS* 3.3 11.2 - - + +
169E VAL* 4.5 6.7 - - + -
175E VAL* 4.2 26.0 - - + -
177E PHE* 3.9 10.3 - - + -
218E MET* 4.5 10.8 - - - -
221E VAL* 4.5 10.5 - - + -
225E ASP* 3.5 34.3 - - + +
226E LYS* 3.2 8.7 - - - +
227E GLY 2.9 29.1 + - - +
229E TYR* 3.6 28.5 - - + +
244E TYR 4.1 0.2 + - - -
245E HIS* 1.3 75.1 - - - +
247E ASP* 1.3 77.5 + - - +
248E VAL* 4.4 7.0 - - + -
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Residues in contact with ASP 247 (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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151A MET* 3.5 30.1 - - + +
166E LEU* 4.5 11.6 - - + +
167E HIS 2.9 11.0 + - - +
168E ALA* 3.2 4.5 - - + -
169E VAL 3.0 26.0 + - - -
226E LYS* 3.3 38.2 + - - +
246E LEU* 1.3 76.5 - - - +
248E VAL* 1.3 75.7 + - - +
249E VAL* 4.2 1.4 + - - +
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Residues in contact with VAL 248 (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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169E VAL* 3.4 4.5 - - + +
171E ALA* 3.3 38.8 - - + +
221E VAL* 4.1 19.7 - - + +
222E VAL* 3.1 37.9 - - - +
223E PRO* 3.7 16.8 - - + +
225E ASP* 4.4 7.6 - - + -
226E LYS* 4.6 6.9 - - - +
246E LEU* 4.4 8.5 - - + -
247E ASP* 1.3 84.7 + - - +
249E VAL* 1.3 66.7 + - - +
250E GLU 4.3 0.3 + - - -
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Residues in contact with VAL 249 (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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149A LEU* 3.9 30.1 - - + -
150A PRO* 4.0 15.0 - - + +
151A MET* 4.2 28.0 - - + -
169E VAL 3.0 5.9 + - - -
170E PRO* 3.1 7.3 - - - +
171E ALA* 2.7 27.1 + - - -
247E ASP* 5.0 2.0 - - - +
248E VAL* 1.3 78.6 - - - +
250E GLU* 1.3 71.0 + - - +
251E ARG* 3.7 14.8 + - - +
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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