Contacts of the strand formed by residues 243 - 253 (chain E) in PDB entry 3V56
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 ASN 243 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D ILE 3.4 2.2 - - - -
234D GLN* 3.4 7.6 - - - +
235D ASN* 2.7 45.6 + - - +
499D SO4 3.5 12.3 + - - -
200E LEU* 3.6 3.8 - - - +
201E TYR* 2.8 40.0 + - - +
234E GLN* 3.9 21.1 - - + +
235E ASN 2.9 27.5 + - - -
236E MET* 3.5 20.2 - - - +
237E PRO* 4.2 0.6 - - - +
242E ASN* 1.3 71.3 - - - +
244E SER* 1.3 60.0 + - - +
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Residues in contact with SER 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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231D ARG 4.6 1.3 - - - -
232D CYS* 3.4 17.9 - - - -
233D ILE 2.9 32.4 + - - -
234D GLN* 3.4 15.4 - - - +
245D CYS* 4.8 2.8 - - - -
198E GLN* 3.9 21.3 + - - -
199E VAL 3.2 10.1 - - - -
200E LEU* 3.8 14.9 - - - +
234E GLN* 4.2 3.8 + - - +
243E ASN* 1.3 73.7 - - - +
245E CYS* 1.3 61.7 + - - +
246E TYR 4.3 0.2 - - - -
276E VAL* 5.0 0.9 - - - -
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Residues in contact with CYS 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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198E GLN* 3.2 23.7 - - - -
199E VAL 2.9 8.8 + - - -
201E TYR* 4.2 13.7 - - + -
210E HIS* 3.2 10.7 - - - -
232E CYS* 2.0 49.6 - - + -
233E ILE 4.0 2.7 - - - -
234E GLN* 3.7 28.9 - - + -
243E ASN 4.0 0.2 + - - -
244E SER* 1.3 75.0 - - - +
246E TYR* 1.3 61.3 + - - +
244F SER* 3.9 11.9 - - - -
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Residues in contact with TYR 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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194D PHE* 4.0 4.7 - - - -
246D TYR* 3.4 54.0 + + + +
248D ALA* 3.2 44.0 - - + +
194E PHE* 4.0 9.0 - - - -
196E TYR* 3.4 30.8 - - + +
197E GLY 3.4 12.8 - - - -
198E GLN* 3.7 18.8 + - + +
232E CYS* 3.4 10.2 - - - -
244E SER 4.3 0.2 - - - -
245E CYS* 1.3 75.4 - - - +
247E SER* 1.3 60.4 + - - +
248E ALA* 3.6 16.5 - - + +
278E PHE* 4.3 3.1 - + - -
198F GLN* 4.0 0.3 - - - +
246F TYR* 3.6 33.4 + + + +
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Residues in contact with SER 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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196E TYR* 3.6 0.3 - - - -
197E GLY 3.1 30.7 + - - +
210E HIS* 4.9 4.5 + - - -
212E ILE* 3.9 8.3 - - - +
230E PHE* 3.9 14.0 - - - +
231E ARG 4.2 1.9 + - - -
232E CYS* 3.9 16.8 - - - -
246E TYR* 1.3 79.5 - - - +
248E ALA* 1.3 64.0 + - - +
198F GLN* 2.7 32.3 + - - -
246F TYR* 4.4 2.2 - - - -
278F PHE* 3.7 8.5 - - - -
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Residues in contact with ALA 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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194E PHE* 3.6 18.6 - - + -
195E ILE 3.1 15.5 - - - +
196E TYR* 3.7 2.5 - - + -
230E PHE* 4.4 7.2 - - - -
246E TYR* 3.6 26.2 - - + +
247E SER* 1.3 78.4 + - - +
249E GLY* 1.3 57.3 + - - +
196F TYR* 4.5 0.5 - - - -
246F TYR* 3.3 17.4 + - - +
278F PHE* 3.1 26.3 - - - -
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Residues in contact with GLY 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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194E PHE* 3.5 9.2 - - - -
195E ILE* 2.9 31.5 + - - +
230E PHE* 3.4 23.3 - - - -
248E ALA* 1.3 75.6 - - - +
250E ILE* 1.3 66.8 + - - -
148F GLN* 4.1 4.3 - - - -
196F TYR* 4.4 9.2 - - - -
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Residues in contact with ILE 250 (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 TYR* 4.3 7.6 - - + -
193E PHE 3.3 11.9 - - - +
194E PHE* 4.2 13.7 - - + -
230E PHE* 3.7 5.1 - - - -
249E GLY* 1.3 78.9 - - - +
251E ALA* 1.3 70.4 + - - +
284E LEU* 3.8 26.0 - - + -
146F CYS* 4.3 14.1 - - + -
148F GLN* 3.1 27.6 + - - -
172F PHE* 3.6 26.4 - - + -
196F TYR* 3.3 31.4 - - + +
282F LEU* 4.1 23.8 - - + -
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Residues in contact with ALA 251 (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 TYR* 3.4 3.5 - - - -
193E PHE* 2.8 35.5 + - - +
195E ILE* 3.8 20.6 - - + -
229E LEU* 4.1 27.6 - - + -
230E PHE* 4.6 2.5 - - + -
250E ILE* 1.3 79.3 - - - +
252E LYS* 1.4 61.5 + - - +
253E LEU* 3.7 8.1 + - + +
172F PHE* 5.1 3.8 - - - -
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Residues in contact with LYS 252 (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 THR* 4.0 23.6 - - - -
191E GLY* 3.3 16.4 - - - +
192E TYR* 3.7 47.3 + - + -
214E ARG* 3.9 17.2 + - - -
251E ALA* 1.4 70.9 - - - +
253E LEU* 1.3 66.4 + - - +
254E GLU* 5.7 3.8 - - + -
172F PHE* 5.7 3.1 - - + -
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Residues in contact with LEU 253 (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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178E LEU* 5.7 0.2 - - + -
187E VAL* 3.8 20.6 - - + -
190E THR* 3.3 6.3 - - - +
191E GLY 2.7 32.4 + - - +
193E PHE* 3.6 30.2 - - + -
195E ILE* 3.8 12.6 - - + -
214E ARG* 3.8 32.1 - - + +
229E LEU* 4.4 1.3 - - + -
251E ALA* 4.1 17.0 - - + +
252E LYS* 1.3 84.0 - - - +
254E GLU* 1.3 61.5 + - - +
257E ASP* 3.8 3.4 - - + +
259E LEU* 3.7 35.2 - - + -
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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