Contacts of the strand formed by residues 243 - 253 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D LEU* 3.6 4.4 - - - +
201D TYR* 2.8 39.4 + - - +
234D GLN* 4.0 18.2 - - + +
235D ASN 2.9 27.9 + - - -
236D MET* 3.5 20.8 - - - +
237D PRO* 4.2 1.8 - - - +
242D ASN* 1.4 71.5 - - - +
244D SER* 1.3 60.6 + - - +
499D SO4 3.1 15.4 + - - -
233F ILE 3.5 2.0 - - - -
234F GLN* 3.4 7.0 - - - +
235F ASN* 2.8 41.2 + - - +
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Residues in contact with SER 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLN* 3.9 21.9 + - - -
199D VAL 3.3 10.8 - - - -
200D LEU* 3.7 15.1 - - - +
234D GLN* 4.1 4.6 + - - +
243D ASN* 1.3 73.9 - - - +
245D CYS* 1.3 62.1 + - - +
276D VAL* 5.0 0.7 - - - -
231F ARG 4.6 1.3 - - - -
232F CYS* 3.4 17.4 - - - -
233F ILE 2.9 33.4 + - - -
234F GLN* 3.4 15.1 - - - +
245F CYS* 4.8 3.3 - - - -
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Residues in contact with CYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLN* 3.2 23.5 - - - -
199D VAL 2.9 8.8 + - - -
201D TYR* 4.2 15.0 - - + -
210D HIS* 3.2 10.6 - - + -
232D CYS* 2.0 48.7 - - + -
233D ILE 4.0 2.9 - - - -
234D GLN* 3.7 28.0 - - + -
243D ASN 4.1 0.4 + - - -
244D SER* 1.3 75.0 - - - +
246D TYR* 1.3 61.3 + - - +
244E SER* 3.9 12.3 - - - -
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Residues in contact with TYR 246 (chain D).
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 9.9 - - - -
196D TYR* 3.4 26.6 - - + +
197D GLY 3.4 11.7 - - - -
198D GLN* 3.7 22.2 - - + +
232D CYS* 3.4 11.3 - - - -
244D SER 4.2 0.4 - - - -
245D CYS* 1.3 75.5 - - - +
247D SER* 1.3 60.4 + - - +
248D ALA* 3.6 19.8 - - + +
278D PHE* 4.3 3.4 - + - -
198E GLN* 4.0 0.3 - - - +
246E TYR* 3.4 57.8 + + + +
194F PHE* 4.5 1.6 - - - -
246F TYR* 3.5 35.0 - + + +
248F ALA* 3.3 41.3 + - - +
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Residues in contact with SER 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D TYR* 3.6 0.5 - - - -
197D GLY 3.1 31.7 + - - +
210D HIS* 4.9 5.2 - - - -
212D ILE* 3.9 7.3 - - - +
230D PHE* 3.9 15.0 - - - +
231D ARG 4.2 2.3 + - - -
232D CYS* 3.9 16.6 - - - -
246D TYR* 1.3 79.6 - - - +
248D ALA* 1.3 62.9 + - - +
198E GLN* 2.7 32.2 + - - -
246E TYR* 4.4 1.8 - - - -
278E PHE* 3.8 7.8 - - - -
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Residues in contact with ALA 248 (chain D).
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* 3.6 25.8 - - + -
195D ILE 3.1 15.9 - - - +
196D TYR* 3.7 2.9 - - + -
230D PHE* 4.5 6.5 - - - +
246D TYR* 3.6 14.8 - - + +
247D SER* 1.3 78.9 + - - +
249D GLY* 1.3 58.5 + - - +
196E TYR* 4.4 0.2 - - - -
246E TYR* 3.2 22.4 - - - +
278E PHE* 3.1 26.6 - - - -
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Residues in contact with GLY 249 (chain D).
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* 3.4 8.9 - - - -
195D ILE* 2.9 31.4 + - - +
230D PHE* 3.4 22.6 - - - -
248D ALA* 1.3 74.6 - - - +
250D ILE* 1.3 63.7 + - - -
148E GLN* 4.0 4.0 - - - -
196E TYR* 4.1 11.4 - - - -
278E PHE* 4.5 0.2 - - - -
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Residues in contact with ILE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D TYR* 4.5 3.1 - - + -
193D PHE 3.3 11.2 - - - +
194D PHE* 4.4 10.8 - - + -
230D PHE* 3.7 5.2 - - - -
249D GLY* 1.3 77.7 - - - +
251D ALA* 1.3 66.2 + - - +
284D LEU* 3.8 24.7 - - + -
146E CYS* 3.9 17.7 - - + -
147E LEU 5.5 0.7 - - - +
148E GLN* 2.9 19.8 + - - +
172E PHE* 3.3 36.4 - - + -
196E TYR* 3.2 35.4 + - + +
281E ALA 4.4 1.3 - - - +
282E LEU* 3.9 25.8 - - + -
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D TYR* 4.4 1.8 - - - -
193D PHE* 2.7 38.8 + - - -
195D ILE* 3.3 26.0 - - + -
229D LEU* 4.0 20.4 - - + -
230D PHE* 4.6 2.5 - - + -
250D ILE* 1.3 76.4 - - - +
252D LYS* 1.3 61.7 + - - +
253D LEU* 3.4 17.7 + - + +
172E PHE* 4.3 5.4 - - - -
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Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D GLY 3.6 7.2 - - - +
192D TYR* 3.1 48.4 + - + +
214D ARG* 3.8 17.5 + - - -
229D LEU* 5.8 0.7 - - - +
251D ALA* 1.3 71.2 - - - +
253D LEU* 1.4 66.2 + - - +
172E PHE* 4.1 32.6 - - + -
173E LYS 5.6 1.1 - - - -
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LEU* 5.7 0.2 - - + -
187D VAL* 3.9 18.8 - - + -
190D THR* 3.4 5.1 - - - +
191D GLY 2.8 34.4 + - - +
193D PHE* 3.6 33.8 - - + -
195D ILE* 3.8 7.2 - - + -
214D ARG* 3.7 30.1 - - + +
229D LEU* 4.2 1.6 - - + -
251D ALA* 3.4 18.4 + - + +
252D LYS* 1.4 82.1 - - - +
254D GLU* 1.3 62.9 + - - +
257D ASP* 3.8 6.3 - - + +
259D LEU* 3.8 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