Contacts of the strand formed by residues 243 - 253 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.6 3.7 - - - +
201A TYR* 2.8 38.8 + - - +
234A GLN* 3.9 18.6 - - + +
235A ASN 2.9 27.5 + - - -
236A MET* 3.5 21.1 - - - +
237A PRO* 4.2 0.8 - - - +
242A ASN* 1.3 70.7 - - - +
244A SER* 1.3 60.5 + - - +
499A SO4 3.0 17.6 + - - -
233C ILE 3.5 2.7 - - - -
234C GLN* 3.4 4.9 - - - +
235C ASN* 2.7 47.0 + - - +
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN* 4.0 21.8 + - - -
199A VAL 3.3 10.1 - - - -
200A LEU* 3.8 14.9 - - - +
234A GLN* 4.1 4.6 + - - +
243A ASN* 1.3 74.9 - - - +
245A CYS* 1.3 60.5 + - - +
246A TYR 4.3 0.2 - - - -
276A VAL* 5.0 0.9 - - - -
231C ARG 4.6 0.9 - - - -
232C CYS* 3.4 17.2 - - - -
233C ILE 2.8 35.9 + - - -
234C GLN* 3.4 15.4 - - - +
245C CYS* 4.8 2.6 - - - -
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Residues in contact with CYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN* 3.2 22.8 - - - -
199A VAL 2.9 9.2 + - - -
201A TYR* 4.2 14.4 - - + -
210A HIS* 3.2 10.9 - - - -
232A CYS* 2.0 48.5 - - + -
233A ILE 4.0 2.7 - - - -
234A GLN* 3.7 28.7 - - + -
243A ASN 4.1 0.2 + - - -
244A SER* 1.3 76.0 - - - +
246A TYR* 1.3 60.9 + - - +
244B SER* 3.9 12.8 - - - -
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PHE* 4.0 10.2 - - - -
196A TYR* 3.4 26.7 - - + +
197A GLY 3.4 11.2 - - - -
198A GLN* 3.7 27.3 + - + +
232A CYS* 3.4 9.4 - - - -
244A SER 4.3 0.2 - - - -
245A CYS* 1.3 76.7 - - - +
247A SER* 1.3 58.9 + - - +
248A ALA* 3.6 22.7 - - + +
278A PHE* 4.2 4.3 - + - -
198B GLN* 4.0 0.9 - - - +
246B TYR* 3.5 52.3 + + + +
194C PHE* 4.5 1.7 - - - -
246C TYR* 3.6 28.3 + + + +
248C ALA* 3.4 39.9 + - + +
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A TYR* 3.6 0.3 - - - -
197A GLY 3.1 32.0 + - - +
210A HIS* 5.0 4.7 - - - -
212A ILE* 3.8 8.0 - - - +
230A PHE* 3.9 14.4 - - - +
231A ARG 4.2 3.2 + - - -
232A CYS* 4.0 16.1 - - - -
246A TYR* 1.3 81.5 - - - +
248A ALA* 1.3 63.6 + - - +
198B GLN* 2.7 30.3 + - - -
246B TYR* 4.4 2.2 - - - -
278B PHE* 3.7 8.3 - - - -
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PHE* 3.6 17.7 - - + -
195A ILE 3.1 15.9 - - - +
196A TYR* 3.7 3.1 - - + -
212A ILE* 5.2 0.2 - - - -
230A PHE* 4.4 6.3 - - - -
246A TYR* 3.6 27.1 - - + +
247A SER* 1.3 78.6 + - - +
249A GLY* 1.3 58.4 + - - +
196B TYR* 4.3 1.4 - - - -
246B TYR* 3.4 16.8 + - - +
278B PHE* 3.1 26.3 - - - -
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Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PHE 3.6 0.3 - - - +
194A PHE* 3.4 9.0 - - - -
195A ILE 2.8 30.9 + - - +
230A PHE* 3.3 24.5 - - - -
248A ALA* 1.3 75.5 - - - +
250A ILE* 1.3 63.1 + - - -
148B GLN* 3.9 5.4 - - - -
196B TYR* 4.2 9.4 - - - -
278B PHE* 4.7 0.2 - - - -
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR* 4.3 6.1 - - + -
193A PHE 3.4 12.6 - - - +
194A PHE* 4.3 13.2 - - + -
230A PHE* 3.7 5.1 - - - -
249A GLY* 1.3 78.5 - - - +
251A ALA* 1.3 66.9 + - - +
284A LEU* 3.8 28.5 - - + -
146B CYS* 3.9 25.6 - - + -
147B LEU 5.6 0.2 - - - +
148B GLN* 3.0 29.1 + - - +
172B PHE* 3.4 27.8 - - + -
196B TYR* 3.3 28.9 - - + +
281B ALA 4.8 0.9 - - - +
282B LEU* 4.4 11.7 - - + -
220F PHE* 4.0 3.1 - - - -
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR* 3.5 5.9 - - - -
193A PHE* 2.9 32.5 + - - +
195A ILE* 4.0 9.0 - - + -
229A LEU* 3.9 39.0 - - + -
230A PHE* 4.6 2.5 - - + -
250A ILE* 1.3 78.2 - - - +
252A LYS* 1.3 64.4 + - - +
253A LEU* 3.5 9.6 + - + +
220F PHE* 3.7 12.8 - - + -
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR* 3.9 24.9 - - - -
191A GLY* 3.4 18.6 - - - +
192A TYR* 3.7 36.5 + - + +
214A ARG* 3.8 17.8 + - - +
251A ALA* 1.3 73.4 - - - +
253A LEU* 1.3 67.7 + - - +
254A GLU* 5.2 6.7 - - + +
220F PHE* 3.4 32.7 - - + -
254F GLU* 3.9 26.4 + - - +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 5.7 0.2 - - + -
187A VAL* 3.8 25.6 - - + -
190A THR* 3.4 4.6 - - - +
191A GLY 2.9 32.9 + - - +
193A PHE* 3.8 25.4 - - + -
195A ILE* 4.0 7.9 - - + -
214A ARG* 3.7 28.3 - - + +
229A LEU* 4.3 2.0 - - + -
251A ALA* 4.0 19.3 - - + +
252A LYS* 1.3 86.8 - - - +
254A GLU* 1.3 62.5 + - - +
257A ASP* 3.7 7.9 - - + +
259A LEU* 3.7 36.8 - - + -
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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