Contacts of the helix formed by residues 345 - 355 (chain B) in PDB entry 1PV7
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 PHE 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B LEU* 3.3 50.0 - - + -
215B GLU* 3.2 31.6 - - + -
216B LEU* 3.8 28.9 - - + -
219B GLN* 4.0 3.8 - - - -
221B LYS* 5.4 0.9 - - - -
341B PHE* 5.1 1.1 - + + -
342B GLU* 2.6 69.7 + - + +
343B VAL 2.9 1.4 - - - -
344B ARG* 1.3 91.3 - - + +
346B SER* 1.3 64.3 + - - -
347B ALA 3.3 2.0 - - - -
348B THR* 2.9 7.3 + - - -
349B ILE* 2.7 32.3 + - + +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B SER* 5.8 2.3 - - - -
337B ILE* 4.8 9.8 - - - +
341B PHE* 6.0 0.4 - - - +
342B GLU 4.3 0.8 + - - -
343B VAL* 3.5 17.4 + - - +
345B PHE* 1.3 72.5 - - - +
347B ALA* 1.3 77.1 + - - +
349B ILE* 2.8 24.4 + - - +
350B TYR* 3.0 28.9 + - - -
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B SER* 4.5 18.8 - - - -
207B ALA* 4.2 17.3 - - - +
208B PHE* 4.7 4.0 - - + -
344B ARG 5.1 2.0 + - - +
345B PHE 3.3 0.8 - - - -
346B SER* 1.3 83.0 + - - +
348B THR* 1.3 58.0 + - - +
350B TYR* 3.5 6.8 + - - +
351B LEU* 2.7 44.7 + - + +
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Residues in contact with THR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ALA 4.4 0.9 + - - -
208B PHE* 3.3 24.9 - - + +
209B SER 5.0 0.4 - - - +
212B LEU* 3.5 16.0 - - + +
213B ALA* 4.3 22.2 - - + +
216B LEU* 3.3 25.8 - - + -
344B ARG 4.4 3.8 + - - -
345B PHE* 2.9 13.7 + - - -
347B ALA* 1.3 72.0 - - - +
349B ILE* 1.3 58.6 + - - +
351B LEU* 3.8 8.5 - - + -
352B VAL* 2.6 45.8 + - + +
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LEU* 4.2 13.2 - - + +
222B LEU* 5.6 5.4 - - + -
225B LEU* 5.3 5.6 - - + -
337B ILE* 3.1 50.5 - - + -
341B PHE* 3.3 36.3 - - + -
345B PHE* 2.7 30.5 + - + +
346B SER 2.8 8.7 + - - +
348B THR* 1.3 71.3 - - - +
350B TYR* 1.3 60.0 + - + +
352B VAL* 5.1 0.2 - - - -
353B CYS* 2.3 54.0 + - + +
354B PHE* 4.9 4.5 - - + -
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Residues in contact with TYR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B PHE* 3.7 29.3 - - - +
337B ILE* 3.0 32.1 - - + +
346B SER* 3.0 20.6 + - - -
347B ALA* 3.9 7.9 - - - +
349B ILE* 1.3 76.9 - - + +
351B LEU* 1.3 69.9 + - + +
354B PHE* 2.6 47.6 + + + +
355B CYS* 3.0 7.3 + - - -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PRO* 5.2 15.5 - - + -
65B LEU* 5.3 4.0 - - + -
208B PHE* 3.2 60.8 - - + -
347B ALA* 2.7 33.4 + - + +
348B THR* 3.5 3.8 - - - +
350B TYR* 1.3 80.0 - - + +
352B VAL* 1.3 61.4 + - + +
355B CYS* 3.2 13.1 + - + +
356B PHE* 2.9 27.5 + - - +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE* 6.5 0.9 - - + -
213B ALA* 5.0 4.9 - - + -
216B LEU* 5.0 3.6 - - + -
217B PHE* 3.7 38.8 - - + -
222B LEU* 4.6 14.6 - - + -
348B THR* 2.6 35.3 + - + +
349B ILE* 5.1 0.2 - - - -
351B LEU* 1.3 78.3 - - + +
353B CYS* 1.3 59.6 + - - +
356B PHE* 4.0 8.9 - - + -
357B PHE* 2.9 48.1 + - + +
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Residues in contact with CYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B LEU* 3.7 20.4 - - + -
225B LEU* 4.7 10.3 - - - -
226B SER* 3.0 41.5 - - - -
229B VAL* 4.7 4.4 - - - +
230B ILE* 4.7 4.3 - - - +
349B ILE* 2.3 37.5 + - + +
352B VAL* 1.3 72.2 - - - +
354B PHE* 1.3 78.1 + - + +
357B PHE* 3.5 17.6 - - - +
358B LYS* 3.8 6.6 + - - +
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Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 5.0 6.5 - - + -
229B VAL* 3.3 40.4 - - + -
233B SER* 5.7 1.3 - - - -
329B LEU* 6.3 0.2 - - + -
333B CYS* 3.4 28.0 - - + -
337B ILE* 5.2 6.7 - - + -
349B ILE* 4.9 7.9 - - + -
350B TYR* 2.6 41.4 + + + +
353B CYS* 1.3 94.1 - - + +
355B CYS* 1.3 58.5 + - - +
358B LYS* 3.3 38.1 - - + +
359B GLN* 3.9 9.9 + - - +
2F GAL 5.6 2.5 - - - -
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Residues in contact with CYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B SER 4.2 11.2 - - - -
57B LEU* 3.1 23.5 - - - +
60B GLN* 4.8 11.2 - - - -
61B PRO* 3.1 40.8 - - + -
350B TYR 3.0 5.7 + - - +
351B LEU* 3.4 20.4 - - + +
354B PHE* 1.3 77.0 - - - +
356B PHE* 1.3 63.7 - - - +
357B PHE 3.3 0.9 - - - -
359B GLN* 3.6 17.1 - - - +
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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