Contacts of the strand formed by residues 339 - 350 (chain B) in PDB entry 1PXV
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 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B ALA 3.5 8.1 - - - -
327B GLN* 4.3 4.9 - - - -
337B HIS* 4.0 3.4 + - - +
338B LEU* 1.3 71.6 - - - +
340B HIS* 1.3 57.8 + - - -
387B TYR* 6.0 0.4 - - - -
92D SER* 3.8 4.2 + - - -
93D SER 5.1 1.0 + - - -
96D GLY 4.4 13.0 + - - -
97D ILE* 4.0 6.5 - - - -
98D GLY 2.9 23.2 + - - -
99D THR* 2.5 23.7 + - - -
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Residues in contact with HIS 340 (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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237B GLN* 3.4 14.4 - - - -
243B ALA* 3.3 28.4 - - + +
324B ILE 3.8 0.3 - - - +
325B LEU* 3.8 0.5 - - - -
326B ALA* 2.8 34.1 + - - +
339B GLY* 1.3 73.4 - - - +
341B ALA* 1.3 66.2 + - - +
342B LEU* 3.8 21.8 - - + -
360B ASN* 2.9 26.3 + - - -
361B PRO* 4.4 0.7 - - + -
362B TRP* 3.4 19.0 + + - -
378B LEU* 4.1 17.0 - - + -
384B TYR* 3.6 22.9 - + + -
97D ILE* 3.7 12.0 - - - +
98D GLY 4.2 1.3 - - - +
99D THR* 3.6 13.6 + - - +
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Residues in contact with ALA 341 (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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243B ALA* 3.5 11.4 - - + +
244B ALA* 3.6 37.9 - - + +
247B SER* 3.3 7.4 + - - -
323B MET* 4.0 11.0 - - - -
324B ILE 3.1 9.6 - - - +
325B LEU* 4.4 3.4 - - + -
340B HIS* 1.3 79.7 + - - +
342B LEU* 1.3 64.0 + - - +
361B PRO* 3.5 13.3 - - - +
97D ILE* 4.1 10.0 - - + +
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Residues in contact with LEU 342 (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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247B SER* 3.2 10.2 + - - -
323B MET* 3.5 5.5 - - - +
324B ILE* 2.7 54.9 + - + +
326B ALA* 4.1 15.0 - - + -
340B HIS* 3.8 18.8 - - + -
341B ALA* 1.3 84.3 - - - +
343B ALA* 1.3 60.9 + - - +
358B TYR* 3.6 22.9 - - + -
359B TRP 3.3 10.3 - - - +
360B ASN* 3.6 28.9 - - + -
361B PRO* 3.9 1.3 - - - -
376B LEU* 4.3 4.9 - - + -
378B LEU* 3.8 15.0 - - + -
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Residues in contact with ALA 343 (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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231B PHE* 4.3 14.6 - - + -
247B SER* 3.6 15.6 + - - +
251B LEU* 3.9 28.0 - - + -
322B ILE 3.9 3.1 - - - -
324B ILE* 4.5 0.7 - - - -
342B LEU* 1.3 74.7 - - - +
344B VAL* 1.3 63.9 + - - +
345B VAL* 3.9 0.9 - - - +
358B TYR* 3.2 6.5 - - - +
359B TRP* 2.7 46.4 + - + +
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Residues in contact with VAL 344 (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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228B LEU* 4.4 5.0 - - - +
231B PHE* 4.7 0.3 - - - -
251B LEU* 3.5 19.8 - - - +
307B PRO* 5.4 0.7 - - + -
312B VAL* 4.0 24.5 - - + -
316B THR* 5.2 1.3 - - - +
322B ILE* 3.0 51.2 + - + +
324B ILE* 3.6 25.8 - - + -
343B ALA* 1.3 73.1 - - - +
345B VAL* 1.3 63.4 + - - +
346B GLY 3.8 13.0 - - - +
356B LEU* 5.6 2.7 - - + -
357B ILE 3.8 8.3 - - - +
358B TYR* 4.3 1.8 - - + +
386B TRP* 3.9 14.1 - - + -
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Residues in contact with VAL 345 (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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227B THR* 3.3 22.2 - - + -
228B LEU* 2.8 36.6 + - - +
231B PHE* 3.8 42.4 - - + -
316B THR* 4.0 1.9 - - - +
343B ALA 3.9 8.7 - - - +
344B VAL* 1.3 78.2 - - - +
346B GLY* 1.3 59.0 + - - +
357B ILE* 2.8 16.1 + - + +
358B TYR 4.1 4.7 - - - -
359B TRP 4.1 0.4 - - - +
366B LEU* 3.7 36.3 - - + -
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Residues in contact with GLY 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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226B ASN 3.2 11.7 - - - -
227B THR* 4.2 2.0 - - - -
312B VAL* 3.6 11.6 - - - +
316B THR* 3.8 15.9 - - - -
344B VAL* 3.8 3.9 - - - +
345B VAL* 1.3 80.5 - - - +
347B ASN* 1.3 64.3 + - - +
356B LEU* 3.6 3.8 - - - -
357B ILE* 2.9 27.5 + - - +
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Residues in contact with ASN 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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224B TYR* 3.8 3.2 - - - -
226B ASN* 2.9 53.0 + - - +
309B TYR* 3.4 32.0 + - + -
312B VAL* 3.8 4.3 - - + +
313B ASP* 2.9 43.4 + - - +
346B GLY* 1.3 76.9 - - - +
348B ALA* 1.3 62.1 + - - +
355B LYS 3.2 15.7 - - - +
356B LEU* 4.0 9.6 - - + +
357B ILE* 3.9 7.7 - - - +
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Residues in contact with ALA 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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222B VAL* 5.0 1.3 - - + -
224B TYR* 3.1 15.7 - - - +
225B GLU* 4.1 8.5 - - + -
309B TYR* 3.3 11.9 - - - -
347B ASN* 1.3 77.4 - - - +
349B LYS* 1.3 58.4 + - - +
350B ILE* 3.9 23.1 - - + -
355B LYS* 2.8 35.9 + - + +
357B ILE* 3.8 17.9 - - + +
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Residues in contact with LYS 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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222B VAL 3.8 0.2 - - - -
223B GLN* 3.0 47.5 + - + +
224B TYR* 2.8 22.6 + - + +
309B TYR* 3.6 12.9 + - + +
348B ALA* 1.3 71.7 - - - +
350B ILE* 1.3 60.6 + - - +
352B ASP* 3.8 34.6 + - - +
353B GLN 3.4 12.8 - - - +
354B GLU* 4.7 9.4 - - + +
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Residues in contact with ILE 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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214A HIS* 5.5 4.9 - - + -
220B ASP* 4.3 14.8 - - + -
221B GLN 3.3 13.9 - - - +
222B VAL* 4.3 16.8 - - + -
348B ALA* 3.9 20.0 - - + -
349B LYS* 1.3 80.1 - - - +
351B ASN* 1.3 88.5 + - - +
352B ASP 3.1 1.6 - - - -
353B GLN* 2.9 25.6 + - - +
355B LYS* 4.1 26.0 - - + -
357B ILE* 5.9 1.8 - - + -
368B ILE* 4.4 26.2 - - + -
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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