Contacts of the strand formed by residues 353 - 359 (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 GLN 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349B LYS* 3.4 4.3 - - - +
350B ILE 2.9 33.2 + - - +
351B ASN* 3.3 21.8 + - - +
352B ASP* 1.3 80.2 - - - +
354B GLU* 1.3 65.5 + - - +
355B LYS* 3.6 30.7 + - - +
370B ASP* 4.0 8.2 + - - +
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Residues in contact with GLU 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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309B TYR* 3.4 54.0 - - + +
310B ASN* 4.7 3.9 - - - +
348B ALA 3.7 3.8 - - - -
349B LYS* 4.7 10.8 - - + +
353B GLN* 1.3 72.4 - - - +
355B LYS* 1.3 62.2 + - - +
370B ASP* 4.2 1.9 - - - +
371B ALA* 3.1 27.2 + - + +
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Residues in contact with LYS 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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309B TYR* 3.6 3.1 - - - -
347B ASN* 3.2 8.8 - - - +
348B ALA* 2.8 36.8 + - + +
350B ILE* 4.1 25.4 - - + -
353B GLN* 3.6 39.8 + - - +
354B GLU* 1.3 80.8 - - - +
356B LEU* 1.3 65.4 + - - +
357B ILE* 5.4 0.7 - - + -
368B ILE* 3.5 30.7 - - + +
369B GLN 3.3 7.4 - - - +
370B ASP* 2.5 31.7 + - - +
371B ALA* 4.1 0.4 - - - +
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Residues in contact with LEU 356 (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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306B VAL* 4.1 7.2 - - + -
307B PRO 4.0 17.3 - - - +
309B TYR* 4.2 16.4 - - + -
312B VAL* 3.8 31.6 - - + -
344B VAL* 5.6 2.5 - - + -
346B GLY 3.6 3.8 - - - +
347B ASN* 4.0 7.6 - - + -
355B LYS* 1.3 81.1 - - - +
357B ILE* 1.3 65.0 + - - +
358B TYR* 4.9 1.3 - - + -
368B ILE* 3.4 3.6 - - - +
369B GLN* 2.7 50.8 + - + +
371B ALA* 4.1 17.7 - - + -
386B TRP* 3.8 34.5 - - + -
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Residues in contact with ILE 357 (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 GLU* 3.8 23.3 - - - +
227B THR* 4.0 11.2 - - + -
344B VAL* 3.7 4.0 - - - +
345B VAL* 2.8 31.0 + - + -
346B GLY 2.9 17.9 + - - +
347B ASN* 3.9 15.0 - - - +
348B ALA* 3.8 25.1 - - + +
350B ILE* 5.9 1.1 - - + -
355B LYS 5.3 0.2 - - - -
356B LEU* 1.3 76.9 - - - +
358B TYR* 1.3 65.5 + - - +
366B LEU* 3.9 31.0 - - + -
367B SER 3.4 12.1 - - - +
368B ILE* 4.7 14.1 - - + -
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Residues in contact with TYR 358 (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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216A HIS* 5.5 0.3 - - - -
324B ILE* 3.9 22.0 - - + -
342B LEU* 3.6 31.4 - - + -
343B ALA 3.2 13.7 - - - +
344B VAL* 4.3 1.1 - - + -
345B VAL* 4.1 6.3 - - - +
356B LEU* 4.3 2.0 - - + -
357B ILE* 1.3 76.7 - - - +
359B TRP* 1.3 63.5 + - - +
360B ASN* 4.6 2.9 - - + -
366B LEU* 3.5 6.1 - - - +
367B SER* 2.8 67.4 + - - -
368B ILE 4.0 4.6 + - - -
369B GLN* 3.8 33.1 + - + -
376B LEU* 4.0 18.6 - - + +
377B HIS 3.9 13.5 + - - -
378B LEU* 3.6 20.7 - - + +
386B TRP* 5.7 2.2 - + + -
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Residues in contact with TRP 359 (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* 4.1 21.5 - + + -
233B ILE* 3.6 41.2 - - + +
234B ARG 5.7 0.7 - - - -
235B GLU* 3.2 30.7 - - + -
246B PHE* 3.6 35.2 - + + -
247B SER 4.3 0.2 - - - -
250B ALA* 3.8 11.9 - - + -
342B LEU* 3.3 4.2 - - - +
343B ALA* 2.7 44.9 + - + +
345B VAL* 4.1 0.4 - - + -
358B TYR* 1.3 78.5 - - - +
360B ASN* 1.3 72.1 + - - +
361B PRO* 3.5 31.8 - - + +
363B ASP 2.9 20.1 + - - -
365B GLU 3.7 12.3 - - - -
366B LEU* 3.9 10.5 - - + -
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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