Contacts of the strand formed by residues 353 - 359 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A LYS* 3.3 4.8 - - - +
350A ILE 2.9 32.1 + - - +
351A ASN* 3.5 21.5 + - - +
352A ASP* 1.3 81.9 - - - +
354A GLU* 1.3 65.7 + - - +
355A LYS* 3.2 32.8 + - + +
370A ASP* 5.3 2.8 + - - -
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Residues in contact with GLU 354 (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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309A TYR* 3.5 52.0 - - + +
310A ASN* 4.9 3.7 - - - +
348A ALA 3.7 4.0 - - - -
349A LYS* 5.1 7.6 - - + -
352A ASP 5.8 0.4 - - - +
353A GLN* 1.3 75.7 - - - +
355A LYS* 1.3 64.1 + - - +
370A ASP* 4.1 1.0 - - - +
371A ALA* 3.0 27.7 + - + +
372A ASP* 5.3 0.5 - - - +
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Residues in contact with LYS 355 (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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309A TYR* 3.5 3.4 - - - -
347A ASN* 3.2 8.8 - - - +
348A ALA* 2.8 37.7 + - + +
350A ILE* 4.0 27.4 - - + -
351A ASN* 6.2 0.4 - - - +
353A GLN* 3.2 46.9 + - - +
354A GLU* 1.3 80.7 + - - +
356A LEU* 1.3 64.1 - - - +
357A ILE* 5.6 0.4 - - + -
368A ILE* 3.7 28.3 - - + -
369A GLN 3.2 9.9 - - - +
370A ASP* 2.6 28.7 + - - +
371A ALA* 4.1 0.7 - - - +
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Residues in contact with LEU 356 (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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306A VAL* 4.2 7.0 - - + -
307A PRO 4.1 16.6 - - - +
309A TYR* 4.2 16.8 - - + -
312A VAL* 3.9 27.8 - - + -
344A VAL* 5.5 2.0 - - + -
346A GLY 3.5 4.0 - - - +
347A ASN* 3.9 13.0 - - + -
355A LYS* 1.3 83.1 - - - +
357A ILE* 1.3 64.0 + - - +
358A TYR* 5.1 1.3 - - + -
368A ILE* 3.5 3.8 - - - +
369A GLN* 2.7 45.5 + - + +
371A ALA* 4.2 16.2 - - + -
386A TRP* 3.7 34.8 - - + -
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Residues in contact with ILE 357 (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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225A GLU* 4.0 17.5 - - + +
227A THR* 3.6 24.2 - - + -
344A VAL* 3.7 4.5 - - - +
345A VAL* 2.7 41.4 + - + -
346A GLY 2.8 17.1 + - - +
347A ASN* 3.9 24.5 - - - +
348A ALA* 4.0 9.2 - - + -
350A ILE* 6.1 0.4 - - + -
355A LYS 5.4 0.2 - - - -
356A LEU* 1.3 76.8 - - - +
358A TYR* 1.3 60.1 + - - +
366A LEU* 4.1 24.0 - - + -
367A SER 3.4 12.1 - - - +
368A ILE* 4.9 12.1 - - + -
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Residues in contact with TYR 358 (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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324A ILE* 3.9 20.4 - - + -
342A LEU* 3.8 30.5 - - + -
343A ALA 3.2 13.7 - - - +
344A VAL* 4.3 1.1 - - + -
345A VAL* 4.0 5.8 - - - +
356A LEU* 4.5 1.1 - - + -
357A ILE* 1.3 77.5 - - - +
359A TRP* 1.3 62.8 + - - +
360A ASN* 4.5 3.4 - - + -
366A LEU* 3.6 4.3 - - - +
367A SER* 2.8 73.6 + - - -
368A ILE 4.1 4.5 + - - -
369A GLN* 3.7 34.1 + - + -
376A LEU* 3.8 15.9 - - + +
377A HIS 3.9 14.2 + - - -
378A LEU* 3.4 21.8 - - + +
386A TRP* 5.6 2.2 - + + -
216B HIS* 5.4 0.3 - - - -
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Residues in contact with TRP 359 (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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231A PHE* 4.1 21.1 - + + -
233A ILE* 3.5 40.0 - - + +
234A ARG 5.7 0.4 - - - -
235A GLU* 3.2 30.7 - - + -
246A PHE* 3.7 37.9 - + + -
247A SER 4.4 0.4 - - - -
250A ALA* 3.8 12.6 - - + -
342A LEU* 3.5 3.6 - - - +
343A ALA* 2.8 42.0 + - + +
345A VAL* 4.1 0.2 - - + -
358A TYR* 1.3 77.6 - - - +
360A ASN* 1.3 73.1 + - - +
361A PRO* 3.5 29.0 - - + +
363A ASP 2.9 20.5 + - - -
365A GLU 3.7 12.3 - - - -
366A LEU* 3.9 12.1 - - + -
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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