Contacts of the helix formed by residues 352 - 360 (chain A) in PDB entry 1JPW
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 SER 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A GLN* 5.6 0.7 - - - -
313A LEU* 4.3 13.2 - - - +
316A LEU* 3.5 22.3 - - - +
350A CYS* 3.2 9.2 + - - -
351A SER* 1.3 78.6 + - - +
353A ASN* 1.3 66.8 + - - +
354A LYS 3.5 1.5 - - - +
355A PRO* 3.9 18.9 - - - +
356A ALA* 4.2 5.9 + - - +
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Residues in contact with ASN 353 (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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312A LYS* 3.7 12.0 + - - +
316A LEU* 2.9 41.1 - - - +
321A PRO* 3.9 6.6 - - - +
347A LEU* 3.1 50.6 - - + +
350A CYS* 2.9 30.5 - - - +
352A SER* 1.3 80.8 - - - +
354A LYS* 1.3 65.0 + - - +
356A ALA* 2.8 14.7 + - - +
357A ILE* 2.9 15.6 + - + +
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Residues in contact with LYS 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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347A LEU 4.4 1.0 + - - -
348A SER 3.1 25.4 - - - +
349A VAL* 4.9 5.4 - - - +
350A CYS 3.7 14.4 + - - +
351A SER* 5.6 3.1 - - - +
352A SER 5.3 0.2 - - - +
353A ASN* 1.3 75.9 - - - +
355A PRO* 1.3 70.4 - - + +
357A ILE* 2.9 8.6 + - - +
358A VAL* 2.8 29.4 + - - +
387A ASN* 3.0 22.8 + - - +
388A LEU* 3.7 18.6 - - + -
390A ASP* 2.8 30.1 + - - -
391A ALA* 3.8 22.0 - - + -
21D PHE 4.5 8.4 + - - -
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Residues in contact with PRO 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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351A SER 5.6 0.9 - - - -
352A SER* 3.9 17.9 - - - +
353A ASN 3.8 0.7 - - - -
354A LYS* 1.3 95.2 - - + +
356A ALA* 1.3 55.7 + - - +
358A VAL* 4.1 8.7 - - + +
359A GLU* 2.7 38.9 + - + +
391A ALA* 4.8 11.2 - - + +
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Residues in contact with ALA 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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316A LEU* 3.3 30.3 - - + -
321A PRO* 4.0 12.8 - - + +
322A GLN* 5.0 0.3 + - - +
352A SER 4.2 3.5 + - - +
353A ASN 2.8 14.6 + - - +
355A PRO* 1.3 76.4 - - - +
357A ILE* 1.3 62.5 + - - +
359A GLU* 4.2 3.1 - - - +
360A ALA* 3.3 25.5 + - - +
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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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321A PRO* 4.2 18.4 - - + -
325A VAL* 4.0 20.2 - - + -
344A LEU* 4.2 26.5 - - + +
347A LEU* 4.2 24.7 - - + -
348A SER* 4.3 3.4 - - - +
353A ASN* 3.3 17.9 - - + +
354A LYS 2.9 5.2 + - - +
356A ALA* 1.3 77.5 - - - +
358A VAL* 1.3 59.1 + - - +
360A ALA* 3.6 5.0 + - - +
361A GLY 3.7 0.2 + - - -
362A GLY* 2.8 34.5 + - - -
366A LEU* 4.8 3.6 - - + -
388A LEU* 3.6 37.0 - - + -
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Residues in contact with VAL 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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354A LYS 2.8 22.2 + - - +
355A PRO* 3.1 9.2 + - + +
357A ILE* 1.3 74.1 - - - +
359A GLU* 1.3 61.7 + - - +
361A GLY* 3.2 14.0 + - - -
362A GLY 3.8 2.0 + - - +
363A MET* 4.2 17.1 + - + +
364A GLN* 4.8 1.9 - - - +
388A LEU* 4.3 18.6 - - + +
391A ALA* 4.2 15.5 - - + +
392A ALA* 4.0 21.8 - - + -
395A GLN* 3.0 45.7 - - + +
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Residues in contact with GLU 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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355A PRO* 2.7 21.7 + - + +
356A ALA* 4.4 3.4 - - - +
358A VAL* 1.3 68.8 - - - +
360A ALA* 1.3 60.3 + - - +
361A GLY* 3.0 6.8 + - - -
395A GLN* 4.1 22.2 + - - +
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Residues in contact with ALA 360 (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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322A GLN* 3.8 35.4 - - + +
325A VAL* 3.9 9.6 - - + +
329A ARG* 3.3 24.4 + - - -
356A ALA 3.3 19.0 + - - +
357A ILE 4.1 4.7 - - - +
358A VAL 3.3 0.8 - - - -
359A GLU* 1.3 76.0 - - - +
361A GLY* 1.3 58.4 + - - +
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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