Contacts of the helix formed by residues 355 - 368 (chain A) in PDB entry 5UDJ
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 ASN 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A TYR* 3.0 30.5 + - + +
353A ALA* 3.4 6.2 - - + +
354A GLY* 1.3 74.4 - - - +
356A HIS* 1.3 63.0 + - - +
357A ARG* 3.3 10.2 + - - +
358A LYS* 2.9 37.5 + - - +
359A ALA* 3.1 18.9 + - - +
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Residues in contact with HIS 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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351A ILE* 4.7 11.0 + - - +
354A GLY* 3.6 22.3 + - - -
355A ASN* 1.3 76.6 - - - +
357A ARG* 1.3 58.5 + - - +
359A ALA* 3.4 5.1 + - - -
360A GLU* 2.9 31.4 + - - +
387A PHE* 3.5 19.9 - + + -
391A GLN* 3.5 47.7 + - + +
392A LYS* 4.8 15.2 + - + +
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Residues in contact with ARG 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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355A ASN* 3.3 7.4 + - - +
356A HIS* 1.3 77.7 - - - +
358A LYS* 1.3 62.5 + - + +
360A GLU* 3.4 29.8 + - - +
361A GLU* 3.0 35.5 + - - +
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Residues in contact with LYS 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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330A GLU* 4.1 5.2 + - - -
350A TYR* 3.2 49.6 + - + -
355A ASN* 2.9 31.9 + - - +
357A ARG* 1.3 77.5 - - + +
359A ALA* 1.3 66.9 + - - +
361A GLU* 3.3 35.9 + - - +
362A ASN* 3.0 32.5 + - - +
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Residues in contact with ALA 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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347A ALA* 3.6 24.1 - - - +
350A TYR* 3.7 8.4 - - + +
351A ILE* 3.8 18.8 - - + -
355A ASN 3.1 14.7 + - - +
356A HIS* 3.6 8.5 - - - +
358A LYS* 1.3 76.7 - - - +
360A GLU* 1.3 63.8 + - - +
362A ASN* 3.2 3.8 + - - +
363A PHE* 2.9 31.4 + - + -
387A PHE* 4.0 9.4 - - + -
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Residues in contact with GLU 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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356A HIS 2.9 17.9 + - - +
357A ARG* 3.5 31.3 + - - +
359A ALA* 1.3 75.8 - - - +
361A GLU* 1.3 58.1 + - - +
363A PHE* 3.2 4.6 + - - +
364A GLN* 2.8 58.7 + - + +
384A TYR* 2.7 29.9 + - - -
387A PHE* 3.7 15.9 - - + -
388A GLN* 3.9 4.0 + - - -
392A LYS* 5.5 4.0 - - + +
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Residues in contact with GLU 361 (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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357A ARG* 3.0 26.6 + - - +
358A LYS* 3.3 37.0 - - - +
359A ALA 3.2 0.2 - - - -
360A GLU* 1.3 77.8 - - - +
362A ASN* 1.3 68.5 + - - +
364A GLN* 3.3 7.6 + - - +
365A LYS* 3.1 38.7 + - + +
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Residues in contact with ASN 362 (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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330A GLU* 4.8 1.6 + - - -
343A HIS* 3.7 22.5 + - + +
346A LEU* 3.5 24.0 - - - +
347A ALA* 3.8 18.8 - - + -
350A TYR* 3.7 24.2 - - - -
358A LYS* 3.0 24.3 + - - +
361A GLU* 1.3 87.4 + - - +
363A PHE* 1.3 65.8 + - - +
365A LYS* 3.3 18.5 + - - +
366A LEU* 3.0 27.5 + - - +
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Residues in contact with PHE 363 (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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344A LEU* 3.8 22.7 - - + -
347A ALA* 4.0 17.7 - - + -
348A ARG* 4.7 4.5 - - + -
351A ILE* 4.2 15.7 - - + -
359A ALA* 2.9 30.9 + - + -
360A GLU 3.6 3.1 - - - +
362A ASN* 1.3 77.3 - - - +
364A GLN* 1.3 62.4 + - - +
366A LEU* 3.0 14.1 + - + +
367A LEU* 2.9 28.0 + - + +
380A ILE* 4.5 4.9 - - + -
383A HIS* 3.8 18.8 - - + -
384A TYR* 3.4 56.5 - + + -
387A PHE* 3.9 24.2 - + + -
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Residues in contact with GLN 364 (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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360A GLU* 2.8 44.8 + - + +
361A GLU* 3.6 7.4 - - - +
362A ASN 3.2 0.4 - - - -
363A PHE* 1.3 76.8 - - - +
365A LYS* 1.3 62.5 + - + +
367A LEU* 3.3 25.2 + - - +
368A CYS* 3.6 19.2 + - - -
384A TYR* 3.2 19.8 + - - -
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Residues in contact with LYS 365 (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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333A VAL* 5.6 2.8 - - - +
343A HIS* 3.9 23.5 - - + +
361A GLU* 3.1 25.9 + - + +
362A ASN* 3.5 30.7 + - - +
363A PHE 3.2 0.2 - - - -
364A GLN* 1.3 77.5 - - + +
366A LEU* 1.3 61.1 + - - +
368A CYS* 3.2 17.6 + - - +
369A MET* 3.4 25.1 - - + +
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Residues in contact with LEU 366 (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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340A GLU* 3.4 26.9 - - - +
343A HIS* 3.7 15.5 - - + +
344A LEU* 3.7 38.8 - - + +
347A ALA* 4.8 0.7 - - + -
362A ASN 3.0 20.2 + - - +
363A PHE* 3.0 18.1 + - + +
365A LYS* 1.3 76.7 - - - +
367A LEU* 1.3 63.0 + - - +
369A MET* 3.0 34.1 + - - +
377A MET* 3.7 11.1 - - - +
380A ILE* 3.8 33.8 - - + +
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Residues in contact with LEU 367 (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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363A PHE 2.9 18.2 + - - +
364A GLN* 3.7 27.8 - - - +
365A LYS 3.2 0.6 - - - -
366A LEU* 1.3 76.2 - - - +
368A CYS* 1.3 60.4 + - - +
369A MET 3.4 1.1 + - - +
377A MET* 4.3 12.6 - - - +
380A ILE* 3.9 15.7 - - + -
381A HIS* 3.5 37.4 - - + +
384A TYR* 3.9 31.2 - - + -
401A HIS* 4.0 11.2 - - + +
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Residues in contact with CYS 368 (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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364A GLN* 3.6 15.9 - - - -
365A LYS* 3.2 9.8 + - - +
366A LEU 3.1 0.8 - - - -
367A LEU* 1.3 78.8 - - - +
369A MET* 1.3 64.2 + - + +
370A LYS* 4.0 16.1 + - - +
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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