Contacts of the helix formed by residues 397 - 413 (chain A) in PDB entry 5OIV
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 TRP 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LEU* 3.9 13.0 - - + -
337A GLU* 3.7 24.2 - - - -
341A LEU* 3.9 25.7 - - + +
392A PHE* 3.0 49.9 + + - +
395A ARG* 3.4 55.3 + - + +
396A GLY* 1.3 78.3 - - - +
398A ALA* 1.3 64.6 + - - +
399A GLU 3.3 2.7 - - - -
400A ARG* 3.3 37.5 + - + +
401A ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 398 (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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393A ALA* 5.1 5.2 - - - +
396A GLY 3.0 9.4 + - - +
397A TRP* 1.3 74.5 - - - +
399A GLU* 1.3 59.3 + - - +
401A ALA* 3.7 6.1 - - - +
402A ARG* 2.9 29.6 + - - +
393B ALA* 4.2 27.1 - - + +
394B ARG* 5.3 0.7 - - - +
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Residues in contact with GLU 399 (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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397A TRP 3.3 0.4 - - - -
398A ALA* 1.3 80.7 - - - +
400A ARG* 1.3 63.0 + - + +
402A ARG* 2.8 43.6 + - - +
403A LEU* 3.0 38.4 + - + +
502A GOL 2.8 27.1 + - - -
125B ARG* 4.3 2.6 + - - +
128B GLU* 3.6 38.9 - - + +
131B ARG* 5.7 1.3 - - - +
132B THR* 4.0 7.6 - - - +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 3.9 26.6 - - - +
345A GLU* 2.8 22.3 + - - +
392A PHE* 4.1 11.7 - - + -
397A TRP* 3.3 52.8 + - + +
399A GLU* 1.3 76.9 - - + +
401A ALA* 1.3 62.8 + - - +
403A LEU* 3.3 5.6 + - + -
404A LEU* 3.2 22.7 + - - +
511A GLY 3.4 30.8 - - - +
512A GLY* 3.4 38.0 + - - -
272B ASP* 5.5 0.8 + - - -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A SER* 2.9 48.8 + - - +
392A PHE* 4.1 5.3 - - + +
393A ALA* 3.6 20.6 - - + +
397A TRP 3.0 17.5 + - - +
398A ALA* 3.7 4.5 - - - +
400A ARG* 1.3 77.9 - - - +
402A ARG* 1.3 61.5 + - - +
404A LEU* 3.3 1.6 + - - +
405A ARG* 3.0 13.0 + - - +
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Residues in contact with ARG 402 (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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398A ALA 2.9 17.7 + - - +
399A GLU* 2.8 44.1 + - - +
401A ALA* 1.3 80.0 - - - +
403A LEU* 1.3 76.0 + - - +
405A ARG* 3.3 16.3 + - - +
406A GLN* 2.9 57.0 + - + +
502A GOL 3.3 37.9 + - - -
132B THR* 4.1 5.3 - - - +
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Residues in contact with LEU 403 (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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358A GLY 5.4 0.7 - - - -
399A GLU* 3.0 40.5 + - + +
400A ARG* 4.6 3.8 - - + -
401A ALA 3.3 0.2 - - - -
402A ARG* 1.3 98.1 - - - +
404A LEU* 1.3 64.0 + - - +
406A GLN* 3.8 19.8 + - - +
407A GLU* 3.0 31.2 + - + +
511A GLY* 3.7 23.6 - - - +
132B THR* 4.4 12.8 - - + -
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Residues in contact with LEU 404 (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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350A CYS* 4.9 0.4 - - - -
358A GLY 4.0 17.7 - - - +
359A LEU* 3.7 13.1 - - + +
360A ILE* 4.4 22.0 - - + -
385A THR* 3.5 19.5 - - + +
388A PHE* 3.8 12.8 - - + -
389A SER* 3.7 32.1 - - - +
392A PHE* 3.8 27.1 - - + -
400A ARG 3.2 13.7 + - - +
401A ALA 3.7 7.4 - - - +
403A LEU* 1.3 77.7 - - - +
405A ARG* 1.3 55.8 + - - +
408A GLY 2.9 24.3 + - - -
511A GLY* 4.0 16.6 - - - +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A SER* 4.0 4.0 + - - +
401A ALA 3.0 17.1 + - - +
402A ARG* 3.7 15.4 + - - +
404A LEU* 1.3 77.6 - - - +
406A GLN* 1.3 63.4 + - - +
408A GLY 3.3 0.5 + - - -
409A LEU* 2.8 47.1 + - + +
444A TRP* 2.7 72.2 + - + +
445A LEU* 3.7 16.8 + - - +
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Residues in contact with GLN 406 (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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402A ARG* 2.9 48.7 + - + +
403A LEU* 3.8 18.3 - - - +
405A ARG* 1.3 82.2 - - - +
407A GLU* 1.3 81.4 + - - +
409A LEU* 3.5 7.4 + - - +
410A ARG* 3.0 28.2 + - + +
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Residues in contact with GLU 407 (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 TYR* 3.3 4.4 - - - -
358A GLY* 2.8 35.9 + - - +
359A LEU* 3.6 24.3 - - + +
403A LEU* 3.0 20.9 + - + +
406A GLN* 1.3 93.4 + - - +
408A GLY* 1.3 61.4 + - - +
410A ARG* 2.9 44.0 + - - +
411A GLN* 2.9 29.8 + - - +
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Residues in contact with GLY 408 (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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359A LEU* 3.8 14.3 - - - +
385A THR* 4.3 1.8 - - - -
404A LEU 2.9 17.8 + - - -
405A ARG 3.7 1.1 - - - -
407A GLU* 1.3 77.6 - - - +
409A LEU* 1.3 56.6 + - - +
411A GLN* 3.3 6.7 + - - +
412A ALA* 3.0 29.3 + - - +
444A TRP* 3.7 23.3 - - - -
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Residues in contact with LEU 409 (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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12A LEU* 4.4 9.7 - - + +
405A ARG* 2.8 56.0 + - + +
406A GLN* 3.8 4.9 - - - +
408A GLY* 1.3 74.6 - - - +
410A ARG* 1.3 65.5 + - - +
412A ALA* 3.3 3.0 + - - +
413A SER* 3.0 25.2 + - - -
441A VAL* 4.3 15.0 - - + -
444A TRP* 3.8 24.4 - - + -
445A LEU* 3.8 37.2 - - + -
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Residues in contact with ARG 410 (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 LYS* 3.4 19.0 + - - +
357A TYR* 3.1 31.7 + - + -
406A GLN* 3.0 19.3 + - + +
407A GLU* 2.9 40.2 + - - +
409A LEU* 1.3 76.5 - - - +
411A GLN* 1.3 62.3 + - - +
413A SER* 2.9 26.7 + - - +
414A ASP 4.7 0.2 + - - -
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Residues in contact with GLN 411 (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 TYR* 3.6 39.9 + - + -
359A LEU* 3.7 16.3 - - + +
380A VAL* 3.5 26.4 - - - +
382A PRO* 3.8 16.6 - - - +
385A THR* 5.2 0.3 + - - -
407A GLU 2.9 17.8 + - - +
408A GLY* 3.6 7.2 - - - +
410A ARG* 1.3 77.4 - - - +
412A ALA* 1.3 59.9 + - - +
413A SER 3.4 0.7 + - - -
414A ASP* 3.2 18.7 + - - +
421A TYR* 3.5 54.2 + - + +
422A GLU 5.4 1.0 + - - -
423A PRO* 6.2 0.2 - - - +
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Residues in contact with ALA 412 (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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12A LEU* 3.4 11.5 - - + +
382A PRO* 6.1 2.7 - - + -
408A GLY 3.0 17.2 + - - +
409A LEU* 3.3 5.6 + - - +
410A ARG 3.3 0.2 - - - -
411A GLN* 1.3 73.2 - - - +
413A SER* 1.3 55.6 + - - +
414A ASP* 3.1 9.6 - - - +
415A GLY* 2.9 20.4 + - - -
416A SER 4.6 0.2 + - - -
417A PHE* 5.1 4.9 + - + -
421A TYR* 4.0 10.7 + - + +
437A THR* 5.3 7.6 - - + -
441A VAL* 3.6 31.2 - - + -
444A TRP* 5.3 1.1 - - + -
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Residues in contact with SER 413 (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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6A SER* 3.2 20.6 - - - -
7A PHE* 2.9 40.7 + - - +
12A LEU* 4.0 13.9 - - - -
409A LEU 3.0 15.2 + - - -
410A ARG* 2.9 21.8 + - - +
411A GLN 3.2 1.4 - - - -
412A ALA* 1.3 77.1 - - - +
414A ASP* 1.3 60.0 + - - +
415A GLY 3.2 1.2 + - - -
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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