Contacts of the helix formed by residues 381 - 396 (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 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A ILE 4.7 3.9 + - - +
362A SER* 4.0 3.5 + - - +
375A TYR* 2.9 36.4 + + - -
376A TRP* 3.3 64.2 - + + -
379A PRO 3.3 16.1 + - - -
380A VAL* 1.3 74.8 - - - +
382A PRO* 1.3 68.9 - - - +
383A VAL* 4.0 20.0 - - + -
384A LEU* 3.0 22.2 + - + +
385A THR* 3.1 14.0 + - - -
419A GLU* 3.4 42.4 - - + -
420A TYR* 3.4 28.1 - + + +
436A TRP* 3.9 14.4 - + - -
504A GOL 5.9 2.0 - - - -
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Residues in contact with PRO 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL 3.5 9.6 - - - +
381A TRP* 1.3 80.9 - - - +
383A VAL* 1.3 61.9 + - - +
385A THR* 3.2 10.0 + - - +
386A TRP* 2.9 24.1 + - - +
411A GLN* 3.8 11.4 - - - +
412A ALA* 6.1 3.1 - - + -
418A ALA 4.2 0.2 - - - +
419A GLU 3.6 17.0 - - - +
421A TYR* 3.7 30.1 - - + -
437A THR* 3.9 32.3 - - + +
440A ALA* 4.4 8.1 - - + +
444A TRP* 4.3 9.3 - - + -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 5.4 5.2 - - + -
46A PHE* 3.5 39.3 - - + -
376A TRP* 4.5 7.9 - - + -
381A TRP* 4.0 18.2 - - + -
382A PRO* 1.3 78.0 - - - +
384A LEU* 1.3 63.4 + - + +
386A TRP* 3.4 6.1 + - - +
387A LEU* 3.0 26.0 + - + +
436A TRP* 3.6 62.6 + - + +
440A ALA* 5.4 0.4 - - - -
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Residues in contact with LEU 384 (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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42A TRP* 5.0 7.9 - - + -
181A MET* 4.3 9.9 - - + -
254A PHE* 3.9 32.1 - - + -
321A ALA* 4.0 27.4 - - + -
360A ILE* 5.3 11.2 - - + +
362A SER* 4.9 7.6 - - - -
376A TRP* 3.9 34.1 - - + -
381A TRP* 3.0 13.9 + - + +
383A VAL* 1.3 80.5 - - + +
385A THR* 1.3 68.4 + - - +
387A LEU* 3.8 9.1 - - + +
388A PHE* 2.9 40.3 + - + -
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Residues in contact with THR 385 (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* 3.5 35.6 - - + +
360A ILE* 5.1 8.0 + - - +
380A VAL* 4.2 10.2 - - - +
381A TRP 3.1 13.3 + - - -
382A PRO* 3.5 12.1 - - - +
384A LEU* 1.3 75.3 - - - +
386A TRP* 1.3 63.3 + - - +
388A PHE* 4.0 4.2 - - - +
389A SER* 2.9 23.4 + - - -
404A LEU* 3.5 25.6 - - + +
408A GLY* 4.3 2.2 - - - -
411A GLN* 5.2 0.2 + - - -
444A TRP* 3.8 17.5 - - + -
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Residues in contact with TRP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.7 29.8 - + + -
49A ILE* 3.8 27.6 - - + -
121A ILE* 4.0 14.6 - - + -
125A ARG* 4.7 2.9 - - + -
382A PRO 2.9 12.6 + - - +
383A VAL* 3.6 8.5 - - - +
384A LEU 3.2 0.2 - - - -
385A THR* 1.3 76.1 - - - +
387A LEU* 1.3 75.1 + - + +
389A SER* 3.3 1.9 + - - -
390A TRP* 2.9 58.8 + + + -
440A ALA* 3.8 29.8 - - + -
443A ASP* 2.8 40.4 + - + +
444A TRP* 3.4 36.7 - + + +
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 4.9 4.7 - - + -
46A PHE* 4.6 18.4 - - + -
118A VAL* 4.9 3.8 - - + -
121A ILE* 4.1 21.5 - - + -
254A PHE* 4.1 21.3 - - + -
258A ILE* 4.0 31.2 - - + -
328A LEU* 4.6 4.7 - - + -
383A VAL 3.0 17.0 + - - +
384A LEU* 3.9 10.1 - - + +
386A TRP* 1.3 91.6 - - + +
388A PHE* 1.3 58.7 + - + +
390A TRP* 3.4 1.1 + - + +
391A CYS* 2.9 47.3 + - - -
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Residues in contact with PHE 388 (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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254A PHE* 3.7 34.8 - + - -
321A ALA* 3.8 18.8 - - + -
324A PHE* 3.7 25.6 - + + -
328A LEU* 3.6 24.7 - - + -
344A LEU* 5.5 0.4 - - + -
360A ILE* 3.6 22.9 - - + -
384A LEU* 2.9 45.2 + - + +
385A THR 4.0 0.7 - - - +
387A LEU* 1.3 73.0 - - + +
389A SER* 1.3 61.8 + - - +
392A PHE* 2.8 56.4 + + + -
404A LEU* 3.8 18.4 - - + -
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A THR 2.9 18.7 + - - -
386A TRP 3.8 2.9 - - - -
388A PHE* 1.3 77.4 - - - +
390A TRP* 1.3 57.2 + - - +
393A ALA* 2.9 26.3 + - - +
401A ALA* 2.9 37.2 + - - +
404A LEU* 3.7 18.7 - - - +
405A ARG* 4.0 9.7 + - - +
444A TRP* 4.2 13.7 + - - -
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Residues in contact with TRP 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.8 44.6 - - + -
124A GLN* 3.9 29.2 - - + +
125A ARG* 3.8 20.4 - - - +
128A GLU* 5.1 0.8 + - - -
261A VAL* 4.1 8.1 - - + -
265A VAL* 4.0 17.3 - - + -
386A TRP* 2.9 50.4 + + + +
387A LEU* 3.9 1.6 - - + +
389A SER* 1.3 77.2 - - - +
391A CYS* 1.3 75.0 + - - +
393A ALA* 3.4 8.7 + - + +
394A ARG* 3.1 48.5 + - + +
443A ASP* 5.4 1.3 - - - -
398B ALA* 6.3 1.9 - - + +
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Residues in contact with CYS 391 (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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121A ILE* 5.0 0.4 - - - -
258A ILE* 6.5 0.2 - - - -
261A VAL* 4.6 13.7 - - - -
328A LEU* 3.7 47.0 - - + +
387A LEU* 2.9 34.0 + - - +
388A PHE 3.9 0.9 - - - +
390A TRP* 1.3 97.8 - - - +
392A PHE* 1.3 64.1 + - + +
394A ARG* 3.2 9.2 + - - +
395A ARG* 3.0 25.9 + - - +
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Residues in contact with PHE 392 (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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327A LEU* 3.8 31.0 - - + -
328A LEU* 4.8 0.7 - - + -
341A LEU* 5.0 0.2 - - + -
344A LEU* 3.7 33.0 - - + -
360A ILE* 5.3 0.4 - - + -
388A PHE* 2.8 51.0 + + - +
389A SER 3.7 3.8 - - - +
391A CYS* 1.3 74.1 - - + +
393A ALA* 1.3 66.4 + - - +
395A ARG* 3.0 9.1 + - - +
397A TRP* 3.0 49.6 + + + +
400A ARG* 4.1 18.6 - - + -
401A ALA* 4.1 10.5 - - + +
404A LEU* 3.8 26.0 - - + -
511A GLY* 4.6 6.7 - - - -
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Residues in contact with ALA 393 (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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389A SER 2.9 16.8 + - - +
390A TRP* 3.7 9.4 - - + +
391A CYS 3.3 0.2 - - - -
392A PHE* 1.3 76.3 - - - +
394A ARG* 1.3 57.8 + - - +
396A GLY* 3.0 17.2 + - - -
397A TRP 4.4 4.5 - - - +
398A ALA* 5.1 3.7 + - - +
401A ALA* 3.6 15.6 - - + +
393B ALA 4.1 2.8 - - - +
396B GLY* 3.4 12.6 - - - +
398B ALA* 4.3 21.6 - - + +
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Residues in contact with ARG 394 (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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124A GLN* 5.4 2.4 + - - +
261A VAL* 4.0 24.4 + - - +
264A GLN* 3.1 46.3 + - - +
265A VAL* 3.9 13.1 - - - +
268A GLU* 4.4 8.1 + - - -
328A LEU 4.1 15.2 + - - -
329A CYS* 5.4 2.8 + - - +
390A TRP* 3.1 45.4 + - + +
391A CYS* 3.5 10.4 + - - +
392A PHE 3.1 0.6 - - - -
393A ALA* 1.3 73.6 - - - +
395A ARG* 1.3 70.4 + - - +
396A GLY 3.1 0.7 - - - -
395B ARG 4.3 2.4 - - - +
396B GLY* 3.3 24.4 - - - +
398B ALA* 5.7 0.9 - - - -
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Residues in contact with ARG 395 (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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327A LEU 2.8 39.6 + - - +
328A LEU 3.9 12.6 - - - -
329A CYS 4.9 1.1 - - - -
330A GLY* 3.5 25.6 - - - +
331A GLY 4.9 1.4 - - - +
337A GLU* 2.8 41.2 + - - -
391A CYS 3.0 19.8 + - - +
392A PHE 3.0 7.8 + - - +
394A ARG* 1.3 83.7 - - - +
396A GLY* 1.3 57.9 + - - +
397A TRP* 3.4 43.8 + - + +
394B ARG 4.3 2.9 - - - +
395B ARG 5.1 2.3 - - - +
396B GLY* 4.4 1.3 - - - -
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Residues in contact with GLY 396 (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 3.0 10.0 + - - -
394A ARG 3.1 1.8 + - - -
395A ARG* 1.3 78.9 - - - +
397A TRP* 1.3 62.6 + - - +
398A ALA* 3.0 9.3 + - - +
393B ALA 3.4 15.0 - - - +
394B ARG* 3.3 39.7 - - - +
396B GLY* 3.7 2.4 - - - -
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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
------------------------------------------------------------
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