Contacts of the helix formed by residues 397 - 413 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU* 3.9 18.4 - - + -
337B GLU* 3.7 23.1 - - - -
341B LEU* 4.0 19.3 - - + +
392B PHE* 3.0 50.1 + + - +
393B ALA* 4.2 0.8 + - - -
395B ARG* 3.3 51.8 + - + +
396B GLY* 1.3 79.0 - - - +
398B ALA* 1.3 64.9 + - - +
399B GLU 3.4 1.8 - - - -
400B ARG* 3.7 42.0 - - + +
401B ALA* 3.0 23.3 + - - +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TRP* 6.3 1.6 - - + +
393A ALA* 4.3 26.9 - - + +
394A ARG* 5.4 0.4 - - - +
393B ALA* 5.1 5.2 - - - +
396B GLY 3.0 10.1 + - - +
397B TRP* 1.3 76.1 - - - +
399B GLU* 1.3 58.7 + - - +
401B ALA* 3.3 6.0 + - - +
402B ARG* 2.9 29.6 + - - +
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 4.4 2.1 + - - -
128A GLU* 3.5 39.6 - - + +
131A ARG* 5.6 2.0 - - - +
132A THR* 4.0 6.9 - - - +
501A GOL 2.8 27.6 + - - -
397B TRP 3.4 0.6 - - - -
398B ALA* 1.3 75.7 - - - +
400B ARG* 1.3 65.8 + - + +
402B ARG* 2.9 43.9 + - - +
403B LEU* 2.9 43.7 + - + +
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASP* 5.5 6.3 + - - -
338B ARG* 6.1 1.0 - - - +
341B LEU* 3.9 39.2 - - - +
344B LEU* 5.4 1.3 - - - -
345B GLU* 2.6 33.7 + - - +
392B PHE* 4.1 15.9 - - + -
397B TRP* 3.4 50.1 + - + +
399B GLU* 1.3 78.7 - - + +
401B ALA* 1.3 62.9 + - - +
403B LEU* 3.4 10.8 + - + +
404B LEU* 3.3 26.2 + - - +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B SER* 3.3 33.6 - - - +
392B PHE* 4.1 5.7 - - + +
393B ALA* 3.6 20.6 - - + +
397B TRP 3.0 17.2 + - - +
398B ALA 3.6 4.3 - - - +
399B GLU 3.2 0.2 - - - -
400B ARG* 1.3 76.6 - - - +
402B ARG* 1.3 64.7 + - - +
404B LEU* 3.3 3.9 + - - +
405B ARG* 3.0 22.9 + - - +
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Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 4.0 6.5 - - - +
501A GOL 3.6 37.2 + - - -
398B ALA 2.9 18.5 + - - +
399B GLU* 2.9 43.3 + - - +
401B ALA* 1.3 79.0 - - - +
403B LEU* 1.3 76.4 + - - +
405B ARG* 3.4 17.3 + - - +
406B GLN* 2.9 54.7 + - + +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A THR* 4.4 11.9 - - + -
358B GLY 5.3 1.6 - - - +
399B GLU* 2.9 41.6 + - + +
400B ARG* 3.8 9.4 - - + +
401B ALA 3.3 0.2 - - - -
402B ARG* 1.3 96.0 - - - +
404B LEU* 1.3 64.1 + - + +
406B GLN* 3.4 19.4 + - - +
407B GLU* 3.0 32.4 + - + +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B CYS* 5.0 4.7 - - - -
358B GLY 3.9 18.4 - - - +
359B LEU* 3.7 13.4 - - + +
360B ILE* 4.3 22.0 - - + +
385B THR* 3.5 20.0 - - + +
388B PHE* 3.9 9.9 - - + -
389B SER* 3.9 24.7 - - - +
392B PHE* 3.6 37.7 - - + -
400B ARG 3.3 8.7 + - - +
401B ALA 3.7 6.1 - - - +
402B ARG 3.3 0.2 - - - -
403B LEU* 1.3 76.2 - - - +
405B ARG* 1.3 61.7 + - - +
407B GLU* 3.4 0.4 + - - -
408B GLY 2.8 24.6 + - - -
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B SER* 4.4 2.8 - - - -
401B ALA 3.0 16.5 + - - +
402B ARG* 3.6 16.2 + - - +
404B LEU* 1.3 76.3 - - - +
406B GLN* 1.3 62.4 + - - +
408B GLY* 3.2 1.0 + - - -
409B LEU* 2.9 46.3 + - + +
444B TRP* 2.5 72.2 + - + +
445B LEU* 3.8 15.4 + - - +
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ARG* 2.9 46.1 + - + +
403B LEU* 3.7 18.8 - - - +
404B LEU 3.3 0.2 - - - -
405B ARG* 1.3 82.7 - - - +
407B GLU* 1.3 81.5 + - - +
409B LEU* 3.4 7.6 + - - +
410B ARG* 2.9 39.6 + - + +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS 4.6 0.2 - - - +
357B TYR* 3.3 6.7 - - + -
358B GLY* 2.8 36.0 + - - +
359B LEU* 3.5 25.3 - - + +
403B LEU* 3.0 22.1 + - + +
406B GLN* 1.3 91.8 + - - +
408B GLY* 1.3 61.0 + - - +
410B ARG* 3.0 48.6 + - - +
411B GLN* 2.9 29.5 + - - +
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Residues in contact with GLY 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.8 14.1 - - - +
382B PRO* 6.2 0.2 - - - +
385B THR* 4.3 2.0 - - - -
404B LEU 2.8 19.0 + - - -
405B ARG 3.2 1.5 + - - -
407B GLU* 1.3 77.7 - - - +
409B LEU* 1.3 55.7 + - - +
411B GLN* 3.5 5.8 + - - +
412B ALA* 3.0 29.8 + - - +
444B TRP* 3.7 22.0 - - - -
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.5 9.2 - - + +
405B ARG* 2.9 54.6 + - + +
406B GLN* 3.8 6.3 - - - +
408B GLY* 1.3 74.6 - - - +
410B ARG* 1.3 64.6 + - - +
412B ALA* 3.3 3.4 + - - +
413B SER* 3.0 24.4 + - - -
441B VAL* 4.2 14.6 - - + -
444B TRP* 3.8 25.4 - - + -
445B LEU* 3.8 37.7 - - + -
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS* 4.2 19.0 + - - +
357B TYR* 3.3 34.5 + - + -
406B GLN* 2.9 26.2 + - + +
407B GLU* 3.0 46.2 + - - +
409B LEU* 1.3 77.1 - - - +
411B GLN* 1.3 61.0 + - - +
413B SER* 2.7 26.5 + - - -
414B ASP 4.7 0.2 + - - -
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Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B TYR* 3.5 39.3 + - + +
359B LEU* 3.6 16.7 - - + +
380B VAL* 3.6 25.5 - - - +
382B PRO* 3.8 15.4 - - - +
385B THR* 5.2 0.5 + - - -
407B GLU 2.9 16.4 + - - +
408B GLY* 3.7 7.0 - - - +
410B ARG* 1.3 78.5 - - - +
412B ALA* 1.3 60.5 + - - +
413B SER 3.3 0.7 + - - -
414B ASP* 3.4 15.2 + - - +
421B TYR* 3.4 55.1 + - + +
422B GLU 5.3 1.4 + - - -
423B PRO* 6.1 0.2 - - - +
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.5 12.1 - - + +
382B PRO* 6.1 2.9 - - + -
408B GLY 3.0 16.9 + - - +
409B LEU* 3.7 6.3 - - - +
410B ARG 3.3 0.2 - - - -
411B GLN* 1.3 73.3 - - - +
413B SER* 1.3 56.0 + - - +
414B ASP* 3.1 10.2 - - - +
415B GLY* 3.0 19.8 + - - -
416B SER 4.7 0.2 + - - -
417B PHE* 5.1 4.4 + - + +
421B TYR* 4.1 10.5 + - + +
437B THR* 5.3 7.4 - - + -
441B VAL* 3.6 31.2 - - + -
444B TRP* 5.3 1.3 - - + -
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B SER* 3.2 20.7 - - - -
7B PHE* 2.9 40.1 + - - +
12B LEU* 4.1 13.2 - - - -
409B LEU 3.0 11.8 + - - -
410B ARG* 2.7 22.6 + - - -
411B GLN 3.2 1.6 - - - -
412B ALA* 1.3 75.1 - - - +
414B ASP* 1.3 59.4 + - - +
415B GLY 3.2 1.1 + - - -
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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