Contacts of the helix formed by residues 394 - 411 (chain B) in PDB entry 4OL0
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 ASP 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 4.7 12.1 + - - -
391B GLU* 3.8 22.5 + - + +
392B GLU 3.4 1.2 - - - -
393B THR* 1.3 84.5 - - + +
395B ASP* 1.3 76.7 + - - +
396B PHE* 3.3 13.4 + - - +
397B GLY 2.8 22.3 + - - +
398B GLU* 2.8 17.0 + - - +
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Residues in contact with ASP 395 (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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145A GLN* 4.5 5.9 + - - -
147A TYR* 3.5 20.8 + - - -
163A TRP* 5.0 6.7 - - - -
166A ARG* 3.3 26.6 + - - -
336B TYR* 3.7 19.3 + - + +
393B THR 4.0 0.4 + - - -
394B ASP* 1.3 82.0 + - - +
396B PHE* 1.3 56.7 + - - +
398B GLU* 3.1 20.7 + - - +
399B PHE* 2.9 27.0 + - - +
402B ARG* 4.2 2.6 + - - -
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.9 32.4 + + + -
379B HIS 3.5 19.3 - - - -
380B CYS 4.1 3.8 - - - -
381B GLN 3.4 22.0 - - - -
382B LEU* 3.6 30.1 - - + -
383B GLU* 6.0 1.1 - - - -
394B ASP* 3.3 12.5 - - - +
395B ASP* 1.3 79.2 - - - +
397B GLY* 1.3 57.6 + - - +
399B PHE* 3.3 17.4 + + - +
400B ARG* 2.8 58.9 + - + +
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Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLU 3.9 18.8 + - - -
392B GLU* 3.9 11.0 - - - -
394B ASP* 2.8 14.1 + - - +
396B PHE* 1.3 77.9 - - - +
398B GLU* 1.3 51.8 + - - -
400B ARG* 3.0 12.7 + - - +
401B MET* 2.8 37.8 + - - +
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Residues in contact with GLU 398 (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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145A GLN* 4.7 4.5 + - - -
146A TYR 5.5 0.5 - - - +
147A TYR* 3.5 22.6 + - - -
159A LYS* 3.3 29.0 - - - -
392B GLU 4.0 4.3 + - - +
393B THR* 3.7 10.5 - - - +
394B ASP 2.8 16.4 + - - +
395B ASP* 3.3 24.9 - - - +
397B GLY* 1.3 70.9 - - - +
399B PHE* 1.3 58.5 + - - +
401B MET* 3.1 14.8 + - + +
402B ARG* 2.8 53.7 + - - +
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 3.5 61.0 - + + -
339B VAL 5.0 1.1 - - - -
340B GLU* 4.1 14.6 - - + +
343B PHE* 3.9 16.6 - + - -
376B LEU* 5.3 1.1 - - + -
379B HIS* 3.8 40.8 - + + -
380B CYS* 4.7 1.3 - - - -
395B ASP 2.9 11.0 + - - +
396B PHE* 3.4 20.6 - + - +
398B GLU* 1.3 76.7 - - - +
400B ARG* 1.3 63.8 + - + +
402B ARG* 3.1 14.6 + - - +
403B VAL* 2.8 53.9 + - + +
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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
----------------------------------------------------------
380B CYS* 3.3 33.5 + - - +
382B LEU* 4.9 3.9 - - - +
390B PRO* 3.7 27.2 + - - +
396B PHE* 2.8 42.1 + - + +
397B GLY* 3.0 10.6 + - - +
399B PHE* 1.3 80.9 - - + +
401B MET* 1.3 58.5 + - + +
403B VAL* 3.4 5.4 + - - +
404B SER* 2.8 28.6 + - - -
438B GLU* 2.8 42.6 + - - -
442B PHE* 3.3 46.2 - - + +
479B TYR* 6.1 1.2 - - - -
480B THR* 4.6 0.6 + - - -
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Residues in contact with MET 401 (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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155A TYR* 5.4 7.4 - - - +
392B GLU* 3.4 42.4 - - + +
397B GLY 2.8 25.7 + - - +
398B GLU* 3.1 13.2 + - + +
400B ARG* 1.3 71.4 - - + +
402B ARG* 1.3 59.7 + - - +
404B SER* 3.2 8.7 + - - -
405B ASP* 2.8 37.5 + - - +
442B PHE* 4.8 4.3 - - + -
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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
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139A HIS* 4.0 22.2 + - - -
145A GLN* 5.4 4.2 + - - +
146A TYR 5.8 1.6 + - - -
336B TYR* 5.7 0.2 - - - -
340B GLU* 2.9 39.6 + - - +
343B PHE* 4.2 19.3 - - + -
347B TYR* 4.0 2.5 + - - +
395B ASP 4.2 2.4 + - - -
398B GLU* 2.8 50.6 + - - +
399B PHE* 3.4 11.6 - - - +
401B MET* 1.3 73.8 - - - +
403B VAL* 1.3 60.4 + - - +
405B ASP* 3.2 12.0 + - - +
406B LEU* 2.9 29.6 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE* 3.7 15.9 - - + -
376B LEU* 3.9 18.4 - - + +
380B CYS* 3.6 24.5 - - - -
399B PHE* 2.8 58.3 + - + +
400B ARG 3.6 6.5 - - - +
402B ARG* 1.3 71.3 - - - +
404B SER* 1.3 59.9 + - - +
406B LEU* 3.2 4.3 + - - +
407B VAL* 2.8 46.0 + - + +
442B PHE* 5.4 0.4 - - + -
443B ILE* 4.6 3.4 - - + -
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG 2.8 15.5 + - - -
401B MET* 3.3 12.1 - - - -
403B VAL* 1.3 76.7 - - - +
405B ASP* 1.3 59.4 + - - +
407B VAL* 3.2 10.1 - - - +
408B LYS* 2.8 40.7 + - - +
442B PHE* 4.0 19.3 - - - -
446B ALA* 3.2 22.2 - - - +
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Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B TYR* 3.3 14.8 - - - +
401B MET* 2.8 25.7 + - - +
402B ARG* 3.2 11.7 + - + +
404B SER* 1.3 75.6 + - - +
406B LEU* 1.3 57.6 + - - +
408B LYS* 3.2 15.2 + - - +
409B ASP* 2.9 34.5 + - - +
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Residues in contact with LEU 406 (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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343B PHE* 3.4 47.8 - - + +
346B TRP* 4.1 8.7 - - + -
347B TYR* 3.0 49.8 + - + +
372B LEU* 4.7 2.2 - - + -
376B LEU* 3.9 16.2 - - + -
402B ARG 2.9 19.5 + - - +
403B VAL* 3.7 4.7 - - - +
405B ASP* 1.3 72.2 - - - +
407B VAL* 1.3 59.6 + - + +
409B ASP* 3.2 4.9 + - - +
410B LEU* 2.9 49.4 + - + +
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Residues in contact with VAL 407 (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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373B LEU* 3.7 33.2 - - + -
376B LEU* 3.9 14.1 - - + -
403B VAL* 2.8 38.1 + - + +
404B SER* 3.2 18.4 - - - +
406B LEU* 1.3 70.5 - - - +
408B LYS* 1.3 70.3 + - - +
410B LEU 4.4 0.9 - - - +
411B ILE* 3.3 32.6 + - + +
443B ILE* 4.7 23.6 - - + -
446B ALA* 4.4 11.4 - - + -
447B ILE* 5.0 3.8 - - + -
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Residues in contact with LYS 408 (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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404B SER* 2.8 28.5 + - - +
405B ASP* 3.2 15.1 + - - +
407B VAL* 1.3 77.7 - - - +
409B ASP* 1.3 64.2 + - - +
411B ILE* 3.2 21.7 - - - +
445B ALA 5.7 0.4 + - - -
446B ALA* 3.4 38.7 - - - +
447B ILE* 5.5 0.4 - - - -
450B SER* 5.1 6.7 + - - +
487B GLU* 5.4 6.7 + - - -
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Residues in contact with ASP 409 (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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134A LYS* 4.8 6.1 - - - -
347B TYR* 3.5 29.1 - - + -
405B ASP* 2.9 15.3 + - - +
406B LEU 3.4 8.1 - - - +
408B LYS* 1.3 82.4 - - - +
410B LEU* 1.3 59.1 - - + +
411B ILE* 3.1 2.9 + - - +
412B PHE* 2.7 37.6 + - + -
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Residues in contact with LEU 410 (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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346B TRP* 3.7 27.1 - - + +
347B TYR* 5.2 1.8 - - + -
350B GLY* 3.9 20.2 - - - -
369B ILE* 4.3 21.5 - - + +
372B LEU* 3.5 32.5 - - + -
373B LEU* 4.3 14.4 - - + -
406B LEU* 2.9 39.7 + - + +
407B VAL 3.4 2.2 + - - +
409B ASP* 1.3 75.2 - - + +
411B ILE* 1.3 58.4 + - - +
412B PHE* 2.9 13.6 + - + -
413B LEU* 3.0 26.6 + - + +
414B ILE 4.2 0.5 + - - -
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Residues in contact with ILE 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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373B LEU* 4.1 18.4 - - + -
407B VAL* 3.3 13.4 + - - +
408B LYS* 3.2 28.5 - - - +
409B ASP 3.1 3.1 + - - +
410B LEU* 1.3 72.6 - - - +
412B PHE* 1.3 67.5 + - + +
413B LEU 3.2 0.7 - - - -
414B ILE* 2.8 31.1 + - + +
416B SER* 3.8 17.9 + - - -
419B CYS* 4.6 9.6 - - + -
447B ILE* 3.9 39.0 - - + -
450B SER* 4.5 19.3 - - - +
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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