Contacts of the helix formed by residues 404 - 423 (chain A) in PDB entry 4P0S
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 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A GLU* 3.9 11.2 - - - +
370A GLU* 4.5 1.8 - - + +
402A THR* 3.3 2.6 - - - +
403A ALA* 1.3 84.8 - - - +
405A ILE* 1.3 64.7 + - - +
406A LYS* 3.2 19.0 + - - +
407A GLU* 3.3 15.0 + - - +
408A SER* 2.8 27.2 + - - -
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Residues in contact with ILE 405 (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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285A PRO* 5.3 13.0 - - + +
286A GLU 5.6 0.4 - - - -
287A LEU* 4.6 27.6 - - + +
290A GLU* 5.8 3.8 - - + -
334A ARG* 3.8 18.2 - - - +
336A ARG* 5.2 2.9 - - - +
369A GLU* 2.8 33.7 - - - +
404A ASP* 1.3 77.4 - - - +
406A LYS* 1.3 51.5 + - - +
408A SER* 3.0 9.7 - - - -
409A ALA* 2.5 35.1 + - + +
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU* 3.5 29.2 + - + +
293A ARG* 2.9 40.2 - - - +
294A LEU* 4.8 1.9 - - + +
404A ASP* 3.2 13.2 + - - +
405A ILE* 1.3 75.5 - - - +
407A GLU* 1.3 62.5 + - + +
409A ALA* 3.3 5.9 + - - +
410A ALA* 2.9 28.5 + - + +
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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
----------------------------------------------------------
400A LYS* 6.0 1.9 - - - -
402A THR* 3.9 18.9 + - + +
403A ALA* 4.0 24.7 + - - +
404A ASP* 3.3 12.2 + - - +
406A LYS* 1.3 79.9 - - + +
408A SER* 1.3 52.5 + - - +
410A ALA* 3.3 6.8 - - - +
411A TYR* 2.4 40.6 + - + +
370B PHE* 5.3 4.9 - - - -
405B ARG* 3.4 28.1 + - - -
409B GLU* 5.3 3.6 - - - +
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 5.5 0.9 - - - -
334A ARG* 5.7 4.2 - - - -
367A LEU* 4.3 19.0 - - - +
369A GLU* 4.0 13.9 + - - +
402A THR* 3.2 16.1 - - - +
404A ASP 2.8 18.9 + - - -
405A ILE* 3.0 19.6 - - - -
407A GLU* 1.3 75.8 - - - +
409A ALA* 1.3 63.6 + - - +
411A TYR* 3.9 5.5 - - - +
412A LEU* 3.0 30.6 + - - +
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.8 20.1 - - + +
290A GLU* 3.6 30.1 - - + -
291A LEU* 4.0 16.0 - - + +
294A LEU* 4.2 7.4 - - + -
405A ILE* 2.5 18.8 + - + +
406A LYS 3.3 4.9 + - - +
408A SER* 1.3 74.2 - - - +
410A ALA* 1.3 57.3 + - - +
412A LEU* 3.2 5.4 + - - +
413A ALA* 2.8 27.4 + - - +
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Residues in contact with ALA 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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294A LEU* 4.1 15.0 - - + +
406A LYS* 2.9 20.8 + - + +
407A GLU* 3.4 8.5 - - - +
409A ALA* 1.3 75.3 - - - +
411A TYR* 1.3 60.3 + - - +
413A ALA* 3.1 9.7 + - - +
414A LEU* 2.8 37.4 + - + +
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Residues in contact with TYR 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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332A VAL* 5.8 0.4 - - + -
365A VAL* 4.6 7.4 - - + +
367A LEU* 3.7 28.7 - - + -
398A PHE* 3.7 2.4 - - - -
400A LYS* 3.3 52.0 - - + +
402A THR* 4.8 4.7 - - - +
407A GLU* 2.4 27.7 + - + +
408A SER* 3.9 4.7 - - - +
410A ALA* 1.3 70.9 - - - +
412A LEU* 1.3 66.2 + - + +
413A ALA 3.1 0.2 + - - -
414A LEU* 3.1 4.4 + - - +
415A LEU* 2.9 44.4 + - + +
409B GLU* 5.9 0.4 - - - -
412B LEU* 6.1 1.1 - - + -
413B VAL* 4.3 17.7 - - + -
416B GLN* 2.2 46.4 + - - -
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Residues in contact with LEU 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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271A LEU* 4.1 28.5 - - + -
287A LEU* 4.5 10.3 - - + -
291A LEU* 4.4 13.0 - - + -
308A PHE* 3.7 53.4 - - + -
310A TRP* 4.0 4.5 - - + -
332A VAL* 4.9 11.2 - - + -
367A LEU* 4.7 13.7 - - + -
408A SER* 3.0 19.6 + - - +
409A ALA 3.5 5.6 - - - +
411A TYR* 1.3 77.3 - - - +
413A ALA* 1.3 53.9 + - - +
415A LEU* 3.8 9.1 - - + +
416A THR* 2.4 38.2 + - - -
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 4.4 11.7 - - + +
296A VAL* 3.8 27.1 - - + +
409A ALA 2.8 14.2 + - - +
410A ALA* 3.2 13.9 - - - +
412A LEU* 1.3 77.4 - - - +
414A LEU* 1.3 67.3 + - + +
416A THR* 2.9 8.6 + - - -
417A ARG* 2.8 28.6 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ALA* 2.8 26.4 + - + +
411A TYR* 4.0 1.3 - - - +
413A ALA* 1.3 74.8 - - + +
415A LEU* 1.3 60.4 - - - +
417A ARG* 3.7 9.6 - - + +
418A GLY* 2.8 23.4 + - - -
406B VAL* 5.1 6.3 - - + +
409B GLU* 4.5 5.6 - - + -
410B GLU* 3.6 46.6 - - + +
413B VAL* 2.9 31.1 - - + +
414B ASP* 5.1 0.2 - - - +
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 3.6 27.1 - - + -
330A HIS* 5.0 2.2 - - + -
332A VAL* 4.4 13.0 - - + -
365A VAL* 5.4 0.7 - - + -
411A TYR* 2.9 43.7 + - + +
412A LEU* 3.8 9.4 - - + +
414A LEU* 1.3 77.5 - - - +
416A THR* 1.3 63.9 + - - +
418A GLY 3.1 0.7 + - - -
419A LEU* 3.0 8.5 + - - +
413B VAL* 3.4 8.6 - - + +
416B GLN* 3.3 39.7 - - + +
417B LEU* 3.0 54.4 - - + +
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Residues in contact with THR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 4.8 3.1 - - + +
271A LEU* 4.0 18.2 - - + +
296A VAL* 4.9 6.7 - - + +
297A THR* 4.3 20.0 - - - +
310A TRP* 3.0 35.3 + - + +
412A LEU 2.4 26.0 + - - -
413A ALA* 2.9 8.4 + - - -
415A LEU* 1.3 78.4 - - - +
417A ARG* 1.3 56.4 + - - +
419A LEU* 3.0 6.7 + - - +
420A GLN* 2.9 36.4 + - + +
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Residues in contact with ARG 417 (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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413A ALA 2.8 17.1 + - - +
414A LEU* 3.8 12.3 - - + +
416A THR* 1.3 69.8 - - - +
418A GLY* 1.3 65.7 + - - +
420A GLN* 2.6 59.7 + - - +
421A ARG* 3.0 39.1 + - + +
424A GLN* 4.1 17.2 - - - +
410B GLU* 6.0 2.0 - - - +
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Residues in contact with GLY 418 (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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414A LEU 2.8 14.0 + - - -
415A LEU 3.1 4.2 + - - -
417A ARG* 1.3 77.9 - - - +
419A LEU* 1.3 49.8 + - - +
421A ARG* 3.0 9.6 + - - +
422A LEU* 2.5 34.7 + - - +
414B ASP* 4.0 18.6 - - - -
417B LEU* 3.6 16.8 - - - -
418B HIS* 4.4 5.2 - - - -
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Residues in contact with LEU 419 (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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269A VAL* 4.4 8.4 - - + +
310A TRP* 3.5 46.2 - - + -
328A LEU* 3.7 30.3 - - + -
330A HIS* 4.4 11.0 - - - +
415A LEU 3.0 15.4 + - - +
416A THR* 3.0 6.7 + - - +
418A GLY* 1.3 74.6 - - - +
420A GLN* 1.3 67.1 + - - +
422A LEU* 3.0 37.5 + - + +
423A TYR* 3.2 20.4 + - + +
417B LEU* 3.9 21.8 - - + -
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Residues in contact with GLN 420 (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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268A ARG* 6.1 1.2 - - - +
269A VAL* 3.3 48.6 + - + +
295A HIS 5.7 0.9 - - - +
297A THR* 3.5 26.1 + - - +
416A THR* 2.9 20.3 + - + +
417A ARG* 2.6 59.3 + - - +
419A LEU* 1.3 76.7 - - - +
421A ARG* 1.4 58.4 - - - +
423A TYR* 4.1 0.7 + - - +
424A GLN* 3.2 32.5 + - - +
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Residues in contact with ARG 421 (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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417A ARG* 3.0 34.1 + - + +
418A GLY* 3.4 6.1 - - - +
420A GLN* 1.4 76.3 - - - +
422A LEU* 1.3 65.6 + - - +
423A TYR 3.3 0.7 - - - -
424A GLN* 4.0 15.8 + - - +
329B LYS* 4.3 11.2 - - - +
344B GLN* 4.9 4.0 - - - +
410B GLU* 5.1 4.1 + - - -
414B ASP* 3.0 45.3 + - - +
418B HIS* 4.1 18.5 + - + -
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Residues in contact with LEU 422 (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 HIS* 5.3 0.2 - - + -
418A GLY 2.5 18.0 + - - +
419A LEU* 3.0 28.0 + - + +
421A ARG* 1.3 76.8 - - - +
423A TYR* 1.3 73.1 + - + +
424A GLN 3.8 0.3 + - - +
426A HIS* 3.6 17.9 + - + -
448A ASN* 4.1 11.7 - - + +
449A PRO* 3.7 26.9 - - + +
417B LEU* 3.6 23.3 - - + +
418B HIS* 3.1 39.9 + - + +
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Residues in contact with TYR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TYR* 2.7 35.4 + - + +
269A VAL* 5.9 4.5 - - + -
328A LEU* 3.9 33.9 - - + +
329A ASP* 4.6 5.5 + - - +
419A LEU* 3.2 20.1 + - + +
420A GLN 4.6 1.1 - - - +
422A LEU* 1.3 98.7 - - + +
424A GLN* 1.3 61.9 + - - +
426A HIS* 3.0 22.7 + - + +
428A LEU* 3.6 30.1 - - + -
448A ASN* 5.2 2.6 + - - -
449A PRO* 4.7 8.0 - - + +
450A LEU* 2.7 44.3 + - - +
451A CYS* 4.8 2.5 - - - -
453A LEU* 4.2 14.0 - - + +
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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