Contacts of the helix formed by residues 404 - 423 (chain B) in PDB entry 3P0U
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 TYR 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B MET* 3.2 35.8 - - + +
397B PRO* 3.5 30.3 - - + -
398B GLU 5.1 0.7 - - - -
399B TYR* 4.5 15.4 + - + -
400B LEU 3.7 23.8 - - - -
401B ASN* 3.9 26.5 + - - -
402B VAL* 3.1 24.2 - - + +
403B HIS* 1.3 73.1 - - - +
405B ILE* 1.3 69.7 + - + +
406B CYS 3.1 1.6 - - - -
407B GLU* 3.0 13.2 + - + +
408B SER* 2.9 26.9 + - - -
456B VAL* 3.9 17.5 - - - +
458B SER* 5.2 4.3 + - - -
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ASN* 4.1 16.8 - - - +
402B VAL 4.4 8.3 - - - +
403B HIS* 4.1 27.4 - - + +
404B TYR* 1.3 85.4 - - + +
406B CYS* 1.3 60.0 + - - +
408B SER* 3.8 6.5 - - - +
409B ALA* 2.8 31.3 + - - +
458B SER* 3.8 38.8 - - - +
461B THR* 5.0 9.0 - - + +
580B LEU 4.5 15.9 - - - +
581B PHE* 4.2 15.5 - - + +
583B THR* 5.2 0.2 - - + -
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Residues in contact with CYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B HIS* 3.4 15.2 + - + +
404B TYR 3.1 0.4 - - - -
405B ILE* 1.3 82.6 - - - +
407B GLU* 1.3 55.7 - - - +
409B ALA* 3.5 2.9 - - - +
410B SER* 2.9 37.8 + - - -
581B PHE 3.3 16.2 - - - +
582B PHE* 4.0 14.1 - - - -
584B GLY* 3.5 43.7 - - - +
585B LEU* 3.9 9.2 - - - -
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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
----------------------------------------------------------
397B PRO* 4.6 5.4 - - + -
403B HIS 4.3 0.2 + - - -
404B TYR* 3.0 20.3 + - + +
406B CYS* 1.3 78.0 - - - +
408B SER* 1.3 54.3 - - - +
410B SER* 3.0 9.7 + - - -
411B ARG* 2.6 79.8 + - - +
414B PHE* 5.6 2.4 - - - -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B MET* 3.1 43.2 - - - +
397B PRO* 3.9 3.5 - - - +
404B TYR* 2.9 22.3 + - - -
405B ILE* 3.9 7.2 - - - -
407B GLU* 1.3 72.6 - - - +
409B ALA* 1.3 66.7 + - - +
411B ARG* 3.2 10.3 + - - +
412B LEU* 2.9 23.4 + - - +
455B GLN* 4.9 11.5 - - - +
458B SER* 5.6 4.9 - - - -
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ILE 2.8 21.6 + - - +
406B CYS* 3.5 5.4 - - - +
408B SER* 1.3 73.7 - - - +
410B SER* 1.3 51.8 + - - +
412B LEU* 3.1 2.0 + - - -
413B LEU* 2.7 32.1 + - - +
446B PHE* 3.2 18.9 - - + -
581B PHE* 3.6 24.4 - - + -
582B PHE* 3.2 25.8 - - + -
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Residues in contact with SER 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B CYS* 2.9 24.1 + - - -
407B GLU* 3.0 15.2 + - - -
409B ALA* 1.3 69.6 - - - +
411B ARG* 1.3 59.1 + - - +
412B LEU 3.0 1.6 - - - -
413B LEU* 4.1 4.0 - - - +
414B PHE* 2.7 63.3 + - - -
582B PHE* 3.3 18.6 - - - -
585B LEU* 6.0 0.7 - - - +
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Residues in contact with ARG 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER* 5.1 7.4 - - - -
395B PRO* 2.8 56.0 + - + +
396B MET* 4.6 4.8 - - + -
397B PRO* 3.1 39.6 - - - +
407B GLU* 2.6 48.1 + - - +
408B SER* 3.4 10.8 - - - +
410B SER* 1.3 73.2 - - - +
412B LEU* 1.3 56.9 + - - +
414B PHE* 4.5 6.0 - - - +
415B LEU* 3.3 26.2 + - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B MET* 4.5 8.7 - - + -
394B SER* 5.0 6.5 - - - -
408B SER 2.9 12.7 + - - +
409B ALA* 3.5 7.4 - - - +
411B ARG* 1.3 77.0 - - - +
413B LEU* 1.3 56.3 + - - +
415B LEU* 3.3 7.2 + - + +
416B SER* 2.7 48.7 + - - +
446B PHE* 3.6 23.3 - - + +
449B GLY* 4.1 7.6 - - - +
450B LEU* 3.4 40.2 - - + -
452B GLN* 4.0 28.0 - - - +
455B GLN* 4.4 11.2 - - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ALA 2.7 20.9 + - - +
410B SER* 3.7 6.3 - - - +
412B LEU* 1.3 74.4 - - - +
414B PHE* 1.3 59.5 + - + +
416B SER* 3.4 4.9 - - - -
417B MET* 2.8 58.6 + - + +
442B TRP* 4.1 26.7 - - + +
446B PHE* 3.9 11.4 - - + -
582B PHE* 3.8 18.6 - - + -
591B ILE* 3.6 40.2 - - + -
594B ILE* 4.4 8.1 - - + -
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLU* 5.6 2.5 - - - -
410B SER* 2.7 49.7 + - - +
411B ARG* 4.4 5.8 - - - +
413B LEU* 1.3 72.2 - - + +
415B LEU* 1.3 59.5 + - - +
417B MET* 3.8 17.1 - - + +
418B HIS* 2.9 49.7 + + + -
594B ILE* 4.1 29.6 - - + -
597B TYR* 5.9 5.4 - + - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B THR 5.2 4.5 - - - +
392B MET* 3.4 34.5 - - + +
393B PRO* 3.9 29.2 - - + +
394B SER* 4.0 19.7 - - - +
395B PRO* 5.3 1.3 - - + -
411B ARG 3.3 17.6 + - - +
412B LEU* 3.3 8.8 + - + +
414B PHE* 1.3 80.0 - - - +
416B SER* 1.3 51.1 + - - +
418B HIS* 3.0 7.7 + - + -
419B TRP* 2.6 38.6 + - + +
452B GLN* 4.8 0.4 - - - +
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B MET* 3.8 15.2 - - - +
412B LEU* 2.7 41.8 + - - +
413B LEU* 3.4 8.7 - - - -
415B LEU* 1.3 71.9 - - - +
417B MET* 1.3 66.0 + - - +
419B TRP* 3.1 6.7 + - - +
420B ALA* 3.1 22.0 + - - +
442B TRP 5.8 0.2 - - - -
445B LEU* 4.3 24.8 + - - +
446B PHE* 4.2 13.1 - - - -
449B GLY* 5.1 1.2 - - - -
515B LYS* 5.2 3.2 - - - +
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Residues in contact with MET 417 (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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413B LEU* 2.8 56.8 + - + +
414B PHE* 4.1 21.8 - - + +
416B SER* 1.3 77.6 - - - +
418B HIS* 1.3 66.1 + - + +
420B ALA* 3.3 8.0 + - - +
421B ARG* 3.3 20.4 + - - +
426B PHE* 5.8 0.9 - - - -
438B VAL* 3.8 25.3 - - + +
442B TRP* 5.1 2.9 - - + -
445B LEU* 5.5 2.7 - - + -
594B ILE* 5.3 3.6 - - + +
595B ILE* 4.0 39.5 - - + +
598B ILE* 5.7 12.2 - - + +
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Residues in contact with HIS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PHE* 2.9 37.3 + + + +
415B LEU* 3.0 8.3 + - + +
417B MET* 1.3 78.6 - - + +
419B TRP* 1.3 64.0 + - - +
421B ARG* 2.8 38.4 + - - +
422B SER* 3.2 20.4 + - - -
598B ILE* 3.6 22.1 - - + +
599B LEU* 4.5 19.8 + - + +
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Residues in contact with TRP 419 (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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388B PHE* 4.9 2.5 - + - -
389B LYS* 3.4 40.8 + - + +
391B THR 4.5 8.7 - - - -
392B MET* 4.3 30.4 - - + +
415B LEU* 2.6 20.0 + - + +
416B SER* 3.1 11.4 + - - +
418B HIS* 1.3 74.1 - - - +
420B ALA* 1.3 93.3 + - + +
421B ARG 3.1 0.2 + - - -
422B SER* 2.9 26.8 + - - -
423B ILE* 3.7 10.6 + - + +
445B LEU* 5.4 3.1 - - + -
509B TYR* 5.5 0.8 - + - -
512B ALA* 3.2 46.1 - - + +
515B LYS* 3.6 34.5 - - + -
516B ALA* 4.3 7.2 - - + -
519B LEU* 4.6 7.0 - - + -
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Residues in contact with ALA 420 (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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416B SER 3.1 10.1 + - - +
417B MET* 3.8 9.2 - - - +
418B HIS 3.3 0.4 - - - -
419B TRP* 1.3 93.5 - - + +
421B ARG* 1.3 58.4 + - - +
423B ILE* 2.8 25.0 - - - +
426B PHE* 3.0 21.1 - - + -
438B VAL* 5.7 2.9 - - + -
445B LEU* 4.4 6.7 - - + -
519B LEU* 3.4 33.0 - - + -
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Residues in contact with ARG 421 (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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417B MET 3.3 11.9 + - - +
418B HIS* 2.8 38.6 + - - +
419B TRP 3.1 1.0 - - - -
420B ALA* 1.3 76.9 - - - +
422B SER* 1.3 65.6 + - - +
423B ILE 3.2 7.9 + - - +
426B PHE* 3.8 17.7 - - + -
427B GLN* 3.5 35.7 - - + +
434B ASN* 5.8 0.9 - - - +
598B ILE* 2.8 51.4 + - + +
599B LEU* 3.9 19.8 - - - +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PHE* 3.7 28.8 + - - -
389B LYS* 3.2 25.1 + - - +
418B HIS 3.2 10.9 + - - -
419B TRP* 2.9 20.2 + - - -
421B ARG* 1.3 79.7 - - - +
423B ILE* 1.3 64.4 + - - +
424B PRO* 3.2 10.7 - - - +
427B GLN* 5.4 1.7 - - - +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B HIS* 3.6 28.3 - - + +
389B LYS* 3.5 18.2 - - + +
419B TRP* 3.7 10.0 + - + +
420B ALA* 2.8 32.8 - - - +
421B ARG 3.6 3.6 - - - +
422B SER* 1.3 80.6 + - - +
424B PRO* 1.4 72.7 - - + +
425B ALA* 3.0 35.7 - - + +
426B PHE* 3.0 29.9 - - + +
427B GLN* 3.6 2.0 + - - +
516B ALA* 6.5 0.9 - - + -
519B LEU* 4.5 3.8 - - + -
520B PHE* 4.3 16.6 - - + -
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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
------------------------------------------------------------
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