Contacts of the helix formed by residues 399 - 414 (chain B) in PDB entry 5U03
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 CYS 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B GLY* 3.9 11.2 - - - -
372B GLY 5.4 1.8 - - - -
398B VAL* 1.3 70.4 - - - +
400B LEU* 1.3 77.9 + - - +
402B MET 2.9 3.5 + - - +
403B GLN* 2.8 35.3 + - - +
479B ARG 4.5 4.9 - - - -
480B HIS* 4.0 20.6 - - - -
523B VAL 2.7 16.0 + - - -
524B GLN* 3.1 25.3 + - - +
526B HIS* 4.0 19.3 - - + -
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Residues in contact with LEU 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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369B VAL* 6.4 0.2 - - + -
370B PRO 4.2 2.0 - - - +
371B GLY* 3.7 15.0 - - - -
372B GLY* 3.8 27.8 - - - +
373B PHE 5.6 0.2 - - - -
374B GLY 4.7 11.9 - - - +
378B THR* 5.6 1.3 - - - +
381B LYS* 4.5 16.6 - - + -
398B VAL 2.8 1.2 + - - -
399B CYS* 1.3 83.9 - - - +
401B GLY* 1.4 54.2 + - - +
403B GLN* 2.9 22.6 + - + +
404B LEU* 2.7 63.2 + - + +
421B SER* 5.7 2.2 - - - +
423B GLU* 4.1 15.0 - - - +
424B PHE* 4.5 12.8 - - + -
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Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B VAL* 3.4 39.3 - - - -
370B PRO 3.7 2.0 + - - -
385B ILE* 3.9 4.5 - - - +
395B PHE* 4.2 1.3 - - - -
397B GLY* 4.1 6.7 - - - -
398B VAL 2.9 7.2 + - - -
400B LEU* 1.4 79.7 - - - +
402B MET* 1.3 56.1 + - - +
404B LEU* 3.3 4.3 + - - +
405B ALA* 2.9 28.4 + - - +
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Residues in contact with MET 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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397B GLY* 4.1 3.4 - - - +
398B VAL 3.8 5.7 - - - +
399B CYS 2.9 10.0 + - - +
401B GLY* 1.3 74.8 - - - +
403B GLN* 1.3 63.1 + - - +
405B ALA* 3.1 8.8 + - - +
406B VAL* 3.1 24.8 + - + +
484B VAL* 5.0 6.3 - - + -
499B PHE* 4.6 12.3 - - + -
509B MET* 4.3 9.6 - - + +
510B GLU 3.7 17.3 - - - +
511B ILE 4.2 1.6 - - - +
512B VAL* 3.8 36.8 - - + +
522B GLY* 3.3 31.4 - - - +
523B VAL* 3.5 18.8 - - - +
524B GLN* 3.4 23.1 - - + +
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Residues in contact with GLN 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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399B CYS* 2.8 30.2 + - - +
400B LEU* 3.3 24.8 - - + +
402B MET* 1.3 75.6 - - - +
404B LEU* 1.3 63.2 + - + +
406B VAL* 3.3 9.3 + - - +
407B VAL* 3.2 23.7 + - - +
421B SER* 4.9 0.2 + - - -
423B GLU* 4.0 5.5 - - - +
433B VAL* 3.3 40.1 - - + +
480B HIS* 5.0 1.6 - - - +
481B ARG 5.6 0.2 - - - +
482B PHE* 3.5 24.8 + - - +
483B GLU* 5.9 2.7 - - - -
484B VAL* 6.4 2.7 - - + -
524B GLN* 3.2 29.1 + - - +
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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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369B VAL* 5.2 0.7 - - + -
378B THR* 3.7 27.8 - - + -
381B LYS* 4.0 35.2 - - + -
382B ILE* 4.1 13.7 - - + +
385B ILE* 3.8 15.9 - - + -
400B LEU* 2.7 44.7 + - + +
401B GLY* 3.8 3.1 - - - +
403B GLN* 1.3 76.7 - - + +
405B ALA* 1.3 60.2 + - - +
407B VAL* 3.1 12.1 + - + +
408B GLU* 2.7 30.1 + - - +
420B ASN* 6.1 0.4 - - - +
421B SER* 5.2 11.0 - - - -
424B PHE* 5.5 2.7 - - + -
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Residues in contact with ALA 405 (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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385B ILE* 3.7 16.8 - - + +
395B PHE* 4.2 8.5 - - + -
401B GLY 2.9 15.1 + - - +
402B MET* 3.1 12.3 + - + +
404B LEU* 1.3 76.8 - - - +
406B VAL* 1.3 57.8 + - + +
408B GLU* 3.2 4.7 + - - +
409B PHE* 2.9 28.8 + - - +
497B LEU* 6.3 1.1 - - - -
512B VAL* 6.1 2.7 - - + -
520B PHE* 4.0 31.7 - - + -
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Residues in contact with VAL 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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402B MET* 3.1 22.7 + - + +
403B GLN* 3.6 9.0 - - - +
404B LEU 3.2 0.2 - - - -
405B ALA* 1.3 77.5 - - + +
407B VAL* 1.3 60.6 + - - +
409B PHE* 3.2 8.1 + - - +
410B SER* 3.0 21.6 + - - +
432B VAL* 3.5 23.3 - - + -
484B VAL* 4.9 11.9 - - + -
492B LEU* 3.9 26.7 - - + -
497B LEU* 4.2 16.6 - - + -
499B PHE* 4.4 16.6 - - + -
512B VAL* 5.1 5.6 - - + -
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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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382B ILE* 4.8 5.4 - - + -
403B GLN 3.2 14.5 + - - +
404B LEU* 3.1 14.5 + - + +
406B VAL* 1.3 76.7 - - - +
408B GLU* 1.3 63.3 + - - +
410B SER* 3.1 6.4 + - - -
411B ARG* 2.8 54.1 + - - +
419B ALA* 3.7 16.4 - - + +
420B ASN* 4.1 11.0 - - - +
421B SER* 4.5 2.7 - - - +
432B VAL* 3.8 17.7 - - + -
433B VAL* 3.8 21.1 - - + -
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Residues in contact with GLU 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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382B ILE* 3.6 32.5 - - + +
385B ILE* 3.9 14.8 - - + +
386B ALA* 3.3 22.4 - - + +
389B ARG* 2.8 46.5 + - - -
404B LEU 2.7 16.5 + - - +
405B ALA 3.2 9.2 + - - +
407B VAL* 1.3 72.6 - - - +
409B PHE* 1.3 65.3 + - - +
411B ARG* 3.1 7.3 + - - +
412B ASN* 2.8 42.2 + - - +
520B PHE* 5.0 0.5 - - - -
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Residues in contact with PHE 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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389B ARG* 4.9 9.6 - - - +
405B ALA 2.9 12.9 + - - +
406B VAL 3.4 9.2 - - - +
408B GLU* 1.3 83.0 + - - +
410B SER* 1.3 57.4 + - - +
413B VAL* 2.7 78.8 + - + +
414B LEU* 4.5 2.7 - - + -
492B LEU* 3.6 30.5 - - + -
495B GLN* 3.8 25.4 - - + -
496B GLY* 4.5 3.4 - - - -
497B LEU* 3.8 23.6 - - + -
514B LEU* 3.8 31.0 - - + -
520B PHE* 6.5 0.9 - + + -
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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
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406B VAL* 3.0 15.0 + - - +
407B VAL 3.5 7.9 - - - -
409B PHE* 1.3 76.2 - - - +
411B ARG* 1.3 64.2 + - - +
414B LEU* 2.9 44.4 + - - +
415B GLY 2.9 6.8 + - - -
416B TRP* 3.0 14.5 + - - -
419B ALA* 4.0 18.2 - - - -
432B VAL* 4.0 11.3 - - - +
488B TRP* 5.8 0.9 - - - +
492B LEU* 4.2 10.4 - - - +
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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
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378B THR* 6.3 0.2 - - - +
382B ILE* 3.5 30.4 - - - +
407B VAL* 2.8 27.6 + - - +
408B GLU* 3.1 9.2 + - - +
410B SER* 1.3 76.6 - - - +
412B ASN* 1.3 63.5 + - - +
415B GLY* 3.2 19.4 - - - -
416B TRP 3.1 22.9 - - - +
417B GLN* 2.7 49.0 + - - +
419B ALA* 2.8 27.9 + - + +
420B ASN* 3.3 28.7 + - - +
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Residues in contact with ASN 412 (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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382B ILE* 5.5 2.6 - - - +
386B ALA* 4.1 10.3 - - - +
389B ARG* 3.6 10.5 + - - +
408B GLU* 2.8 42.5 + - - +
411B ARG* 1.3 78.9 - - - +
413B VAL* 1.4 63.7 + - - +
415B GLY* 4.5 1.1 - - - -
417B GLN* 3.1 22.4 + - - +
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Residues in contact with VAL 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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389B ARG* 3.9 22.7 - - - +
409B PHE* 2.7 55.6 + - + +
412B ASN* 1.4 78.5 - - - +
414B LEU* 1.4 60.2 + - - +
415B GLY 3.2 1.1 + - - -
495B GLN* 3.6 25.1 - - - +
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Residues in contact with LEU 414 (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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409B PHE* 4.5 5.6 - - + -
410B SER* 2.9 20.9 + - - +
413B VAL* 1.4 77.1 - - - +
415B GLY* 1.3 62.0 + - - +
416B TRP* 3.3 58.9 + - + -
491B CYS* 4.5 8.1 - - + +
492B LEU* 3.7 25.8 - - + -
495B GLN* 3.8 35.2 - - + +
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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