Contacts of the helix formed by residues 399 - 414 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371C GLY* 3.9 11.4 - - - -
372C GLY 5.4 2.5 - - - -
398C VAL* 1.3 70.2 - - - +
400C LEU* 1.3 76.7 + - - +
402C MET 2.9 3.3 + - - +
403C GLN* 2.8 36.0 + - - +
479C ARG 4.5 4.5 - - - -
480C HIS* 4.0 21.3 - - - -
523C VAL 2.7 16.4 + - - -
524C GLN* 3.1 24.1 + - - +
526C HIS* 4.0 19.1 - - + -
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Residues in contact with LEU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C VAL* 6.4 0.2 - - + -
370C PRO 4.2 1.6 - - - +
371C GLY* 3.7 14.8 - - - -
372C GLY* 3.8 28.9 - - - +
373C PHE* 4.9 0.4 - - - +
374C GLY 4.7 11.2 - - - +
378C THR* 5.5 1.6 - - - +
381C LYS* 4.5 16.6 - - + -
398C VAL 2.8 1.2 + - - -
399C CYS* 1.3 83.9 - - - +
401C GLY* 1.3 53.3 + - - +
403C GLN* 2.9 21.7 + - + +
404C LEU* 2.7 64.1 + - + +
421C SER* 5.7 2.0 - - - +
423C GLU* 4.1 15.3 - - - +
424C PHE* 4.5 12.6 - - + -
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Residues in contact with GLY 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C VAL* 3.4 38.8 - - - -
370C PRO 3.7 2.2 + - - -
385C ILE* 3.9 4.5 - - - +
395C PHE* 4.2 0.9 - - - -
397C GLY* 4.1 6.3 - - - -
398C VAL 2.9 6.9 + - - -
400C LEU* 1.3 80.1 - - - +
402C MET* 1.3 55.6 + - - +
404C LEU* 3.3 5.0 + - - +
405C ALA* 2.9 28.9 + - - +
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Residues in contact with MET 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C GLY* 4.1 3.6 - - - +
398C VAL 3.8 5.5 - - - +
399C CYS 2.9 9.8 + - - +
401C GLY* 1.3 75.3 - - - +
403C GLN* 1.3 62.8 + - - +
405C ALA* 3.1 8.1 + - - +
406C VAL* 3.1 24.9 + - + +
484C VAL* 5.0 6.1 - - + -
499C PHE* 4.6 11.9 - - + -
509C MET* 4.3 10.1 - - + +
510C GLU 3.7 17.0 - - - +
511C ILE 4.2 1.6 - - - +
512C VAL* 3.8 36.3 - - + +
522C GLY* 3.3 31.6 - - - +
523C VAL* 3.5 19.5 - - - +
524C GLN* 3.4 23.1 - - + +
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Residues in contact with GLN 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C CYS* 2.8 29.4 + - - +
400C LEU* 3.3 24.4 - - + +
402C MET* 1.3 75.7 - - - +
404C LEU* 1.3 62.2 + - + +
406C VAL* 3.3 8.9 + - - +
407C VAL* 3.2 23.4 + - - +
421C SER* 4.9 0.2 + - - -
423C GLU* 4.0 5.9 - - - +
433C VAL* 3.3 40.9 - - + +
480C HIS* 5.0 1.4 - - - +
482C PHE* 3.5 25.1 + - - +
483C GLU* 5.9 2.5 - - - -
484C VAL* 6.4 2.7 - - + -
524C GLN* 3.2 28.7 + - - +
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Residues in contact with LEU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C VAL* 5.2 0.7 - - + -
378C THR* 3.7 27.8 - - + -
381C LYS* 4.0 35.2 - - + -
382C ILE* 4.1 14.4 - - + +
385C ILE* 3.8 16.4 - - + -
400C LEU* 2.7 45.0 + - + +
401C GLY* 3.8 3.1 - - - +
403C GLN* 1.3 75.6 - - + +
405C ALA* 1.3 60.1 + - - +
407C VAL* 3.1 11.7 + - + +
408C GLU* 2.7 29.8 + - - +
420C ASN* 6.1 0.7 - - - +
421C SER* 5.2 11.7 - - - -
424C PHE* 5.5 2.2 - - + -
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Residues in contact with ALA 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C ILE* 3.7 16.8 - - + +
395C PHE* 4.2 9.0 - - + -
401C GLY 2.9 14.5 + - - +
402C MET* 3.1 11.8 + - + +
404C LEU* 1.3 78.4 - - - +
406C VAL* 1.3 57.9 + - + +
408C GLU* 3.2 5.0 + - - +
409C PHE* 2.9 27.9 + - - +
497C LEU* 6.0 1.7 - - + +
512C VAL* 6.1 3.1 - - + -
520C PHE* 4.0 31.5 - - + -
522C GLY* 6.3 0.4 - - - -
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Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C MET* 3.1 22.5 + - + +
403C GLN* 3.6 9.2 - - - +
404C LEU 3.2 0.2 - - - -
405C ALA* 1.3 76.7 - - + +
407C VAL* 1.3 62.5 + - - +
409C PHE* 3.2 8.5 + - - +
410C SER* 3.0 21.6 + - - +
432C VAL* 3.5 22.9 - - + -
484C VAL* 4.9 11.7 - - + -
492C LEU* 3.9 26.5 - - + -
497C LEU* 4.2 16.2 - - + -
499C PHE* 4.4 16.8 - - + -
512C VAL* 5.1 5.8 - - + -
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Residues in contact with VAL 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C ILE* 4.8 4.9 - - + -
403C GLN 3.2 13.9 + - - +
404C LEU* 3.1 14.0 + - + +
406C VAL* 1.3 77.6 - - - +
408C GLU* 1.3 64.0 + - - +
410C SER* 3.1 6.7 + - - +
411C ARG* 2.8 54.2 + - - +
419C ALA* 3.7 15.9 - - + +
420C ASN* 4.1 10.5 - - - +
421C SER* 4.5 2.9 - - - +
432C VAL* 3.8 18.4 - - + -
433C VAL* 3.8 21.1 - - + -
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Residues in contact with GLU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C ILE* 3.6 33.2 - - + +
385C ILE* 3.9 14.5 - - + +
386C ALA* 3.3 23.8 - - + +
389C ARG* 2.8 47.1 + - - -
404C LEU 2.7 17.5 + - - +
405C ALA 3.4 9.2 - - - +
407C VAL* 1.3 71.8 - - - +
409C PHE* 1.3 65.2 + - - +
411C ARG* 3.1 7.4 + - - +
412C ASN* 2.8 40.5 + - - +
520C PHE* 5.0 0.5 - - - -
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Residues in contact with PHE 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ARG* 4.9 9.9 - - - +
405C ALA 2.9 12.9 + - - +
406C VAL 3.2 9.6 + - - +
408C GLU* 1.3 83.4 + - - +
410C SER* 1.3 58.5 + - - +
413C VAL* 2.7 77.0 + - + +
414C LEU* 4.5 2.9 - - + -
492C LEU* 3.6 31.4 - - + -
495C GLN* 3.8 26.5 - - + -
496C GLY* 4.5 3.4 - - - -
497C LEU* 3.8 24.5 - - + -
514C LEU* 3.8 31.0 - - + -
520C PHE* 6.5 1.1 - + + -
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Residues in contact with SER 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C VAL* 3.0 15.9 + - - +
407C VAL 3.5 8.1 - - - -
409C PHE* 1.3 74.9 - - - +
411C ARG* 1.3 62.1 + - - +
414C LEU* 2.9 45.8 + - - +
415C GLY 2.9 7.1 + - - -
416C TRP* 3.0 15.1 + - - -
419C ALA* 4.0 17.9 - - - -
432C VAL* 4.0 11.8 - - - +
488C TRP* 5.8 0.7 - - - +
492C LEU* 4.2 10.0 - - - +
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Residues in contact with ARG 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C ILE* 3.5 30.6 - - - +
407C VAL* 2.8 30.4 + - - +
408C GLU* 3.6 9.4 - - - +
410C SER* 1.3 76.6 - - - +
412C ASN* 1.3 62.6 + - - +
415C GLY* 3.2 18.9 - - - -
416C TRP 3.1 23.3 - - - +
417C GLN* 2.7 46.9 + - - +
419C ALA* 2.8 27.4 + - + +
420C ASN* 3.3 28.5 + - - +
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Residues in contact with ASN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C ILE* 5.5 2.2 - - - +
386C ALA* 4.1 9.9 - - - +
389C ARG* 3.6 10.5 + - - +
408C GLU* 2.8 42.1 + - - +
411C ARG* 1.3 80.3 - - - +
413C VAL* 1.3 64.6 + - - +
415C GLY* 4.5 0.9 - - - -
417C GLN* 3.1 23.1 + - - +
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Residues in contact with VAL 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ARG* 3.9 22.4 - - - +
409C PHE* 2.7 56.5 + - + +
412C ASN* 1.3 79.0 - - - +
414C LEU* 1.4 60.9 + - - +
415C GLY* 3.2 1.7 + - - -
495C GLN* 3.6 24.7 - - - +
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Residues in contact with LEU 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C PHE* 4.5 5.4 - - + -
410C SER* 2.9 21.1 + - - +
413C VAL* 1.4 75.2 - - + +
415C GLY* 1.3 63.1 + - - +
416C TRP* 3.3 58.9 + - + -
491C CYS* 4.5 7.6 - - + +
492C LEU* 3.7 25.6 - - + -
495C GLN* 3.8 36.3 - - + +
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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