Contacts of the helix formed by residues 399 - 414 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371D GLY* 3.9 12.6 - - - -
372D GLY 5.4 2.2 - - - -
398D VAL* 1.3 71.0 - - - +
400D LEU* 1.3 76.5 + - - +
402D MET 2.9 3.1 + - - +
403D GLN* 2.8 35.7 + - - +
479D ARG 4.5 4.9 - - - -
480D HIS* 4.0 20.4 - - - -
523D VAL 2.7 15.7 + - - -
524D GLN* 3.1 25.2 + - - +
526D HIS* 4.0 19.3 - - + -
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Residues in contact with LEU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D VAL* 6.3 0.2 - - + -
370D PRO 4.2 2.0 - - - +
371D GLY* 3.7 14.4 - - - -
372D GLY* 3.8 28.7 - - - +
373D PHE* 5.4 0.2 - - - -
374D GLY 4.7 12.1 - - - +
378D THR* 5.6 1.1 - - - +
381D LYS* 4.5 17.3 - - + -
398D VAL 2.8 1.2 + - - -
399D CYS* 1.3 85.3 - - - +
401D GLY* 1.4 53.5 + - - +
403D GLN* 2.9 21.8 + - + +
404D LEU* 2.7 64.2 + - + +
421D SER* 5.7 2.2 - - - +
423D GLU* 4.1 14.8 - - - +
424D PHE* 4.5 13.0 - - + -
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Residues in contact with GLY 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D VAL* 3.4 38.8 - - - -
370D PRO 3.7 2.0 + - - -
385D ILE* 3.9 4.3 - - - +
395D PHE* 4.2 0.7 - - - -
397D GLY* 4.1 6.5 - - - -
398D VAL 2.9 6.7 + - - -
400D LEU* 1.4 79.7 - - - +
402D MET* 1.3 55.7 + - - +
404D LEU* 3.3 5.3 + - - +
405D ALA* 2.9 28.9 + - - +
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Residues in contact with MET 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D GLY* 4.1 3.1 - - - +
398D VAL 3.8 5.7 - - - +
399D CYS 2.9 9.8 + - - +
401D GLY* 1.3 75.5 - - - +
403D GLN* 1.3 62.1 + - - +
405D ALA* 3.1 8.3 + - - +
406D VAL* 3.1 25.4 + - + +
484D VAL* 5.0 5.8 - - + -
499D PHE* 4.6 12.1 - - + -
509D MET* 4.3 9.6 - - + +
510D GLU 3.7 17.0 - - - +
511D ILE 4.2 1.6 - - - +
512D VAL* 3.8 36.3 - - + +
522D GLY* 3.3 31.9 - - - +
523D VAL* 3.5 20.0 - - - +
524D GLN* 3.4 24.2 - - + +
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Residues in contact with GLN 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D CYS* 2.8 28.5 + - - +
400D LEU* 2.9 24.6 + - + +
402D MET* 1.3 75.3 - - - +
404D LEU* 1.3 62.9 + - + +
406D VAL* 3.3 10.4 + - - +
407D VAL* 3.2 23.7 + - - +
421D SER* 4.9 0.2 + - - -
423D GLU* 4.0 6.2 - - - +
433D VAL* 3.3 41.8 - - + +
480D HIS* 5.0 1.6 - - - +
482D PHE* 3.5 25.3 + - - +
483D GLU* 5.9 2.7 - - - -
484D VAL* 6.4 2.5 - - + -
524D GLN* 3.2 29.1 + - - +
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Residues in contact with LEU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D VAL* 5.2 0.9 - - + -
378D THR* 3.7 28.3 - - + +
381D LYS* 4.0 35.0 - - + -
382D ILE* 4.1 14.8 - - + +
385D ILE* 3.8 16.1 - - + +
400D LEU* 2.7 47.9 + - + +
401D GLY* 3.8 2.9 - - - +
403D GLN* 1.3 74.0 - - + +
405D ALA* 1.3 61.0 + - - +
407D VAL* 3.1 12.0 + - + +
408D GLU* 2.7 30.1 + - - +
420D ASN* 6.1 0.4 - - - +
421D SER* 5.2 11.2 - - - -
424D PHE* 5.5 2.7 - - + -
433D VAL* 6.1 0.2 - - + -
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Residues in contact with ALA 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ILE* 3.7 17.0 - - + +
395D PHE* 4.2 8.5 - - + -
401D GLY 2.9 14.9 + - - +
402D MET* 3.1 12.1 + - + +
404D LEU* 1.3 77.8 - - - +
406D VAL* 1.3 57.9 + - + +
408D GLU* 3.2 4.9 + - - +
409D PHE* 2.9 28.1 + - - +
497D LEU* 6.3 1.3 - - + -
512D VAL* 6.1 3.6 - - + -
520D PHE* 4.0 30.7 - - + -
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Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D MET* 3.1 22.9 + - + +
403D GLN* 3.6 9.2 - - - +
404D LEU 3.2 0.2 - - - -
405D ALA* 1.3 77.1 - - + +
407D VAL* 1.3 62.7 + - - +
409D PHE* 3.2 9.0 + - - +
410D SER* 3.0 22.2 + - - +
432D VAL* 3.5 23.8 - - + -
433D VAL* 5.9 0.2 - - + -
484D VAL* 4.9 11.4 - - + -
492D LEU* 3.9 26.5 - - + -
497D LEU* 4.2 14.4 - - + -
499D PHE* 4.4 17.7 - - + -
512D VAL* 5.1 5.8 - - + -
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D ILE* 4.8 5.6 - - + -
403D GLN 3.2 14.3 + - - +
404D LEU* 3.1 14.7 + - + +
406D VAL* 1.3 76.6 - - - +
408D GLU* 1.3 62.8 + - - +
410D SER* 3.1 6.8 + - - -
411D ARG* 2.8 54.1 + - - +
419D ALA 3.7 15.3 - - - +
420D ASN* 4.1 10.5 - - - +
421D SER* 4.5 2.9 - - - +
432D VAL* 3.8 17.5 - - + -
433D VAL* 3.8 20.6 - - + -
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Residues in contact with GLU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D ILE* 3.6 33.2 - - + +
385D ILE* 3.9 14.5 - - + +
386D ALA* 3.3 25.0 - - + +
389D ARG* 2.8 45.9 + - - -
404D LEU 2.7 17.4 + - - +
405D ALA 3.2 8.5 + - - +
407D VAL* 1.3 72.2 - - - +
409D PHE* 1.3 63.5 + - - +
411D ARG* 3.1 7.4 + - - +
412D ASN* 2.8 40.8 + - - +
520D PHE* 5.0 0.7 - - - -
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Residues in contact with PHE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ARG* 4.9 9.2 - - - +
405D ALA 2.9 12.5 + - - +
406D VAL 3.4 9.6 - - - +
408D GLU* 1.3 82.3 + - - +
410D SER* 1.3 56.7 + - - +
413D VAL* 2.7 77.8 + - + +
414D LEU* 4.5 2.7 - - + -
492D LEU* 3.6 31.4 - - + -
495D GLN* 3.8 26.7 - - + -
496D GLY* 4.5 3.1 - - - -
497D LEU* 3.8 23.6 - - + -
514D LEU* 3.8 31.2 - - + -
520D PHE* 6.5 0.9 - + + -
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Residues in contact with SER 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D VAL* 3.0 15.5 + - - +
407D VAL 3.1 8.3 + - - -
409D PHE* 1.3 76.0 - - - +
411D ARG* 1.3 62.6 + - - +
414D LEU* 2.9 45.2 + - - +
415D GLY 2.9 6.8 + - - -
416D TRP* 3.0 15.1 + - - -
419D ALA* 4.0 18.6 - - - -
432D VAL* 4.0 11.6 - - - +
488D TRP* 5.8 0.9 - - - +
492D LEU* 4.2 9.7 - - - +
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Residues in contact with ARG 411 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382D ILE* 3.5 30.4 - - - +
407D VAL* 2.8 29.8 + - - +
408D GLU* 3.1 9.4 + - - +
410D SER* 1.3 77.7 - - - +
412D ASN* 1.3 63.4 + - - +
415D GLY* 3.2 19.1 - - - -
416D TRP 3.1 22.0 - - - +
417D GLN* 2.7 46.7 + - - +
418D ASP* 5.7 0.2 - - - +
419D ALA* 2.8 27.0 + - + +
420D ASN* 3.3 29.1 + - - +
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Residues in contact with ASN 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D ILE* 5.5 1.8 - - - +
386D ALA* 4.1 10.1 - - - +
389D ARG* 3.6 10.7 + - - +
408D GLU* 2.8 42.7 + - - +
411D ARG* 1.3 80.4 - - - +
413D VAL* 1.4 64.3 + - - +
415D GLY* 4.5 0.9 - - - -
417D GLN* 3.1 22.5 + - - +
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Residues in contact with VAL 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ARG* 3.9 22.2 - - - +
409D PHE* 2.7 57.6 + - + +
412D ASN* 1.4 78.9 - - - +
414D LEU* 1.3 60.4 + - + +
415D GLY* 3.2 1.9 + - - -
495D GLN* 3.6 24.0 - - - +
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D PHE* 4.5 4.9 - - + -
410D SER* 2.9 21.9 + - - +
413D VAL* 1.3 75.8 - - - +
415D GLY* 1.3 61.6 + - - +
416D TRP* 3.1 58.2 + - + -
491D CYS* 4.5 7.9 - - + +
492D LEU* 3.7 26.0 - - + -
495D GLN* 3.8 35.7 - - + +
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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
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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