Contacts of the helix formed by residues 369 - 383 (chain D) in PDB entry 1SZU
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 369 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344D GLU* 4.9 1.6 - - - +
359D LEU* 3.0 22.1 + - + +
360D PHE 4.1 2.8 - - - +
361D GLU* 3.5 39.1 - - + +
367D LYS 3.3 0.6 + - - -
368D PRO* 1.3 71.3 - - - +
370D ALA* 1.3 58.7 + - - +
371D LYS* 3.1 10.2 + - - +
372D LEU* 2.6 50.4 + - + +
373D THR* 3.0 23.3 + - - -
395D ASN* 3.7 2.4 - - - +
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Residues in contact with ALA 370 (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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368D PRO 3.4 7.3 + - - +
369D ASP* 1.3 74.1 - - - +
371D LYS* 1.3 59.2 + - + +
373D THR* 3.6 1.9 - - - -
374D ALA* 3.1 28.8 + - - +
393D TYR 3.6 19.5 - - - +
394D TYR* 3.5 28.0 - - + +
395D ASN* 4.2 1.0 - - - +
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Residues in contact with LYS 371 (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 ASP* 3.1 6.6 - - - +
370D ALA* 1.3 78.0 - - + +
372D LEU* 1.3 65.1 + - - +
374D ALA* 3.4 6.1 + - - +
375D GLU* 3.1 22.6 + - - +
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Residues in contact with LEU 372 (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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344D GLU* 3.5 41.3 - - + +
359D LEU* 3.9 16.4 - - + -
369D ASP* 2.6 32.7 + - + +
371D LYS* 1.3 71.6 - - - +
373D THR* 1.3 64.0 + - - +
375D GLU* 2.9 16.5 + - + +
376D ILE* 2.9 44.3 + - + +
421D PHE* 4.6 9.0 - - + -
424D ALA* 4.1 18.2 - - + +
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Residues in contact with THR 373 (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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359D LEU* 3.4 21.4 - - - +
369D ASP 3.0 15.9 + - - -
370D ALA 3.6 0.9 - - - -
372D LEU* 1.3 79.0 - - - +
374D ALA* 1.3 62.8 + - - +
376D ILE* 3.3 4.3 + - - +
377D VAL* 3.1 22.3 + - - +
389D SER* 3.7 25.8 - - - +
394D TYR 3.4 23.8 - - - +
395D ASN* 3.1 15.2 - - - -
396D VAL 4.0 6.7 - - - +
397D LEU* 4.0 15.4 - - + +
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Residues in contact with ALA 374 (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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370D ALA 3.1 16.0 + - - +
371D LYS* 3.8 5.8 - - - +
373D THR* 1.3 80.1 - - - +
375D GLU* 1.3 57.0 + - - +
377D VAL* 3.3 9.1 + - - +
378D ALA* 3.0 28.8 + - - +
389D SER* 6.3 0.2 - - - -
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Residues in contact with GLU 375 (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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371D LYS 3.1 12.7 + - - +
372D LEU* 2.9 19.1 + - + +
374D ALA* 1.3 73.3 - - - +
376D ILE* 1.3 61.5 + - - +
378D ALA* 3.2 5.8 + - + +
379D ARG* 2.6 77.9 + - + +
424D ALA* 3.1 22.9 - - + +
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Residues in contact with ILE 376 (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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359D LEU* 4.3 4.3 - - + -
372D LEU* 2.9 33.4 + - + +
373D THR 3.5 6.5 - - - +
375D GLU* 1.3 76.4 - - - +
377D VAL* 1.3 57.9 + - - +
379D ARG* 3.9 4.2 - - - +
380D ALA* 2.8 34.2 + - + +
387D LEU* 4.3 13.2 - - + -
397D LEU* 3.7 21.1 - - + -
417D ILE* 5.2 4.0 - - + -
420D CYS* 3.8 29.3 - - + +
421D PHE* 3.8 48.5 - - + -
424D ALA* 4.4 2.7 - - + -
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Residues in contact with VAL 377 (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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22D ILE* 5.0 7.6 - - + -
23D HIS* 4.0 23.6 - - + -
373D THR 3.1 13.5 + - - +
374D ALA* 3.5 11.2 - - - +
375D GLU 3.2 0.2 - - - -
376D ILE* 1.3 79.1 - - - +
378D ALA* 1.3 62.9 + - - +
380D ALA* 3.7 5.7 - - - +
381D ARG* 3.0 22.5 + - - +
385D LEU 4.7 0.5 - - - +
387D LEU* 4.2 18.1 - - + +
388D LEU* 5.6 0.2 - - - -
389D SER* 4.5 17.7 - - - +
397D LEU* 3.5 22.9 - - + -
1027D EDO 4.1 9.6 - - - -
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Residues in contact with ALA 378 (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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374D ALA 3.0 16.9 + - - +
375D GLU* 3.7 6.1 - - + +
377D VAL* 1.3 78.4 - - - +
379D ARG* 1.3 63.4 + - + +
381D ARG* 3.3 5.4 + - - +
382D ASP* 3.2 27.1 + - - +
1027D EDO 4.0 27.4 - - - +
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Residues in contact with ARG 379 (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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375D GLU* 2.6 60.3 + - + +
376D ILE* 3.9 0.9 - - - +
378D ALA* 1.3 69.2 - - + +
380D ALA* 1.3 67.7 + - - +
382D ASP* 3.0 21.8 + - - +
383D LYS* 3.1 19.1 + - - +
420D CYS* 3.6 37.2 - - + +
423D GLU* 3.3 40.3 + - - +
424D ALA* 3.5 6.1 + - - +
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Residues in contact with ALA 380 (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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376D ILE* 2.8 22.4 + - + +
377D VAL 3.7 3.6 - - - +
379D ARG* 1.3 73.0 - - - +
381D ARG* 1.3 60.8 + - - +
383D LYS* 3.0 8.8 + - - -
384D GLY 3.2 0.5 + - - -
385D LEU* 2.8 45.4 + - + +
387D LEU* 3.7 22.9 - - + -
416D ILE* 4.3 3.6 - - - -
417D ILE* 5.6 0.7 - - + -
420D CYS* 3.3 16.3 - - - -
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Residues in contact with ARG 381 (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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23D HIS* 3.7 11.2 - - + +
24D PRO* 3.4 24.7 + - - +
25D ILE* 3.3 34.4 - - + +
41D ARG* 3.5 12.4 + - - +
43D TYR* 4.0 4.6 + - + -
377D VAL 3.0 11.8 + - - +
378D ALA 3.6 6.7 + - - +
379D ARG 3.1 0.2 - - - -
380D ALA* 1.3 78.3 - - - +
382D ASP* 1.3 71.7 + - - +
384D GLY* 3.0 17.0 + - - -
385D LEU 3.4 10.3 + - - +
386D ILE* 4.2 8.3 - - + -
1006D SO4 3.2 36.9 + - - -
1027D EDO 2.4 53.8 + - - +
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Residues in contact with ASP 382 (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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41D ARG* 2.6 28.2 + - - +
378D ALA* 3.2 14.9 + - - +
379D ARG* 3.0 13.7 + - - +
381D ARG* 1.3 97.4 + - - +
383D LYS* 1.3 56.0 + - + +
384D GLY 3.2 0.7 - - - -
1006D SO4 5.0 4.0 + - - -
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Residues in contact with LYS 383 (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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41D ARG* 3.6 4.3 - - - -
379D ARG* 3.1 8.7 + - - +
380D ALA 3.0 9.7 + - - +
381D ARG 3.0 0.8 - - - -
382D ASP* 1.3 81.3 - - + +
384D GLY* 1.3 59.3 + - - +
385D LEU 3.5 0.4 - - - -
416D ILE* 3.5 34.5 - - + +
419D GLN* 3.2 26.9 + - - +
420D CYS* 3.8 26.5 - - - +
423D GLU* 3.0 40.4 + - - -
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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