Contacts of the helix formed by residues 393 - 406 (chain D) in PDB entry 3IAD
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 SER 393 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D ASN* 4.2 3.5 - - - +
391D ASP 3.9 2.4 + - - -
392D SER* 1.3 70.6 - - - +
394D VAL* 1.3 65.1 + - - +
395D LEU 3.4 2.2 - - - -
396D GLU* 3.2 25.1 + - - -
397D ASN* 2.9 30.6 + - - -
435D LEU* 4.5 9.8 + - - +
438D ASP* 2.6 29.1 + - - +
441D LYS* 3.9 13.9 + - - -
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Residues in contact with VAL 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D ASN* 3.4 16.8 + - + +
378D LEU* 4.3 12.1 - - + -
379D ILE* 4.3 9.0 - - + -
385D LEU* 3.4 40.2 - - + +
386D ALA* 3.5 19.1 - - + +
389D TYR* 3.6 12.5 - - + -
391D ASP* 3.6 35.7 - - - +
392D SER 3.8 3.4 - - - +
393D SER* 1.3 77.3 - - - +
395D LEU* 1.3 64.2 + - - +
398D HIS* 3.3 18.2 + - - +
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Residues in contact with LEU 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D ASP 4.9 1.8 - - - +
370D HIS* 3.7 17.9 - - + +
371D PRO* 3.4 27.4 - - + -
373D VAL 3.1 27.8 - - - +
374D SER* 4.5 0.9 - - - -
375D ASN* 2.7 31.5 + - - +
378D LEU* 3.6 19.3 - - + -
385D LEU* 4.7 9.9 - - + -
394D VAL* 1.3 73.1 - - - +
396D GLU* 1.3 65.0 + - - +
398D HIS* 3.0 9.8 + - + +
399D HIS* 2.8 52.9 + - + +
901D 15X 4.7 2.0 - - - +
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D ASN* 3.0 28.5 + - - -
393D SER* 3.2 22.3 + - - +
395D LEU* 1.3 80.0 - - - +
397D ASN* 1.3 64.7 + - - +
399D HIS* 3.3 15.5 + - + +
400D LEU* 3.2 25.5 + - - +
434D VAL* 3.9 13.1 - - + +
435D LEU* 4.5 9.9 - - + -
437D THR* 3.8 12.1 - - - +
438D ASP* 3.6 38.6 - - - +
439D MET* 4.6 3.6 + - - +
621D MG 3.9 13.5 - - - -
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Residues in contact with ASN 397 (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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389C TYR 4.8 3.5 - - - +
390C ASN* 2.9 36.8 + - - +
392C SER* 5.6 2.4 + - - -
389D TYR* 3.5 37.2 + - + +
392D SER* 2.9 28.1 + - - -
393D SER* 2.9 21.3 + - - +
396D GLU* 1.3 77.6 - - - +
398D HIS* 1.3 57.2 + - - +
400D LEU* 3.5 0.4 + - - -
401D ALA* 3.0 19.9 + - - +
435D LEU* 3.8 16.9 - - - +
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Residues in contact with HIS 398 (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 VAL 4.6 1.6 - - - -
369D ASP* 2.8 43.3 + - + -
385D LEU* 3.4 45.0 - - + +
389D TYR* 3.9 10.8 + - + -
394D VAL 3.3 10.8 + - - +
395D LEU* 3.0 16.3 + - + +
397D ASN* 1.3 77.5 - - - +
399D HIS* 1.3 67.0 + - - +
401D ALA* 3.1 3.9 + - + +
402D VAL* 3.0 44.4 + - + +
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Residues in contact with HIS 399 (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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365D ILE* 3.6 14.4 - - - +
366D HIS 2.9 28.3 - - - +
367D ASP* 3.2 31.7 + - - -
368D VAL* 2.8 36.5 + - - +
369D ASP 4.5 0.7 - - - -
370D HIS* 3.6 26.6 - + + -
395D LEU* 2.8 47.2 + - + +
396D GLU* 3.3 13.2 + - + +
398D HIS* 1.3 73.9 - + - +
400D LEU* 1.3 57.6 + - - +
403D GLY* 3.0 24.9 + - - -
434D VAL* 4.5 4.0 - - + -
621D MG 4.3 5.6 - - - -
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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
----------------------------------------------------------
390C ASN* 3.2 28.3 - - - +
365D ILE* 4.2 4.9 - - + -
396D GLU 3.2 10.6 + - - +
397D ASN 3.7 4.3 - - - +
398D HIS 3.2 0.2 - - - -
399D HIS* 1.3 77.1 - - - +
401D ALA* 1.3 64.3 + - - +
403D GLY 3.3 0.5 + - - -
404D PHE* 3.1 39.9 + - + -
430D VAL* 3.7 23.6 - - + +
431D ILE* 3.9 23.6 - - + +
434D VAL* 3.4 43.3 - - + -
435D LEU* 4.0 15.7 - - + -
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Residues in contact with ALA 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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387C LEU* 3.8 21.2 - - - +
388C MET* 4.5 15.2 - - - +
390C ASN* 3.7 6.7 + - - +
389D TYR* 3.5 24.5 - - - +
397D ASN 3.0 10.9 + - - +
398D HIS* 3.1 9.8 + - - +
400D LEU* 1.3 75.7 - - - +
402D VAL* 1.3 59.3 + - + +
404D PHE 3.7 0.2 + - - -
405D LYS* 3.0 30.7 + - - +
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Residues in contact with VAL 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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318D HIS* 4.7 8.1 - - + -
368D VAL* 3.9 22.4 - - + -
369D ASP* 4.3 12.8 - - + +
398D HIS* 3.0 46.9 + - + +
401D ALA* 1.3 74.3 - - + +
403D GLY* 1.3 67.6 + - - +
405D LYS* 4.2 5.2 - - - -
406D LEU* 2.9 49.6 + - + +
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Residues in contact with GLY 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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311D TYR* 2.9 27.5 + - - -
315D LEU* 4.7 3.6 - - - -
361D PHE* 4.6 4.3 - - - -
365D ILE* 4.1 24.2 - - - -
368D VAL* 3.9 4.0 - - - +
399D HIS 3.0 19.3 + - - -
400D LEU 3.3 2.2 + - - -
402D VAL* 1.3 78.8 - - - +
404D PHE* 1.3 59.8 + - - +
406D LEU* 3.8 5.0 + - - +
407D LEU* 4.0 1.4 + - - +
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Residues in contact with PHE 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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387C LEU* 4.2 15.4 - - + +
390C ASN* 4.8 1.6 - - - -
361D PHE* 4.2 14.1 - + - -
365D ILE* 4.8 2.2 - - + -
400D LEU* 3.1 50.9 + - + +
401D ALA* 5.4 0.2 - - - -
403D GLY* 1.3 72.7 - - - +
405D LYS* 1.3 66.9 + - - +
406D LEU 3.2 0.2 - - - -
407D LEU* 3.1 40.7 + - + +
408D GLN* 4.2 4.5 + - - +
415D PHE* 5.6 0.2 - + - -
426D LEU* 5.1 9.0 - - + -
427D ARG* 3.2 53.4 - - + +
430D VAL* 3.8 26.5 - - + -
431D ILE* 4.5 6.7 - - + -
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Residues in contact with LYS 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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405A LYS* 3.7 18.8 - - - +
408A GLN* 3.7 11.0 + - - +
384B GLU* 3.6 46.6 - - + +
387B LEU* 5.6 4.7 - - - +
384C GLU* 5.1 6.7 - - - +
387C LEU* 4.2 15.7 - - + +
388C MET* 6.0 8.8 - - + +
401D ALA 3.0 22.2 + - - +
402D VAL* 3.8 7.0 - - - +
404D PHE* 1.3 76.4 - - - +
406D LEU* 1.3 59.1 + - + +
408D GLN* 2.8 60.0 + - - +
409D GLU* 4.3 2.4 + - - +
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Residues in contact with LEU 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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311D TYR* 4.0 10.8 - - + -
314D THR* 3.9 11.0 - - + +
315D LEU* 4.0 35.7 - - + -
318D HIS* 3.6 41.5 - - + +
402D VAL* 2.9 38.8 + - + +
403D GLY 3.9 5.2 - - - +
405D LYS* 1.3 72.8 - - + +
407D LEU* 1.3 60.8 + - - +
408D GLN 3.0 7.2 + - - -
409D GLU* 3.2 32.4 + - + +
412D CYS* 3.3 13.3 - - - +
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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
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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