Contacts of the helix formed by residues 419 - 436 (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 THR 419 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417D ASN 3.9 1.3 + - - +
418D LEU* 1.3 75.8 - - - +
420D LYS* 1.3 64.4 + - - +
421D LYS* 3.5 7.7 + - - +
422D GLN* 3.0 41.1 + - - +
423D ARG* 2.9 22.6 + - - +
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Residues in contact with LYS 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU* 3.0 37.5 + - + +
379C ILE 4.7 0.2 + - - -
380C ASN* 2.8 34.1 + - - +
382C ASN* 3.4 14.6 + - - +
419D THR* 1.3 73.0 - - - +
421D LYS* 1.3 63.9 + - - +
423D ARG* 3.1 22.3 + - + +
424D GLN* 3.0 50.4 + - + +
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Residues in contact with LYS 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D THR* 3.3 7.8 + - - +
420D LYS* 1.3 79.4 - - - +
422D GLN* 1.3 61.0 + - - +
424D GLN* 3.7 9.4 + - - +
425D SER* 3.3 20.8 + - - -
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Residues in contact with GLN 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PHE* 3.8 25.1 - - - -
354D LEU* 3.8 22.3 - - + +
417D ASN 4.9 0.3 - - - +
418D LEU* 3.6 21.0 - - + +
419D THR* 3.0 47.0 + - - +
421D LYS* 1.3 74.8 - - - +
423D ARG* 1.3 60.3 + - - +
425D SER* 3.2 3.5 + - - -
426D LEU* 2.9 29.7 + - - +
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Residues in contact with ARG 423 (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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410A GLU* 3.0 40.4 + - - -
382C ASN* 4.0 8.5 - - - +
415D PHE* 3.6 28.0 + - + +
416D GLN* 5.1 2.4 + - - +
418D LEU* 3.4 33.2 + - + -
419D THR 2.9 14.0 + - - +
420D LYS* 3.1 31.3 + - + +
422D GLN* 1.3 75.7 - - - +
424D GLN* 1.3 57.9 + - + +
426D LEU* 3.5 9.8 + - + +
427D ARG* 3.0 29.8 + - - +
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Residues in contact with GLN 424 (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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376C GLN* 4.4 4.0 - - - +
379C ILE* 4.8 7.5 + - + +
380C ASN* 2.6 41.9 + - - +
420D LYS* 3.0 41.8 + - - +
421D LYS* 4.0 9.3 - - - +
423D ARG* 1.3 75.6 - - + +
425D SER* 1.3 64.6 + - - +
427D ARG* 3.4 6.6 + - - +
428D LYS* 3.0 25.8 + - - +
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU* 3.8 13.7 - - - +
421D LYS 3.3 12.0 + - - -
422D GLN 3.2 8.5 + - - -
424D GLN* 1.3 78.2 - - - +
426D LEU* 1.3 63.3 + - - +
428D LYS* 3.6 4.1 + - - +
429D MET* 3.1 40.8 + - - +
469D TYR* 5.7 2.3 - - - -
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Residues in contact with LEU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU* 4.3 12.3 - - + +
357D LEU* 3.6 36.8 - - + -
358D ALA* 4.0 19.5 - - + +
361D PHE* 5.4 0.2 - - + -
404D PHE* 5.1 5.2 - - + -
415D PHE* 3.5 44.9 - - + -
418D LEU* 4.7 4.0 - - + -
422D GLN 2.9 16.4 + - - +
423D ARG* 3.7 7.9 - - + +
425D SER* 1.3 73.4 - - - +
427D ARG* 1.3 68.3 + - - +
429D MET* 3.2 12.9 + - - +
430D VAL* 2.9 35.0 + - + +
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Residues in contact with ARG 427 (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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379C ILE* 5.5 1.3 - - - +
382C ASN* 5.3 9.2 + - - -
386C ALA* 3.1 17.8 + - - +
387C LEU* 3.7 23.3 + - - +
390C ASN* 3.8 12.5 + - - +
391C ASP* 3.1 39.3 + - - +
404D PHE* 3.2 63.3 - - + +
423D ARG 3.0 18.9 + - - +
424D GLN* 3.7 7.2 - - - +
426D LEU* 1.3 78.3 - - + +
428D LYS* 1.3 57.7 + - - +
430D VAL* 3.1 1.7 + - - +
431D ILE* 2.9 44.0 + - + +
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Residues in contact with LYS 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ASP* 5.9 0.9 - - - -
424D GLN 3.0 16.7 + - - +
425D SER* 4.0 4.7 - - - +
427D ARG* 1.3 76.8 - - - +
429D MET* 1.3 57.7 + - - +
431D ILE* 3.4 9.6 + - + +
432D ASP* 3.0 53.6 + - - +
469D TYR* 4.1 18.3 - - + +
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Residues in contact with MET 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU* 4.0 27.8 - - + +
355D GLU* 3.6 33.2 - - + +
358D ALA* 4.0 11.2 - - + -
425D SER* 3.1 40.5 + - - +
426D LEU* 3.6 9.0 - - - +
428D LYS* 1.3 76.7 - - - +
430D VAL* 1.3 58.2 + - - +
432D ASP* 3.4 1.9 + - - +
433D ILE* 2.9 37.9 + - + +
469D TYR* 3.6 33.2 - - + +
473D ILE* 3.9 10.7 - - + +
476D LEU* 4.9 7.6 - - - -
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Residues in contact with VAL 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D ALA* 3.9 28.9 - - + +
361D PHE* 4.0 17.9 - - + -
362D ALA* 4.3 5.6 - - - -
365D ILE* 4.0 15.3 - - + -
400D LEU* 3.7 18.4 - - + -
404D PHE* 3.8 16.4 - - + -
426D LEU* 2.9 27.9 + - + +
427D ARG 3.6 3.6 - - - +
429D MET* 1.3 71.0 - - - +
431D ILE* 1.3 67.1 + - - +
433D ILE* 3.2 5.5 + - - +
434D VAL* 2.9 28.4 + - + +
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Residues in contact with ILE 431 (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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390C ASN* 3.4 40.4 - - + +
391C ASP* 4.0 17.3 - - + +
392C SER* 5.1 2.2 - - - +
400D LEU* 3.9 23.1 - - + +
404D PHE* 4.5 5.4 - - + -
427D ARG* 2.9 34.9 + - + +
428D LYS* 3.7 6.7 - - + +
430D VAL* 1.3 75.7 - - - +
432D ASP* 1.3 67.8 + - - +
435D LEU* 3.0 48.5 + - + +
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Residues in contact with ASP 432 (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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428D LYS* 3.0 36.8 + - - +
429D MET 3.7 4.3 - - - +
431D ILE* 1.3 80.8 - - - +
433D ILE* 1.3 62.5 + - - +
435D LEU* 3.9 7.0 + - - +
436D ALA 3.4 12.5 + - - -
469D TYR* 2.9 27.7 + - - -
473D ILE* 3.8 17.4 - - + +
477D GLN* 3.0 25.6 + - - +
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Residues in contact with ILE 433 (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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358D ALA* 4.3 3.1 - - + +
359D ALA* 3.8 31.4 - - + +
362D ALA* 3.5 21.1 - - + -
429D MET* 2.9 24.4 + - + +
430D VAL 3.7 3.1 - - - +
432D ASP* 1.3 75.0 - - - +
434D VAL* 1.3 64.8 + - - +
436D ALA* 3.2 16.8 + - - +
437D THR* 3.5 8.7 + - + +
473D ILE* 3.9 12.6 - - + -
476D LEU* 3.9 31.4 - - + +
477D GLN* 4.2 11.8 - - - +
480D VAL* 3.6 28.3 - - + -
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Residues in contact with VAL 434 (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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362D ALA* 4.0 30.3 - - + +
365D ILE* 4.4 5.6 - - + -
366D HIS* 4.3 20.4 - - + +
396D GLU* 3.9 17.2 - - + +
399D HIS* 4.5 3.6 - - + -
400D LEU* 3.4 36.3 - - + +
430D VAL* 2.9 20.7 + - + +
433D ILE* 1.3 74.0 - - - +
435D LEU* 1.3 60.5 + - - +
437D THR* 2.4 41.1 + - - +
438D ASP 4.0 0.7 + - - -
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Residues in contact with LEU 435 (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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390C ASN* 5.7 1.3 - - + -
392C SER* 4.9 9.4 - - - +
393D SER* 4.5 10.7 + - - +
396D GLU* 4.5 3.8 - - - -
397D ASN* 3.8 39.0 - - - +
400D LEU* 4.0 14.1 - - + -
431D ILE* 3.0 39.0 + - + +
432D ASP* 4.4 7.6 - - - +
434D VAL* 1.3 76.3 - - - +
436D ALA* 1.3 59.5 + - - +
437D THR 3.2 0.4 - - - -
438D ASP* 3.3 22.6 - - - +
441D LYS* 3.7 15.0 - - - +
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Residues in contact with ALA 436 (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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432D ASP 3.4 13.3 + - - +
433D ILE 3.2 12.1 + - - +
434D VAL 3.1 0.8 - - - -
435D LEU* 1.3 75.4 - - - +
437D THR* 1.3 60.8 + - - +
438D ASP 3.2 8.9 + - - +
441D LYS* 4.6 9.6 - - - +
445D LEU* 3.3 29.4 - - + +
477D GLN* 3.7 34.1 - - + +
481D HIS* 4.5 5.8 + - - -
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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