Contacts of the helix formed by residues 419 - 436 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A ASN 3.8 1.8 + - - +
418A LEU* 1.3 76.4 - - - +
420A LYS* 1.3 59.7 + - - +
421A LYS* 3.3 12.6 + - - +
422A GLN* 2.7 38.9 + - - +
423A ARG* 3.0 27.9 + - - +
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Residues in contact with LYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A THR* 1.3 73.3 - - - +
421A LYS* 1.3 62.0 + - - +
423A ARG* 3.7 22.2 - - + +
424A GLN* 2.9 57.5 + - + +
379B ILE 4.5 0.4 + - - -
380B ASN* 3.5 20.1 + - - -
382B ASN* 2.7 31.3 + - - +
410D GLU* 3.0 32.4 + - + +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A THR* 3.2 11.3 + - - +
420A LYS* 1.3 78.1 - - - +
422A GLN* 1.3 60.9 + - + +
424A GLN* 3.7 7.0 + - - +
425A SER* 3.3 22.2 + - - -
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Residues in contact with GLN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A THR 5.5 1.6 + - - -
301A PHE* 4.1 22.6 - - - -
354A LEU* 3.8 22.3 - - + +
418A LEU* 3.1 26.5 - - + -
419A THR* 2.7 47.6 + - - +
421A LYS* 1.3 73.5 - - + +
423A ARG* 1.3 60.5 - - - +
425A SER* 3.3 1.9 + - - -
426A LEU* 2.8 32.0 + - - +
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Residues in contact with ARG 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ASP* 6.1 0.4 - - - -
415A PHE* 3.6 26.5 + - + +
416A GLN* 5.5 1.6 + - - +
418A LEU* 3.3 34.4 + - + -
419A THR* 3.0 11.8 + - - +
420A LYS* 3.7 32.4 - - + +
422A GLN* 1.3 76.2 - - - +
424A GLN* 1.3 59.0 + - - +
426A LEU* 3.5 6.8 + - + +
427A ARG* 2.9 31.8 + - - +
382B ASN* 4.1 5.9 - - - +
410D GLU* 2.7 43.2 + - - -
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Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 2.9 55.1 + - + +
421A LYS* 4.1 5.6 - - - +
423A ARG* 1.3 75.1 - - - +
425A SER* 1.3 62.3 + - - +
427A ARG* 3.8 6.8 - - - +
428A LYS* 3.1 25.1 + - - +
376B GLN* 4.6 2.6 - - - +
379B ILE* 4.7 7.1 + - - +
380B ASN* 2.7 38.0 + - - +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 3.7 12.7 - - - +
421A LYS 3.3 16.9 + - - -
422A GLN 3.6 3.6 - - - -
423A ARG 3.3 0.2 - - - -
424A GLN* 1.3 77.7 - - - +
426A LEU* 1.3 64.5 + - - +
428A LYS* 3.6 3.6 + - - +
429A MET* 3.2 41.9 + - - +
469A TYR* 6.0 0.9 - - - -
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 4.0 13.4 - - + +
357A LEU* 4.1 14.8 - - + +
358A ALA* 3.5 38.8 - - + +
361A PHE* 5.4 0.7 - - + -
404A PHE* 5.9 2.7 - - + -
415A PHE* 3.5 48.7 - - + -
418A LEU* 4.2 8.1 - - + -
422A GLN 2.8 21.5 + - - +
423A ARG* 3.7 6.3 - - + +
425A SER* 1.3 72.5 - - - +
427A ARG* 1.3 60.2 + - - +
429A MET* 3.2 9.8 + - - +
430A VAL* 2.8 41.1 + - + +
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Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A PHE* 3.2 62.6 - - + +
423A ARG 2.9 20.2 + - - +
424A GLN* 3.8 7.2 - - - +
425A SER 3.3 0.2 - - - -
426A LEU* 1.3 76.2 - - - +
428A LYS* 1.3 58.1 + - - +
430A VAL* 3.2 3.1 + - - +
431A ILE* 2.9 41.1 + - + +
379B ILE* 5.5 1.9 + - - +
382B ASN* 5.8 4.4 + - - -
386B ALA 3.1 27.1 + - - -
387B LEU* 3.6 27.6 + - - +
390B ASN* 3.9 10.3 + - - +
391B ASP* 2.9 34.4 + - - +
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Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A GLN 3.1 15.1 + - - +
425A SER* 4.0 4.5 - - - +
427A ARG* 1.3 78.2 - - - +
429A MET* 1.3 58.1 + - - +
431A ILE* 3.3 8.9 + - + +
432A ASP* 2.9 54.7 + - - +
469A TYR* 3.8 22.4 - - + +
391B ASP* 5.8 0.9 - - - -
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Residues in contact with MET 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 4.1 19.7 - - + +
355A GLU* 3.6 46.0 - - + +
358A ALA* 3.8 10.5 - - + -
425A SER* 3.2 37.0 + - - +
426A LEU* 3.6 5.6 - - - +
428A LYS* 1.3 77.7 - - - +
430A VAL* 1.3 57.3 + - - +
432A ASP* 3.4 1.6 + - - +
433A ILE* 3.0 36.4 + - + +
469A TYR* 3.7 32.1 - - + +
473A ILE* 3.9 16.1 - - + +
476A LEU* 4.9 3.1 - - - -
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ALA* 3.9 15.5 - - - +
361A PHE* 3.9 14.6 - - + -
362A ALA* 3.9 17.3 - - + -
365A ILE* 3.9 28.7 - - + -
400A LEU* 4.0 2.7 - - + -
404A PHE* 3.9 16.6 - - + -
426A LEU* 2.8 44.4 + - + +
427A ARG 3.7 4.0 - - - +
429A MET* 1.3 75.2 - - - +
431A ILE* 1.3 57.9 + - - +
433A ILE* 3.5 1.3 + - - +
434A VAL* 3.0 29.1 + - - +
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Residues in contact with ILE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 3.9 24.4 - - + +
404A PHE* 4.3 6.3 - - + -
427A ARG* 2.9 40.2 + - + +
428A LYS* 3.6 7.0 - - - +
430A VAL* 1.3 75.0 - - - +
432A ASP* 1.3 72.3 + - - +
435A LEU* 3.0 46.5 + - + +
390B ASN* 3.3 41.1 - - + +
391B ASP* 4.0 9.4 - - + +
392B SER* 4.5 2.5 - - - +
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Residues in contact with ASP 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A LYS* 2.9 39.9 + - - +
429A MET 3.8 4.3 - - - +
431A ILE* 1.3 82.2 - - - +
433A ILE* 1.3 61.6 + - - +
435A LEU* 4.3 6.1 - - - +
436A ALA* 3.4 13.3 + - - +
469A TYR* 2.9 28.1 + - - -
473A ILE* 4.0 17.9 - - + +
477A GLN* 3.0 24.0 - - - +
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ALA* 4.1 9.4 - - + +
359A ALA* 3.8 31.0 - - + +
362A ALA* 3.8 13.5 - - + -
429A MET 3.0 22.6 + - - +
430A VAL 3.8 3.1 - - - +
432A ASP* 1.3 75.4 - - - +
434A VAL* 1.3 66.7 + - + +
436A ALA* 3.2 13.2 + - - +
437A THR* 3.5 11.4 + - - +
473A ILE* 4.4 11.2 - - + -
476A LEU* 4.1 28.5 - - + +
477A GLN* 4.1 12.4 - - + +
480A VAL* 3.7 33.4 - - + -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ALA* 3.8 33.0 - - + +
365A ILE* 4.3 7.0 - - + -
366A HIS* 4.1 24.7 - - + +
396A GLU* 3.8 17.9 - - + +
399A HIS* 4.5 2.9 - - + -
400A LEU* 3.5 36.3 - - + +
430A VAL 3.0 17.3 + - - +
433A ILE* 1.3 75.5 - - + +
435A LEU* 1.3 62.1 + - - +
437A THR* 2.5 32.8 + - - +
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A SER* 4.3 15.8 + - - +
396A GLU* 4.5 3.8 - - + -
397A ASN* 3.8 37.5 - - - +
400A LEU* 4.0 13.2 - - + -
431A ILE* 3.0 37.9 + - + +
432A ASP* 4.3 6.5 - - - +
434A VAL* 1.3 76.2 - - - +
436A ALA* 1.3 57.2 + - - +
437A THR 3.1 3.7 + - - -
438A ASP* 3.2 23.2 + - - +
441A LYS* 4.3 8.9 - - - +
390B ASN* 5.7 0.4 - - + -
392B SER* 4.5 12.8 - - - +
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ASP 3.4 16.8 + - - +
433A ILE 3.2 8.1 + - - +
434A VAL 3.2 1.0 - - - -
435A LEU* 1.3 77.2 - - - +
437A THR* 1.3 59.7 + - - +
438A ASP 3.3 6.9 + - - +
441A LYS* 4.6 9.5 - - + +
445A LEU* 3.3 35.8 - - + +
477A GLN* 3.7 26.9 - - + +
481A HIS* 4.3 5.2 + - - +
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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