Contacts of the helix formed by residues 419 - 436 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B ASN 5.3 1.8 - - - +
418B LEU* 1.3 76.3 - - - +
420B LYS* 1.3 65.0 + - - +
421B LYS* 3.7 18.4 + - - +
422B GLN* 2.8 43.2 + - - +
423B ARG* 3.1 22.9 + - - +
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B LEU 4.1 0.2 + - - -
419B THR* 1.3 74.3 - - - +
421B LYS* 1.3 77.6 + - - +
423B ARG* 3.2 9.4 + - - +
424B GLN* 3.1 46.4 + - + +
410C GLU* 2.7 39.7 + - - +
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B THR* 3.3 21.9 + - - +
420B LYS* 1.3 95.1 - - + +
422B GLN* 1.3 57.7 + - + +
424B GLN* 3.6 20.2 + - - +
425B SER* 3.1 29.1 + - - -
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Residues in contact with GLN 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.8 22.9 - - - -
354B LEU* 3.8 23.2 - - + +
417B ASN 4.8 0.3 - - - +
418B LEU* 3.5 24.0 - - + -
419B THR* 2.8 48.5 + - - +
421B LYS* 1.3 76.0 - - + +
423B ARG* 1.3 60.0 + - - +
425B SER* 3.3 2.1 + - - -
426B LEU* 2.8 32.7 + - - +
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B LEU* 4.7 12.1 - - - +
413B ASP* 3.2 36.8 + - - -
415B PHE* 3.7 27.6 + - + +
416B GLN* 4.4 5.3 + - - +
418B LEU* 3.9 22.9 - - + -
419B THR 3.1 19.2 + - - +
420B LYS* 3.2 8.9 + - - +
422B GLN* 1.3 71.9 - - - +
424B GLN* 1.3 61.2 + - - +
426B LEU* 3.3 6.1 + - - +
427B ARG* 2.9 33.6 + - - +
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ASN* 5.2 11.9 + - - +
420B LYS* 3.1 36.8 + - + +
421B LYS* 3.6 28.4 - - - +
423B ARG* 1.3 75.9 - - - +
425B SER* 1.3 62.0 + - - +
427B ARG* 3.4 6.6 + - - +
428B LYS* 3.1 24.1 + - - +
410C GLU* 5.8 0.8 + - - -
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 3.4 20.4 - - - +
421B LYS 3.1 15.5 + - - -
422B GLN 3.5 4.3 - - - -
424B GLN* 1.3 81.1 - - - +
426B LEU* 1.3 61.5 + - - +
428B LYS* 3.4 4.5 + - - +
429B MET* 3.1 37.5 + - - +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 3.7 17.0 - - + +
357B LEU* 4.0 5.4 - - + +
358B ALA* 3.2 44.0 - - + +
361B PHE* 5.7 0.2 - - + -
415B PHE* 3.4 50.3 - - + -
418B LEU* 4.2 10.3 - - + -
422B GLN 2.8 21.5 + - - +
423B ARG* 3.8 4.9 - - - +
425B SER* 1.3 72.9 - - - +
427B ARG* 1.3 57.8 + - - +
429B MET* 3.3 6.3 + - - +
430B VAL* 2.9 41.7 + - + +
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ILE* 5.3 2.6 + - - +
382A ASN* 4.9 7.0 + - - -
386A ALA* 4.2 3.2 + - - +
387A LEU* 3.2 45.0 + - - +
390A ASN* 4.9 1.4 + - - +
391A ASP* 2.6 46.2 + - - -
404B PHE* 4.0 36.1 - - + -
423B ARG 2.9 19.0 + - - +
424B GLN* 3.7 6.9 - - - +
426B LEU* 1.3 78.0 - - - +
428B LYS* 1.3 62.0 + - - +
430B VAL* 4.0 1.0 - - - +
431B ILE* 3.0 45.0 + - - +
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASP* 5.7 5.8 - - - +
424B GLN 3.1 13.2 + - - +
425B SER* 3.9 4.9 - - - +
426B LEU 3.4 0.2 - - - -
427B ARG* 1.3 79.4 - - - +
429B MET* 1.3 62.8 + - - +
431B ILE* 3.6 8.8 + - - +
432B ASP* 3.1 46.8 + - - -
469B TYR* 3.6 27.7 - - + +
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Residues in contact with MET 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 4.0 13.5 - - + -
355B GLU* 3.5 52.9 - - + +
358B ALA* 3.9 16.6 - - + -
425B SER* 3.1 39.4 + - - +
426B LEU* 3.7 3.8 - - - +
428B LYS* 1.3 77.4 - - - +
430B VAL* 1.3 56.6 + - - +
432B ASP* 3.3 3.3 + - - +
433B ILE* 3.0 36.7 + - + +
469B TYR* 3.6 32.8 - - + +
473B ILE* 3.7 6.9 - - + +
476B LEU* 4.7 7.6 - - - -
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA* 3.7 32.3 - - - +
361B PHE* 4.0 17.5 - - + -
362B ALA* 4.2 13.9 - - + -
365B ILE* 3.9 22.9 - - + -
400B LEU* 4.1 2.7 - - + -
404B PHE* 3.9 24.5 - - + -
426B LEU* 2.9 26.3 + - + +
427B ARG 4.0 2.0 - - - +
429B MET* 1.3 72.9 - - - +
431B ILE* 1.3 65.8 + - - +
433B ILE* 3.4 1.0 + - - +
434B VAL* 3.0 24.7 + - + +
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Residues in contact with ILE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ASN* 3.7 37.0 - - + +
391A ASP* 4.5 4.7 - - + +
400B LEU* 3.9 10.4 - - + +
404B PHE* 4.0 16.6 - - + -
427B ARG* 3.0 60.9 + - + +
428B LYS* 3.8 7.2 - - - +
430B VAL* 1.3 77.2 - - - +
432B ASP* 1.3 70.1 + - - +
433B ILE 3.2 0.2 + - - -
435B LEU* 3.0 47.3 + - + +
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Residues in contact with ASP 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B LYS* 3.1 39.2 + - - +
429B MET 3.3 1.5 + - - +
431B ILE* 1.3 86.5 - - - +
433B ILE* 1.3 62.0 + - - +
435B LEU* 4.3 5.4 - - - +
436B ALA 3.4 11.3 + - - -
469B TYR* 2.8 27.5 + - - -
473B ILE* 3.6 21.0 - - + +
477B GLN* 2.8 27.2 + - - +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ALA* 4.4 3.4 - - + +
359B ALA* 4.0 27.8 - - + +
362B ALA* 3.5 21.5 - - + -
429B MET* 3.0 24.8 + - + +
430B VAL 3.8 3.6 - - - +
431B ILE 3.2 0.2 - - - -
432B ASP* 1.3 73.8 - - - +
434B VAL* 1.3 67.6 + - + +
436B ALA* 3.1 17.8 + - - +
437B THR* 3.5 7.6 + - - +
473B ILE* 3.8 15.7 - - + -
476B LEU* 4.1 26.7 - - + +
477B GLN* 4.1 11.6 - - + +
480B VAL* 3.6 31.6 - - + -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ALA* 3.9 32.5 - - + +
365B ILE* 4.2 6.1 - - + -
366B HIS* 4.4 12.8 - - + +
396B GLU* 3.8 18.0 - - - +
399B HIS* 4.4 13.9 - - + -
400B LEU* 3.4 37.7 - - + -
430B VAL* 3.0 18.1 + - + +
433B ILE* 1.3 75.2 - - - +
435B LEU* 1.3 60.9 + - - +
437B THR* 2.5 32.9 + - - +
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Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ASN* 4.6 3.6 - - + -
392A SER* 4.3 15.9 - - - +
393B SER* 4.3 16.6 - - - -
396B GLU* 4.4 4.3 - - + -
397B ASN* 3.5 33.9 - - - +
400B LEU* 3.9 13.5 - - + -
431B ILE* 3.0 39.4 + - + +
432B ASP* 4.3 5.4 - - - +
434B VAL* 1.3 76.4 - - - +
436B ALA* 1.3 56.6 + - - +
437B THR 3.1 0.4 - - - -
438B ASP* 3.2 27.5 + - - +
441B LYS* 3.6 15.0 - - - +
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B ASP 3.4 13.2 + - - +
433B ILE 3.1 13.5 + - - +
435B LEU* 1.3 78.4 - - - +
437B THR* 1.3 58.8 + - - +
438B ASP* 3.2 8.3 + - - +
441B LYS* 4.6 10.3 - - - +
442B HIS* 6.0 0.2 - - - -
445B LEU* 3.3 32.4 - - + +
477B GLN* 3.6 33.9 - - + +
481B HIS* 4.3 5.1 + - - -
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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