Contacts of the helix formed by residues 419 - 436 (chain A) in PDB entry 1IAX
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A ARG* 3.6 3.1 - - - +
418A MET* 1.3 78.4 - - - +
420A ASP* 1.3 66.2 + - - +
421A GLY* 3.0 7.9 - - - +
422A THR* 3.2 15.2 + - - +
423A VAL* 3.1 25.3 + - - +
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Residues in contact with ASP 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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341A LYS* 3.2 27.7 + - - -
342A ARG* 2.6 28.5 + - - +
345A HIS* 5.0 9.4 + - + -
419A ASP* 1.3 73.9 - - - +
421A GLY* 1.3 62.1 + - - +
423A VAL* 3.5 4.0 + - - +
424A ASP* 2.9 33.4 + - - +
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Residues in contact with GLY 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 ASP* 3.0 6.0 - - - +
420A ASP* 1.3 80.7 - - - +
422A THR* 1.3 60.8 + - - +
424A ASP* 3.4 7.7 + - - +
425A ILE* 3.1 30.8 + - - +
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Residues in contact with THR 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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39A PHE* 3.4 34.7 - - + -
49A ILE* 3.9 28.3 - - + -
418A MET* 3.6 17.4 - - + +
419A ASP* 3.2 25.8 + - - +
421A GLY* 1.3 76.9 - - - +
423A VAL* 1.3 56.3 + - - +
425A ILE* 3.1 11.6 + - - +
426A ALA* 2.8 27.4 + - - +
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET* 5.5 1.8 - - + -
342A ARG* 3.7 30.5 - - - +
345A HIS* 4.9 8.7 - - - +
346A PHE* 3.6 35.0 - - + -
415A PHE* 4.7 2.0 - - + +
418A MET* 3.4 24.2 - - + -
419A ASP 3.1 16.2 + - - +
420A ASP* 3.9 6.5 - - - +
421A GLY 3.3 0.4 - - - -
422A THR* 1.3 75.8 - - - +
424A ASP* 1.3 58.3 + - - +
426A ALA* 3.3 7.6 + - - +
427A LEU* 2.8 35.0 + - + +
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Residues in contact with ASP 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A HIS* 2.8 37.4 + - - -
420A ASP* 2.9 20.3 + - - +
421A GLY* 3.8 7.5 - - - +
422A THR 3.2 0.6 - - - -
423A VAL* 1.3 74.2 - - - +
425A ILE* 1.3 57.4 + - - +
427A LEU* 3.2 11.7 + - - +
428A ALA* 2.7 35.6 + - - +
431A ARG* 4.1 6.2 + - - +
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.7 28.5 - - + -
41A PRO* 6.2 0.4 - - + -
45A PRO 4.9 2.7 - - - +
49A ILE* 4.0 6.1 - - + -
421A GLY 3.1 19.3 + - - +
422A THR* 3.1 10.2 + - - +
424A ASP* 1.3 76.5 - - - +
426A ALA* 1.3 63.9 + - - +
428A ALA* 3.1 10.0 + - + +
429A ARG* 3.0 57.2 + - + +
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Residues in contact with ALA 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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49A ILE* 3.8 20.9 - - + -
51A MET* 3.8 33.2 - - + -
346A PHE* 5.3 0.4 - - + -
395A LEU* 3.8 7.3 - - + +
418A MET* 5.7 0.2 - - + -
422A THR 2.8 12.6 + - - +
423A VAL* 3.5 9.4 - - - +
425A ILE* 1.3 77.9 - - - +
427A LEU* 1.3 61.0 + - - +
429A ARG* 3.4 5.1 + - - +
430A ILE* 3.1 29.9 + - + +
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Residues in contact with LEU 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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345A HIS* 4.4 18.8 - - - +
346A PHE* 3.4 42.8 - - + +
349A GLY* 4.1 10.5 - - - -
350A LEU* 4.0 22.7 - - + +
423A VAL* 2.8 36.8 + - + +
424A ASP* 3.5 23.6 - - - +
426A ALA* 1.3 70.6 - - - +
428A ALA* 1.3 55.7 + - - +
430A ILE* 3.0 7.2 + - - +
431A ARG* 2.7 47.8 + - - +
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Residues in contact with ALA 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 ASP 2.7 17.5 + - - +
425A ILE* 3.1 14.4 - - - +
427A LEU* 1.3 73.1 - - - +
429A ARG* 1.3 63.8 + - + +
431A ARG* 3.0 27.1 + - - +
432A ARG* 3.0 29.4 + - + +
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Residues in contact with ARG 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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39A PHE* 4.0 3.8 - - - -
45A PRO 3.1 26.1 + - - -
46A ASN* 3.4 25.2 + - - +
47A GLY 3.2 22.6 + - - -
49A ILE* 3.8 11.8 - - - +
393A VAL* 3.3 30.3 - - + +
394A LYS* 3.3 28.1 + - - +
395A LEU* 4.1 9.9 - - + -
425A ILE* 3.0 31.2 + - + +
426A ALA 3.6 5.8 - - - +
428A ALA* 1.3 75.7 - - + +
430A ILE* 1.3 56.9 + - - +
432A ARG* 3.3 12.8 - - - +
433A PHE* 3.1 27.5 + - - +
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Residues in contact with ILE 430 (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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51A MET* 5.5 1.3 - - - -
346A PHE* 4.5 13.7 - - + -
350A LEU* 3.8 24.7 - - + -
353A VAL* 4.9 2.9 - - + -
355A ILE* 3.7 29.8 - - + -
368A MET* 5.2 11.7 - - + -
393A VAL* 5.0 2.5 - - + -
395A LEU* 3.5 25.4 - - + -
413A VAL* 5.8 1.6 - - + -
426A ALA* 3.1 19.3 + - + +
427A LEU* 3.0 11.3 + - - +
429A ARG* 1.3 73.6 - - - +
431A ARG* 1.3 65.1 + - - +
432A ARG 3.0 1.8 - - - -
433A PHE* 4.5 7.4 - - + -
434A VAL* 3.0 32.7 + - + +
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Residues in contact with ARG 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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349A GLY* 5.5 3.2 + - - -
352A VAL* 5.1 10.2 - - - +
353A VAL* 3.2 36.1 - - + +
424A ASP* 4.1 7.3 + - - +
427A LEU* 2.7 25.1 + - - +
428A ALA* 3.0 40.9 + - - +
430A ILE* 1.3 74.7 - - - +
432A ARG* 1.3 60.8 + - + +
434A VAL* 4.3 1.4 - - - +
435A GLY* 3.2 16.6 + - - -
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Residues in contact with ARG 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 ALA* 3.0 17.2 + - + +
429A ARG* 3.3 15.0 - - - +
430A ILE 3.0 1.0 - - - -
431A ARG* 1.3 74.7 - - - +
433A PHE* 1.3 58.3 + - - +
434A VAL 3.0 1.1 - - - -
435A GLY* 2.5 26.3 + - - -
436A VAL* 2.9 20.8 + - + +
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Residues in contact with PHE 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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370A LEU* 5.7 0.4 - - + -
373A LEU* 3.8 19.7 - - + -
385A LEU* 3.5 31.4 - - + -
388A VAL* 3.3 26.9 - - + -
389A ILE* 4.2 11.9 - - + -
393A VAL* 3.7 27.4 - - + -
429A ARG 3.1 12.7 + - - +
430A ILE* 3.9 7.9 - - + +
432A ARG* 1.3 78.5 - - - +
434A VAL* 1.3 64.1 + - + +
436A VAL* 3.4 10.4 - - - +
437A GLU* 2.8 53.3 - - + +
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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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353A VAL* 3.8 29.6 - - + +
355A ILE* 3.3 35.0 - - + -
373A LEU* 4.8 20.0 - - + -
430A ILE* 3.0 21.1 + - + +
431A ARG 4.3 3.6 - - - +
433A PHE* 1.3 75.9 - - + +
435A GLY* 1.3 68.5 + - - +
437A GLU* 3.4 18.6 + - - +
438A LYS* 4.1 4.9 + - - +
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Residues in contact with GLY 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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431A ARG 3.2 11.5 + - - -
432A ARG* 2.5 15.2 + - - -
434A VAL* 1.3 76.7 - - - +
436A VAL* 1.3 57.7 + - - -
437A GLU 3.0 6.6 + - - -
438A LYS 3.2 18.9 - - - +
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Residues in contact with VAL 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 ARG* 2.9 19.9 + - + +
433A PHE* 3.4 8.4 - - - +
435A GLY* 1.3 68.7 - - - +
437A GLU* 1.3 68.2 - - - +
438A LYS 4.4 0.2 - - - +
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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