Contacts of the helix formed by residues 419 - 436 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO* 5.7 5.7 - - - +
342B ARG* 3.9 2.9 - - - +
418B MET* 1.3 77.9 - - - +
420B ASP* 1.3 66.9 + - - +
421B GLY* 3.7 9.2 - - - +
422B THR* 3.5 16.2 + - - +
423B VAL* 3.0 26.2 + - - +
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Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 2.6 28.7 + - - +
345B HIS* 5.4 7.2 + - + +
419B ASP* 1.3 74.5 - - - +
421B GLY* 1.3 64.4 + - - +
423B VAL* 3.2 4.5 + - - +
424B ASP* 2.9 36.4 + - - +
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Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASP* 3.1 6.0 - - - +
420B ASP* 1.3 82.4 - - - +
422B THR* 1.3 61.2 + - - +
424B ASP* 3.3 8.3 + - - +
425B ILE* 3.1 28.8 + - - +
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.9 23.0 - - + -
41B PRO* 5.9 0.3 - - - +
49B ILE* 3.9 31.4 - - + +
418B MET* 3.4 27.5 - - + +
419B ASP* 3.3 23.4 + - - +
420B ASP 3.3 0.4 - - - -
421B GLY* 1.3 73.8 - - - +
423B VAL* 1.3 58.9 + - - +
425B ILE* 3.0 13.9 + - - +
426B ALA* 2.9 26.7 + - - +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B MET* 5.5 0.2 - - + -
342B ARG* 3.6 32.3 - - - +
345B HIS* 5.2 7.4 - - - +
346B PHE* 3.7 31.6 - - + -
415B PHE* 4.4 2.7 - - + +
418B MET* 3.2 29.4 - - + -
419B ASP 3.0 16.1 + - - +
420B ASP* 3.5 7.2 - - - +
422B THR* 1.3 75.9 - - - +
424B ASP* 1.3 60.0 + - - +
426B ALA* 3.2 8.1 + - - +
427B LEU* 2.7 33.9 + - + +
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Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B HIS* 2.7 39.4 + - - -
420B ASP* 2.9 25.5 + - - +
421B GLY* 3.6 7.5 - - - +
423B VAL* 1.3 76.5 - - - +
425B ILE* 1.3 52.4 + - + +
427B LEU* 3.3 13.7 - - - +
428B ALA* 2.8 32.6 + - - +
431B ARG* 4.6 2.6 + - - -
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.8 28.5 - - + -
45B PRO 5.5 1.8 - - - +
49B ILE* 3.9 14.6 - - + -
421B GLY 3.1 17.9 + - - +
422B THR* 3.0 11.9 + - - +
424B ASP* 1.3 73.8 - - + +
426B ALA* 1.3 56.1 + - - +
427B LEU 3.0 1.3 - - - -
428B ALA* 2.8 9.1 + - + +
429B ARG* 2.7 53.5 + - + +
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.2 10.7 - - + +
51B MET* 3.8 36.1 - - + -
346B PHE* 5.1 0.9 - - + -
395B LEU* 4.0 16.3 - - + +
418B MET* 5.1 0.2 - - + -
422B THR 2.9 11.1 + - - +
423B VAL* 3.4 9.9 - - - +
425B ILE* 1.3 76.9 - - - +
427B LEU* 1.3 58.5 + - - +
429B ARG* 3.3 4.0 + - - +
430B ILE* 2.9 36.5 + - - +
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B HIS* 4.3 14.8 - - + +
346B PHE* 3.9 28.9 - - + -
349B GLY* 3.4 47.1 - - - +
350B LEU* 3.8 12.3 - - + +
353B VAL* 5.4 1.2 - - - +
423B VAL* 2.7 19.8 + - + +
424B ASP* 3.3 24.0 - - - +
426B ALA* 1.3 75.3 - - - +
428B ALA* 1.3 64.6 + - - +
430B ILE* 3.3 6.5 + - + +
431B ARG* 3.1 30.3 + - - +
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ASP 2.8 15.7 + - - +
425B ILE* 2.8 12.3 + - + +
427B LEU* 1.3 76.6 - - - +
429B ARG* 1.3 63.1 + - + +
431B ARG* 3.0 44.4 + - - +
432B ARG* 3.3 9.8 + - - +
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Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.0 5.5 - - - -
45B PRO 3.4 9.5 + - - -
46B ASN* 3.2 36.7 + - - +
47B GLY 3.0 28.7 + - - +
49B ILE* 3.6 20.6 - - - +
393B VAL* 3.6 29.2 - - + +
394B LYS* 3.0 22.1 + - - +
395B LEU* 4.3 8.1 - - + -
425B ILE* 2.7 30.7 + - + +
426B ALA* 3.6 7.6 - - - +
428B ALA* 1.3 74.6 - - + +
430B ILE* 1.3 62.0 + - - +
432B ARG* 3.3 9.7 + - - +
433B PHE* 3.2 20.3 + - - +
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Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B MET* 5.4 1.1 - - - -
346B PHE* 4.2 17.7 - - + -
350B LEU* 4.0 21.1 - - + -
353B VAL* 4.8 2.5 - - + -
355B ILE* 3.4 30.7 - - + -
368B MET* 5.2 12.6 - - + -
393B VAL* 4.7 2.7 - - + -
395B LEU* 3.5 24.7 - - + -
413B VAL* 5.7 1.8 - - + -
426B ALA* 2.9 20.5 + - + +
427B LEU* 3.7 5.8 - - + +
428B ALA 3.2 0.2 - - - -
429B ARG* 1.3 76.2 - - - +
431B ARG* 1.3 63.3 + - - +
433B PHE* 3.3 10.7 + - + +
434B VAL* 3.1 26.6 + - + +
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Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 5.2 9.1 - - - +
353B VAL* 3.3 32.7 - - + +
424B ASP 4.6 3.0 + - - -
427B LEU* 3.1 16.6 + - - +
428B ALA* 3.0 44.0 + - - +
430B ILE* 1.3 77.5 - - - +
432B ARG* 1.3 58.0 + - + +
434B VAL* 4.3 0.5 - - - +
435B GLY* 2.8 28.1 + - - -
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Residues in contact with ARG 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 ALA 3.3 8.4 + - - +
429B ARG* 3.8 9.2 - - - +
430B ILE 3.3 0.2 - - - -
431B ARG* 1.3 77.1 - - + +
433B PHE* 1.3 70.9 + - - +
435B GLY* 4.8 0.7 - - - -
436B VAL* 3.0 32.3 + - + +
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Residues in contact with PHE 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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370B LEU* 5.1 2.2 - - + -
373B LEU* 3.9 13.5 - - + -
385B LEU* 3.5 27.1 - - + -
388B VAL* 3.4 28.7 - - + -
389B ILE* 4.0 17.0 - - + -
392B ASP* 6.3 0.2 - - + -
393B VAL* 3.4 27.6 - - + -
429B ARG 3.2 10.5 + - - +
430B ILE* 3.3 13.9 + - + +
432B ARG* 1.3 82.3 - - - +
434B VAL* 1.3 72.5 + - + +
436B VAL* 2.9 12.7 + - - +
437B GLU* 3.0 40.0 - - - +
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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
----------------------------------------------------------
353B VAL* 3.5 28.9 - - + +
354B GLY 5.9 0.2 - - - -
355B ILE* 3.5 32.8 - - + -
373B LEU* 4.2 26.5 - - + -
430B ILE* 3.1 13.7 + - + +
431B ARG 4.3 1.1 - - - +
433B PHE* 1.3 80.9 - - + +
435B GLY* 1.3 67.9 + - - +
437B GLU* 2.7 30.4 + - + +
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Residues in contact with GLY 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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353B VAL* 5.7 0.4 - - - +
431B ARG 2.8 25.2 + - - -
432B ARG* 3.8 1.8 - - - -
434B VAL* 1.3 75.5 - - - +
436B VAL* 1.3 58.0 + - - +
437B GLU 3.1 5.4 + - - -
438B LYS* 4.6 6.4 + - - +
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Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ARG* 3.0 22.2 + - + +
433B PHE* 2.9 8.8 + - - +
435B GLY* 1.3 75.0 - - - +
437B GLU* 1.3 64.9 + - - +
438B LYS* 3.7 4.4 + - - -
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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