Contacts of the helix formed by residues 421 - 438 (chain B) in PDB entry 1IW1
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 421 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B VAL* 4.3 2.0 - - - +
412B ARG* 3.9 7.0 + - - +
416B ILE* 3.1 21.7 + - + +
419B ASN* 4.2 12.0 + - + +
420B VAL* 1.3 71.4 - - - +
422B GLY* 1.3 56.5 + - - +
423B PRO* 3.6 5.9 - - - +
424B ALA* 3.1 26.8 + - + +
425B LEU* 2.9 28.8 + - - +
492B HIS* 2.7 32.3 + - - -
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Residues in contact with GLY 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B VAL* 3.9 14.4 - - - -
366B SER* 6.0 0.2 - - - -
368B PHE* 3.4 26.4 - - - -
420B VAL 3.2 7.9 + - - -
421B ASP* 1.3 71.7 - - - +
423B PRO* 1.3 72.4 - - - +
425B LEU* 3.1 4.3 + - - +
426B VAL* 2.9 25.5 + - - +
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Residues in contact with PRO 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B PHE* 3.6 19.3 - - + -
421B ASP* 3.6 10.1 - - - +
422B GLY* 1.3 88.3 - - - +
424B ALA* 1.3 61.7 + - - +
426B VAL* 3.3 1.8 + - + +
427B ALA* 3.2 17.0 + - - +
485B LEU* 4.6 1.1 - - + -
489B GLN* 3.8 55.2 - - + +
492B HIS* 4.4 8.1 - - + -
493B LEU* 3.3 28.8 - - + +
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 3.9 3.6 - - - +
416B ILE* 3.7 20.2 - - + -
421B ASP* 3.1 34.1 + - - +
423B PRO* 1.3 76.7 - - - +
425B LEU* 1.3 63.0 + - - +
427B ALA* 3.2 3.6 + - - +
428B HIS* 3.1 28.5 + - - -
492B HIS* 3.9 9.5 - - - +
496B GLU* 3.7 21.5 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 3.9 13.5 - - + -
359B ALA* 3.7 16.4 - - + +
360B VAL* 3.7 38.8 - - + +
363B VAL* 3.7 24.0 - - + -
373B LEU* 3.7 36.6 - - + -
413B LEU* 5.4 1.1 - - + -
416B ILE* 3.9 8.9 - - + +
421B ASP 2.9 14.7 + - - +
422B GLY 3.1 7.4 + - - +
424B ALA* 1.3 77.6 - - - +
426B VAL* 1.3 65.1 + - + +
428B HIS* 3.1 6.2 + - + +
429B HIS* 2.9 24.3 + - + +
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 5.7 0.4 - - + -
368B PHE* 3.8 9.4 - - + -
369B ALA* 3.8 28.5 - - + -
372B LEU* 3.7 22.4 - - + -
373B LEU* 5.0 0.7 - - + -
422B GLY 2.9 17.3 + - - +
423B PRO 3.7 7.2 - - - +
425B LEU* 1.3 80.5 - - + +
427B ALA* 1.3 63.9 + - - +
429B HIS* 3.2 7.5 + - - +
430B TYR* 2.9 24.1 + - + +
476B TYR* 4.5 0.2 + - - -
480B LEU* 3.7 18.6 - - + -
483B LEU* 4.1 8.1 - - + -
493B LEU* 3.9 17.9 - - + -
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Residues in contact with ALA 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 5.4 0.2 - - - -
423B PRO 3.2 10.5 + - - +
424B ALA 3.3 10.1 - - - +
425B LEU 3.2 0.2 - - - -
426B VAL* 1.3 77.4 - - - +
428B HIS* 1.3 61.2 + - - +
430B TYR* 3.4 5.6 + - - +
431B VAL* 3.1 30.2 + - - +
493B LEU* 3.4 34.7 - - + +
496B GLU* 3.7 7.9 - - + -
497B ALA* 3.6 20.9 - - + +
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Residues in contact with HIS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 3.9 18.8 - - + +
409B TYR* 3.7 28.3 + + - +
412B ARG* 4.2 3.0 - - + +
413B LEU* 3.7 11.7 - - + +
416B ILE* 3.4 19.5 - - + +
424B ALA 3.1 20.9 + - - +
425B LEU* 3.1 9.8 + - - +
427B ALA* 1.3 80.3 - - - +
429B HIS* 1.3 61.9 + - - +
431B VAL* 4.0 0.9 - - - +
432B ARG* 3.1 29.3 + - + +
496B GLU* 2.8 32.1 + - + +
500B ALA* 3.5 31.6 - - + +
503B PHE* 4.2 12.3 - + - -
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Residues in contact with HIS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 4.4 2.8 - - - +
360B VAL* 3.9 15.7 - - + +
372B LEU* 3.4 26.9 + - + +
373B LEU* 3.5 31.4 - - + +
374B ASP 4.6 1.2 + - - -
377B LEU* 3.5 24.0 - - + +
425B LEU* 2.9 17.7 + - + +
426B VAL* 3.4 9.6 - - - +
428B HIS* 1.3 73.6 - - - +
430B TYR* 1.3 59.6 + - - +
433B TYR* 2.9 68.4 + + - +
476B TYR* 2.8 26.9 + + - -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ALA 5.1 1.6 - - - -
312B LEU* 3.7 43.4 + - + -
313B LYS* 3.4 15.9 - - - -
316B THR* 4.0 14.9 + - + -
426B VAL 2.9 16.6 + - - +
427B ALA* 3.6 3.1 - - - +
429B HIS* 1.3 75.7 - - - +
431B VAL* 1.3 79.7 + - + +
434B LEU* 3.0 51.7 + - + +
476B TYR* 3.2 18.0 + + + +
480B LEU* 4.1 20.0 - - + -
501B PHE* 4.6 0.8 - + - -
902B HEM 2.6 54.5 + - + +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR* 5.3 0.2 - - - +
427B ALA 3.1 17.5 + - - +
428B HIS 4.0 3.6 - - - +
429B HIS 3.4 0.2 - - - -
430B TYR* 1.3 92.0 - - + +
432B ARG* 1.3 63.8 + - + +
497B ALA* 3.8 25.8 - - + +
500B ALA* 3.9 14.1 - - + -
501B PHE* 3.8 22.0 - - + +
504B ASN* 4.0 16.8 - - - +
902B HEM 3.5 50.0 - - + +
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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
----------------------------------------------------------
349B ALA* 5.7 1.2 - - - +
352B PHE* 4.0 14.8 - - + -
353B TYR* 2.7 38.4 + - + +
356B LEU* 4.0 20.2 - - + -
409B TYR* 3.3 27.1 - - - +
428B HIS 3.1 17.0 + - - +
429B HIS 4.4 0.2 - - - +
431B VAL* 1.3 78.5 - - + +
433B TYR* 1.3 61.8 + - - +
435B GLY* 3.3 2.3 + - - -
436B ASP* 2.9 58.0 + - - +
460B PHE* 4.0 7.1 - - - -
461B TYR* 6.2 0.2 - - - -
504B ASN* 2.9 28.9 + - - +
508B PHE* 5.8 2.6 - - - -
902B HEM 4.4 18.9 - - - +
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Residues in contact with TYR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TYR* 3.7 15.7 - + - -
356B LEU* 3.9 24.5 - - + +
357B GLU* 2.7 37.3 + - - +
360B VAL* 4.6 2.6 - - + +
377B LEU* 3.3 55.9 - - + -
378B ASN* 4.5 2.1 + - - -
379B ARG* 4.0 2.5 - - + -
429B HIS* 2.9 66.3 + + + +
432B ARG* 1.3 69.5 - - - +
434B LEU* 1.3 65.9 + - - +
436B ASP* 3.1 13.7 + - - +
437B LEU* 3.0 30.3 + - + +
463B PHE* 4.9 2.9 - + + -
476B TYR* 5.2 2.5 - - + +
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Residues in contact with LEU 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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429B HIS 4.0 0.8 + - - -
430B TYR* 3.0 48.8 + - + +
433B TYR* 1.3 77.3 - - - +
435B GLY* 1.3 61.7 + - - +
437B LEU* 3.4 9.7 + - + +
438B SER* 2.9 31.6 + - - +
473B LYS* 3.8 34.3 - - + +
476B TYR* 4.0 27.9 + - + -
477B ARG* 4.2 16.2 - - + +
480B LEU* 5.4 0.4 - - + -
902B HEM 3.8 28.3 - - + +
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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
----------------------------------------------------------
431B VAL 3.8 0.8 + - - -
432B ARG 3.3 5.7 + - - -
433B TYR 3.1 0.6 - - - -
434B LEU* 1.3 79.4 - - - +
436B ASP* 1.3 59.9 + - - +
438B SER 3.0 0.2 + - - -
439B GLY* 3.0 11.1 + - - -
440B GLY 2.9 22.3 + - - -
902B HEM 3.2 46.4 + - - +
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Residues in contact with ASP 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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353B TYR* 2.5 36.2 + - - -
379B ARG* 4.2 2.6 - - - +
432B ARG* 2.9 34.3 + - - +
433B TYR* 3.1 14.8 + - - +
435B GLY* 1.3 77.0 - - - +
437B LEU* 1.3 58.3 + - - +
438B SER 3.1 1.3 + - - -
440B GLY* 3.5 16.9 - - - +
441B GLN* 2.9 22.3 + - - -
460B PHE* 3.4 20.7 - - + +
461B TYR* 4.8 2.4 - - + -
463B PHE* 3.8 18.5 - - + -
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 4.2 7.2 - - + -
433B TYR* 3.0 26.0 + - + +
434B LEU* 3.8 18.4 - - + +
435B GLY 3.2 0.2 - - - -
436B ASP* 1.3 76.6 - - - +
438B SER* 1.3 58.3 + - - +
441B GLN* 3.6 17.8 - - - +
463B PHE* 3.6 32.8 - - + -
466B ILE* 4.3 7.9 - - + -
469B LEU* 3.6 33.1 - - + +
472B TYR* 3.9 30.3 - - + -
473B LYS* 3.6 26.6 + - + -
476B TYR* 5.5 2.7 - - + -
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 2.9 16.7 + - - +
435B GLY 3.0 1.8 + - - -
436B ASP 3.1 0.2 - - - -
437B LEU* 1.3 76.6 - - - +
439B GLY* 1.3 67.7 + - - -
440B GLY 3.2 0.2 - - - -
441B GLN* 3.0 22.0 + - - +
442B VAL* 3.8 5.6 + - - +
473B LYS* 3.3 28.6 + - - +
477B ARG* 5.1 2.3 + - - -
902B HEM 3.5 38.9 - - - +
913B SO4 5.3 0.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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