Contacts of the helix formed by residues 403 - 420 (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 SER 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B GLN* 2.9 19.9 + - - +
401B THR* 3.4 2.2 + - - -
402B ALA* 1.3 74.0 - - - +
404B PRO* 1.3 76.6 - - - +
405B ALA* 4.1 1.2 - - - +
406B VAL* 3.0 20.1 + - - +
407B ILE* 2.9 20.8 + - - +
507B VAL* 5.0 1.9 + - - +
510B ASP* 3.0 25.8 + - - +
511B LEU* 6.1 1.1 - - - +
515B LEU* 4.1 19.1 - - - -
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Residues in contact with PRO 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ALA 4.6 0.4 - - - +
403B SER* 1.3 88.0 - - - +
405B ALA* 1.3 60.7 + - - +
407B ILE* 3.3 16.5 + - + +
408B ASP* 3.2 27.9 + - - +
510B ASP* 3.3 14.1 - - - +
515B LEU* 4.3 21.3 - - + -
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B SER* 4.1 0.4 - - - +
404B PRO* 1.3 73.1 - - - +
406B VAL* 1.3 58.3 + - - +
408B ASP* 3.3 9.9 + - - +
409B TYR* 2.9 28.0 + - - +
503B PHE* 4.3 4.0 - - - +
506B GLN* 3.5 44.9 - - + +
507B VAL* 3.6 10.9 - - + +
510B ASP* 2.7 24.0 + - - +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 3.0 42.0 - - + +
351B LEU* 4.2 13.7 - - + -
352B PHE* 4.3 10.3 - - + -
402B ALA* 3.7 15.9 - - + -
403B SER* 3.0 14.2 + - - +
405B ALA* 1.3 73.0 - - - +
407B ILE* 1.3 60.7 + - - +
409B TYR* 4.1 4.5 - - - -
410B VAL* 2.8 44.5 + - + +
507B VAL* 3.8 22.0 - - + -
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ALA* 3.8 28.3 - - + +
403B SER 2.9 14.5 + - - +
404B PRO* 3.4 17.3 - - + +
406B VAL* 1.3 76.9 - - - +
408B ASP* 1.3 64.3 + - - +
410B VAL* 4.0 3.1 - - - +
411B ASN* 2.9 50.9 + - - +
695C GLU* 5.3 9.0 - - - +
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PRO* 3.2 15.0 + - - +
405B ALA* 3.6 9.7 - - - +
406B VAL 3.2 0.2 - - - -
407B ILE* 1.3 84.7 - - - +
409B TYR* 1.3 62.0 + - - +
411B ASN* 3.4 10.5 + - - +
412B ARG* 3.1 22.9 + - - +
503B PHE* 3.8 19.7 - - + -
506B GLN* 5.0 6.6 + - - +
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Residues in contact with TYR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 3.6 42.0 - + + -
356B LEU* 5.5 1.1 - - + +
405B ALA 2.9 16.7 + - - +
406B VAL* 3.6 5.6 - - - +
408B ASP* 1.3 78.0 - - - +
410B VAL* 1.3 57.8 + - - +
412B ARG* 3.2 3.6 + - - +
413B LEU* 2.9 46.9 + - + +
428B HIS* 3.7 27.1 + + - -
431B VAL* 5.3 0.3 - - - +
432B ARG* 3.3 23.7 - - - +
500B ALA* 5.0 1.1 - - - +
503B PHE* 3.7 35.4 - + + -
504B ASN* 3.0 38.0 + - - -
507B VAL* 4.3 9.4 - - + -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 3.9 22.2 - - + +
352B PHE* 4.0 10.5 - - + -
355B ALA* 3.9 6.1 - - + -
402B ALA* 5.6 2.5 - - + -
406B VAL* 2.8 38.7 + - + +
407B ILE* 4.0 3.4 - - - +
409B TYR* 1.3 68.7 - - - +
411B ASN* 1.3 60.5 + - - +
413B LEU* 3.2 6.8 + - - -
414B GLU* 2.8 49.7 + - - +
694C SER* 3.9 10.1 - - - +
695C GLU* 3.9 20.2 - - + +
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Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE* 2.9 40.7 + - - +
408B ASP* 3.6 12.7 + - - +
409B TYR 3.3 0.2 - - - -
410B VAL* 1.3 75.0 - - - +
412B ARG* 1.3 62.2 + - - +
414B GLU* 3.3 6.2 + - - +
415B GLU* 3.0 22.9 + - - +
695C GLU* 2.9 26.2 + - - +
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP 3.1 13.4 + - - +
409B TYR 3.2 7.8 + - - +
411B ASN* 1.3 76.2 - - - +
413B LEU* 1.3 63.2 + - - +
415B GLU* 2.8 50.1 + - - +
416B ILE* 2.9 36.1 + - + +
419B ASN* 5.0 3.2 - - - +
421B ASP* 3.9 10.1 + - - -
424B ALA* 3.9 13.1 - - - +
428B HIS* 4.2 3.6 - - + +
492B HIS* 4.1 8.9 - - - -
496B GLU* 2.8 45.5 + - - +
503B PHE* 3.8 24.5 - - + -
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Residues in contact with LEU 413 (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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352B PHE* 3.5 29.4 - - + +
355B ALA* 4.1 20.4 - - + +
356B LEU* 3.7 27.4 - - + +
359B ALA* 3.7 9.9 - - + +
409B TYR* 2.9 42.5 + - + +
410B VAL 3.7 4.0 - - - +
412B ARG* 1.3 75.7 - - - +
414B GLU* 1.3 58.4 + - - +
416B ILE* 3.4 8.5 + - + +
417B ARG* 3.0 26.5 + - - +
425B LEU* 5.4 0.7 - - + -
428B HIS* 3.7 35.4 - - + +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ALA* 4.6 6.9 - - + +
358B GLN* 4.8 0.2 + - - -
410B VAL* 2.8 30.0 + - + +
411B ASN* 3.8 5.6 - - - +
413B LEU* 1.3 74.3 - - - +
415B GLU* 1.3 60.2 + - - +
417B ARG* 3.4 24.6 + - - +
418B ASP* 2.9 38.2 + - - +
692C GLY 4.5 0.3 - - - +
693C SER* 2.6 29.7 + - - -
694C SER* 2.7 42.5 + - - -
695C GLU* 3.4 7.2 - - - +
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Residues in contact with GLU 415 (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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411B ASN 3.0 12.8 + - - +
412B ARG* 2.8 42.7 + - - +
414B GLU* 1.3 74.5 - - - +
416B ILE* 1.3 58.6 + - - +
418B ASP* 3.3 5.3 + - - +
419B ASN* 2.8 58.0 + - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ALA* 4.3 9.2 - - + -
363B VAL* 5.0 2.0 - - + +
412B ARG* 2.9 36.1 + - + +
413B LEU* 3.6 11.7 - - + +
415B GLU* 1.3 75.9 - - - +
417B ARG* 1.3 57.1 + - - +
419B ASN* 4.9 0.4 - - - +
420B VAL* 2.8 25.3 + - - -
421B ASP* 3.1 37.3 + - + +
424B ALA* 3.7 17.5 - - + -
425B LEU* 3.9 18.6 - - + -
428B HIS* 3.4 37.5 - - + +
496B GLU* 3.8 6.3 - - - +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ALA 5.6 0.4 - - - +
358B GLN* 2.9 59.9 - - - +
359B ALA* 3.9 13.7 - - + +
362B ALA* 3.9 16.4 - - + +
363B VAL* 5.9 0.2 - - - -
413B LEU 3.0 13.6 + - - +
414B GLU* 3.5 33.9 + - - +
416B ILE* 1.3 77.9 - - - +
418B ASP* 1.3 87.2 + - - +
420B VAL* 3.1 20.1 + - - +
688C ASP* 5.4 4.0 + - - +
692C GLY 4.0 19.6 + - - -
693C SER* 4.4 3.4 - - - +
694C SER 4.6 3.0 - - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU* 2.9 24.5 + - - +
415B GLU* 3.8 6.5 - - - +
417B ARG* 1.3 103.6 + - - +
419B ASN* 1.3 66.1 + - - +
420B VAL* 4.1 5.4 - - - +
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Residues in contact with ASN 419 (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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412B ARG* 5.0 3.0 - - - +
415B GLU* 2.8 46.3 + - - +
416B ILE* 4.3 1.8 - - - +
418B ASP* 1.3 76.3 - - - +
420B VAL* 1.3 72.0 + - - +
421B ASP* 4.2 13.1 + - + +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ALA* 4.0 17.3 - - + +
363B VAL* 4.3 12.1 - - + -
366B SER* 3.7 33.7 - - - +
416B ILE 2.8 10.9 + - - -
417B ARG 3.1 14.3 + - - +
418B ASP 4.1 5.6 - - - +
419B ASN* 1.3 83.5 - - - +
421B ASP* 1.3 57.4 + - - +
422B GLY 3.2 6.6 + - - -
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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