Contacts of the helix formed by residues 468 - 482 (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 LYS 468 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 5.4 6.5 - - - +
108A ASP* 3.6 9.6 - - + +
202A VAL* 3.7 33.2 + - + +
203A PHE* 4.3 13.7 - - + -
205A HIS* 5.0 5.9 + - - -
206A GLN* 2.8 51.3 + - + +
466B ILE* 4.2 3.6 - - - +
467B ALA* 1.3 75.0 - - - +
469B LEU* 1.3 65.6 + - - +
470B LYS 3.3 2.5 - - - -
471B VAL* 3.3 25.6 + - + +
472B TYR* 3.0 21.3 + - - +
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Residues in contact with LEU 469 (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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108A ASP* 3.2 14.9 + - - +
111A ASN* 6.3 2.7 - - + +
437B LEU* 3.6 34.3 - - + +
441B GLN* 3.9 33.4 - - + +
463B PHE* 4.9 6.5 - - + -
466B ILE* 3.9 21.8 - - + +
467B ALA 3.3 9.2 + - - +
468B LYS* 1.3 72.2 - - - +
470B LYS* 1.3 57.4 + - - +
472B TYR* 3.7 3.5 - - - +
473B LYS* 2.9 47.5 + - + +
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Residues in contact with LYS 470 (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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104A PRO* 3.5 34.0 - - + +
107A ILE* 3.7 40.4 - - - +
108A ASP* 2.8 30.6 + - - +
914A SO4 5.2 5.9 + - - -
469B LEU* 1.3 73.2 - - - +
471B VAL* 1.3 60.7 + - + +
473B LYS* 3.5 6.8 + - - +
474B ASP* 2.6 38.7 + - - +
913B SO4 3.0 41.7 + - - +
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP* 5.3 0.4 - - - +
206A GLN* 3.7 37.7 - - + +
468B LYS* 3.3 33.9 + - + +
470B LYS* 1.3 80.0 - - + +
472B TYR* 1.3 63.4 + - - +
474B ASP* 3.3 7.6 + - - +
475B GLU* 2.9 49.8 + - + +
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Residues in contact with TYR 472 (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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372B LEU 4.9 1.4 + - - -
374B ASP* 2.7 42.2 + - - +
377B LEU* 3.6 24.3 - - + +
437B LEU* 3.9 21.5 - - + -
466B ILE* 3.6 46.0 - - + -
468B LYS 3.0 9.6 + - - +
469B LEU* 3.7 4.5 - - + +
471B VAL* 1.3 75.5 - - - +
473B LYS* 1.3 59.8 + - + +
475B GLU* 3.2 17.0 + - + +
476B TYR* 2.8 40.8 + + + +
479B LYS* 5.2 10.7 + - - -
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Residues in contact with LYS 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 3.8 18.5 - - + +
437B LEU* 3.6 33.9 + - + +
438B SER* 3.3 32.6 + - - +
469B LEU* 2.9 31.3 + - - +
470B LYS* 4.0 4.5 - - - +
472B TYR* 1.3 77.1 - - - +
474B ASP* 1.3 57.7 + - - +
476B TYR* 3.3 7.7 + - - +
477B ARG* 2.9 41.0 + - - +
902B HEM 5.9 1.2 - - - +
913B SO4 2.8 42.7 + - - +
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Residues in contact with ASP 474 (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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104A PRO* 5.5 3.6 - - - +
470B LYS* 2.6 35.9 + - - +
471B VAL* 3.7 8.2 + - - +
473B LYS* 1.3 75.5 - - - +
475B GLU* 1.3 59.4 + - + +
477B ARG* 3.3 22.4 + - - +
478B GLU* 2.9 36.0 + - + +
913B SO4 4.5 5.4 + - - -
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Residues in contact with GLU 475 (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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471B VAL* 2.9 38.4 + - + +
472B TYR* 3.6 17.3 - - + +
474B ASP* 1.3 76.5 - - + +
476B TYR* 1.3 59.1 + - - +
478B GLU* 3.3 8.4 + - - +
479B LYS* 2.9 46.9 + - - +
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Residues in contact with TYR 476 (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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372B LEU* 3.6 27.0 - - + +
377B LEU* 4.6 3.8 - - + -
426B VAL 4.5 0.2 + - - -
429B HIS* 2.8 41.3 + + - +
430B TYR* 3.2 33.7 + + - +
433B TYR* 5.3 3.4 - - + -
434B LEU* 4.0 25.1 - - + -
437B LEU* 5.5 1.6 - - + -
472B TYR* 2.8 35.4 + + + +
473B LYS* 3.3 10.1 + - - +
475B GLU* 1.3 76.8 - - - +
477B ARG* 1.3 62.3 + - - +
479B LYS* 3.1 13.2 + - + +
480B LEU* 2.9 46.1 + - + +
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Residues in contact with ARG 477 (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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309B ALA* 3.7 26.8 + - + +
310B VAL* 6.5 0.4 - - - -
313B LYS* 5.7 2.4 - - - +
430B TYR* 6.4 0.2 - - + -
434B LEU* 4.2 19.8 - - + +
438B SER* 5.1 1.2 + - - -
473B LYS* 2.9 40.8 + - - +
474B ASP* 3.6 16.4 + - - +
476B TYR* 1.3 75.9 - - - +
478B GLU* 1.3 61.3 + - - +
480B LEU* 3.2 8.8 + - + +
481B ASN* 2.9 34.7 + - - +
902B HEM 2.7 33.9 + - - +
913B SO4 2.9 42.6 + - - -
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Residues in contact with GLU 478 (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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474B ASP* 2.9 23.2 + - + +
475B GLU* 3.6 9.0 - - - +
476B TYR 3.2 0.2 - - - -
477B ARG* 1.3 78.4 - - - +
479B LYS* 1.3 56.1 + - - +
481B ASN* 3.2 23.4 + - - +
482B ASN* 2.9 47.4 + - - +
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Residues in contact with LYS 479 (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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371B SER* 3.0 51.4 + - - +
372B LEU* 3.7 21.1 + - + +
374B ASP* 5.4 2.6 + - - +
472B TYR* 5.2 13.3 + - - -
475B GLU* 2.9 32.0 + - - +
476B TYR* 3.1 12.0 + - + +
478B GLU* 1.3 71.7 - - + +
480B LEU* 1.3 65.3 + - - +
482B ASN* 3.2 8.0 + - - +
483B LEU* 3.1 28.9 + - + +
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Residues in contact with LEU 480 (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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308B LEU* 3.6 21.7 - - + +
309B ALA* 4.2 21.1 - - + +
312B LEU* 3.9 26.5 - - + -
372B LEU* 4.0 14.4 - - + -
426B VAL* 3.7 30.1 - - + -
430B TYR* 4.1 10.8 - - + -
476B TYR* 2.9 42.8 + - + +
477B ARG* 3.2 9.2 + - + +
479B LYS* 1.3 75.7 - - - +
481B ASN* 1.3 63.4 + - - +
483B LEU* 3.2 24.8 + - + +
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Residues in contact with ASN 481 (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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307B GLY* 3.5 13.0 - - - -
308B LEU* 3.2 12.9 + - - +
309B ALA* 2.9 33.9 + - - +
310B VAL* 4.6 2.0 + - - +
477B ARG* 2.9 17.9 + - - +
478B GLU* 3.5 32.9 + - - +
480B LEU* 1.3 76.1 - - - +
482B ASN* 1.3 63.1 + - - +
483B LEU 3.3 5.1 + - - +
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Residues in contact with ASN 482 (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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478B GLU* 2.9 36.2 + - - +
479B LYS* 3.2 7.5 + - - +
480B LEU 3.2 0.6 - - - -
481B ASN* 1.3 79.4 - - - +
483B LEU* 1.3 62.9 + - - +
484B GLU* 3.3 10.0 + - - +
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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