Contacts of the helix formed by residues 459 - 473 (chain A) in PDB entry 6IWQ
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 459 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A GLY* 3.8 3.0 - - - -
458A SER* 1.3 81.5 + - - +
460A PRO* 1.4 76.7 - - - +
461A THR* 2.9 16.2 - - - -
462A LEU* 3.0 27.7 + - - +
463A LYS* 3.1 9.2 + - - +
490A LEU* 4.9 0.2 - - - +
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Residues in contact with PRO 460 (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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410A GLN* 3.8 36.8 - - + +
411A ILE* 4.7 12.6 - - + -
452A PRO* 5.8 2.5 - - + -
454A ILE* 4.5 31.4 - - + +
457A GLY* 3.9 8.9 - - - +
459A SER* 1.4 83.8 - - - +
461A THR* 1.3 60.9 + - - +
463A LYS* 2.8 37.9 + - + +
464A ASN* 2.9 15.4 + - - +
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Residues in contact with THR 461 (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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411A ILE* 5.0 4.0 - - - +
412A TRP* 3.3 45.3 + - + +
413A GLY* 3.7 15.3 - - - -
459A SER* 3.5 15.3 + - - -
460A PRO* 1.3 82.4 - - - +
462A LEU* 1.3 59.9 + - - +
463A LYS 3.0 0.2 - - - -
464A ASN* 3.1 12.9 + - - +
465A TYR* 3.2 29.2 + - + +
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A SER 4.0 11.9 - - - +
459A SER* 3.0 23.0 + - - +
461A THR* 1.3 78.4 - - - +
463A LYS* 1.3 62.0 + - - +
465A TYR* 3.5 12.0 + - + -
466A VAL* 3.3 28.2 + - - +
480A PHE* 4.3 7.0 - - + -
484A ARG* 3.3 44.2 - - - +
486A GLU* 4.0 21.3 - - + +
487A SER* 3.7 24.2 - - - -
490A LEU* 3.9 14.4 - - + -
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Residues in contact with LYS 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 4.9 13.3 - - + +
454A ILE* 5.9 3.0 - - - +
456A VAL 4.6 0.4 + - - -
457A GLY* 2.8 46.2 + - - -
459A SER 3.1 3.4 + - - +
460A PRO* 2.8 23.2 + - + +
462A LEU* 1.3 81.1 - - - +
464A ASN* 1.3 62.8 + - - +
466A VAL* 3.4 5.5 + - - +
467A ARG* 3.2 24.7 + - - +
490A LEU* 4.2 13.2 - - + -
491A PRO* 3.5 28.5 - - - +
492A TYR* 3.9 15.3 - - + +
657A VAL 4.9 1.3 + - - -
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Residues in contact with ASN 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 4.2 0.4 - - - +
408A GLY 4.0 2.1 - - - +
409A LEU* 3.7 18.2 - - + +
410A GLN* 3.1 49.2 + - - +
412A TRP 3.0 25.2 + - - -
413A GLY 3.7 18.4 + - - +
460A PRO 2.9 13.4 + - - +
461A THR* 3.1 6.7 + - - +
463A LYS* 1.3 78.0 - - - +
465A TYR* 1.3 65.5 + - - +
467A ARG* 3.1 7.0 + - - +
468A VAL* 3.1 26.6 + - + +
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Residues in contact with TYR 465 (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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359A SER 4.1 10.1 - - - -
360A MET* 3.8 37.2 + - - -
361A LEU* 4.5 9.3 - - + +
412A TRP* 4.9 3.5 + - - -
413A GLY* 3.8 28.1 - - - -
414A GLY 4.0 10.5 + - - -
417A PHE* 5.5 2.4 - + - -
461A THR* 3.2 25.7 + - + +
462A LEU* 3.7 18.2 - - + +
463A LYS 3.4 0.2 - - - -
464A ASN* 1.3 77.7 - - - +
466A VAL* 1.3 63.9 + - - +
468A VAL* 3.3 3.7 + - - +
469A VAL* 3.0 28.8 + - - +
480A PHE* 3.9 13.9 - + + -
484A ARG* 3.7 29.8 - - - -
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU 3.3 15.3 + - - +
463A LYS* 3.8 7.4 - - - +
464A ASN 3.2 0.6 - - - -
465A TYR* 1.3 78.1 - - - +
467A ARG* 1.3 61.9 + - - +
469A VAL* 3.3 1.7 + - - -
470A GLU* 2.9 25.7 + - + +
480A PHE* 3.9 14.6 - - + -
481A TYR* 3.5 24.2 - - + +
487A SER* 3.7 35.7 - - - +
488A GLN 6.1 0.2 - - - +
490A LEU* 4.4 7.2 - - + +
492A TYR* 3.5 32.1 - - + -
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Residues in contact with ARG 467 (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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406A ASP* 3.0 44.6 + - - +
408A GLY* 3.5 32.7 - - - +
409A LEU* 4.3 6.1 - - + -
463A LYS* 3.2 15.6 + - - +
464A ASN* 3.1 11.5 + - - +
466A VAL* 1.3 78.0 - - - +
468A VAL* 1.3 64.3 + - - +
470A GLU* 4.1 2.1 - - - +
471A VAL* 2.9 25.4 + - - +
492A TYR* 2.9 36.6 + - + +
493A GLY* 3.7 4.4 - - - -
494A ASP 2.8 33.7 + - - +
495A ILE* 3.6 22.8 - - + +
498A LEU* 3.8 4.8 - - - +
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A MET* 3.5 13.2 - - + -
406A ASP* 5.6 0.2 + - - -
409A LEU* 4.6 7.4 - - + -
414A GLY 4.2 16.2 - - - +
415A GLU 4.2 3.1 - - - +
417A PHE* 4.4 0.7 - - + -
418A GLU* 4.0 34.8 - - + +
421A TYR* 3.5 37.2 - - + -
464A ASN 3.1 16.2 + - - +
465A TYR* 3.3 5.8 + - - +
467A ARG* 1.3 75.1 - - - +
469A VAL* 1.3 63.4 + - - +
471A VAL* 3.3 6.9 - - - +
472A TRP* 3.0 26.4 + - + +
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Residues in contact with VAL 469 (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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360A MET* 3.7 19.1 - - + -
465A TYR 3.0 21.2 + - - +
466A VAL* 3.8 4.0 - - + +
468A VAL* 1.3 74.8 - - - +
470A GLU* 1.3 67.8 + - + +
473A TRP* 2.8 47.2 + - + +
474A ASP 4.0 1.2 + - - -
477A LYS* 3.5 35.9 - - + +
480A PHE* 3.7 36.3 - - + -
481A TYR* 5.5 1.1 - - + -
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Residues in contact with GLU 470 (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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466A VAL* 2.9 26.2 + - + +
467A ARG* 4.1 3.1 - - - +
469A VAL* 1.3 78.4 - - + +
471A VAL* 1.3 58.9 + - - +
474A ASP* 4.8 3.1 + - - +
477A LYS* 3.2 41.9 + - - +
481A TYR* 2.5 43.5 + - - +
492A TYR* 4.0 33.1 + - + +
495A ILE* 5.2 6.1 - - + -
499A LYS* 2.9 23.7 + - - +
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Residues in contact with VAL 471 (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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406A ASP* 6.1 0.2 - - - +
418A GLU* 5.8 0.9 - - + -
467A ARG 2.9 21.8 - - - +
468A VAL* 3.3 9.6 - - - +
470A GLU* 1.3 81.7 - - - +
472A TRP* 1.3 81.3 + - + +
474A ASP* 4.5 0.4 - - - +
495A ILE* 4.3 19.3 - - + -
498A LEU* 3.9 34.8 - - + +
499A LYS* 4.1 18.9 + - + +
502A ARG* 2.6 33.9 + - - -
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Residues in contact with TRP 472 (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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418A GLU* 4.1 17.5 + - + +
421A TYR* 4.0 28.7 - + + -
422A LYS* 3.2 38.1 - - + +
425A GLN* 3.7 30.7 - - + +
426A CYS* 3.8 22.2 - - - -
468A VAL* 3.0 23.6 + - + +
471A VAL* 1.3 112.5 - - + +
473A TRP* 1.3 65.6 + - + +
474A ASP 3.4 2.2 - - - -
498A LEU* 4.9 4.4 - - + +
501A PHE* 4.5 8.7 - + - -
502A ARG* 3.2 50.3 + - + -
507A CYS* 4.2 8.1 - - + -
510A PHE* 3.2 17.0 - - - +
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Residues in contact with TRP 473 (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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356A TRP* 4.0 16.8 - + - -
357A ASP 4.6 1.1 - - - -
358A TRP* 3.4 41.1 - + - -
360A MET* 3.8 20.9 - - + +
421A TYR* 3.3 40.5 + + - -
469A VAL* 2.8 40.9 + - + +
472A TRP* 1.3 72.3 - - + +
474A ASP* 1.3 69.9 + - - +
476A TYR* 3.2 33.5 + - + +
477A LYS 4.1 2.5 - - - +
480A PHE* 3.5 37.2 - + + -
510A PHE* 3.4 35.4 - + - +
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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