Contacts of the helix formed by residues 458 - 473 (chain E) 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 458 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E ILE* 5.0 2.0 - - - -
456E VAL 3.6 0.2 + - - -
457E GLY* 1.3 65.7 + - - -
459E SER* 1.3 64.6 + - - +
460E PRO* 3.2 8.0 - - - +
461E THR* 3.4 22.9 + - - +
462E LEU* 3.6 18.5 + - - +
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Residues in contact with SER 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E ILE* 4.1 3.6 - - - +
456E VAL* 2.9 47.8 + - - +
457E GLY* 2.8 8.3 + - - -
458E SER* 1.3 72.8 - - - +
460E PRO* 1.4 69.2 - - - +
462E LEU* 3.4 4.5 + - - +
463E LYS* 2.4 47.0 + - - +
490E LEU* 5.3 1.1 - - - +
657E VAL 4.4 6.7 - - - -
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Residues in contact with PRO 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E GLN* 3.5 24.7 - - + +
411E ILE* 4.1 24.0 - - + +
454E ILE* 4.3 13.2 - - + -
458E SER* 3.3 7.9 - - - +
459E SER* 1.4 95.8 - - - +
461E THR* 1.3 51.5 + - + +
463E LYS* 4.4 5.6 - - + -
464E ASN* 2.6 47.0 + - - +
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Residues in contact with THR 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411E ILE 4.4 6.5 - - - +
412E TRP* 3.4 44.1 - - + +
413E GLY* 4.6 0.9 - - - -
458E SER* 3.4 20.9 + - - +
459E SER 3.4 0.4 - - - -
460E PRO* 1.3 73.8 - - + +
462E LEU* 1.3 60.1 + - - +
464E ASN* 3.6 6.9 - - - +
465E TYR* 2.8 54.1 + - - -
484E ARG* 5.7 0.5 + - - -
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Residues in contact with LEU 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E SER 3.6 10.2 + - - +
459E SER* 3.4 7.6 + - - +
461E THR* 1.3 81.4 + - - +
463E LYS* 1.3 63.4 + - - +
465E TYR* 3.5 3.8 + - + -
466E VAL* 3.3 26.3 + - + +
480E PHE* 4.9 4.7 - - + -
484E ARG* 4.7 20.4 - - + +
486E GLU* 4.8 6.3 - - + +
487E SER* 2.7 30.1 - - - +
490E LEU* 3.0 32.0 - - + +
656E SER* 3.8 22.0 - - - +
657E VAL 5.6 2.2 - - - -
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Residues in contact with LYS 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E GLY* 4.4 12.8 + - - -
459E SER* 2.4 33.5 + - - +
460E PRO* 3.9 4.7 - - + +
462E LEU* 1.3 74.1 - - - +
464E ASN* 1.3 65.1 + - - +
466E VAL* 3.8 3.6 + - - +
467E ARG* 3.3 35.6 + - - +
490E LEU* 4.4 11.0 - - + -
491E PRO 4.1 9.6 + - - +
492E TYR* 3.8 37.9 + - + +
493E GLY* 4.7 5.3 - - - +
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Residues in contact with ASN 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E GLY 4.4 2.3 - - - +
409E LEU* 3.4 27.9 - - + +
410E GLN 3.0 26.5 + - - +
412E TRP 4.0 0.2 - - - -
413E GLY* 2.6 40.0 - - - -
414E GLY 3.9 3.6 - - - +
460E PRO* 2.6 29.2 + - - +
461E THR 3.6 2.2 - - - +
463E LYS* 1.3 83.8 - - - +
465E TYR* 1.3 66.4 + - - +
467E ARG* 3.1 8.5 + - - +
468E VAL* 3.1 27.4 + - - +
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Residues in contact with TYR 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E SER 4.1 7.2 - - - -
360E MET* 3.9 35.4 + - + -
361E LEU* 4.5 9.2 - - + +
412E TRP* 3.7 24.0 - + - -
413E GLY 4.2 2.2 - - - -
414E GLY* 3.5 33.7 - - - -
417E PHE* 5.5 1.8 - + - -
461E THR* 2.8 38.8 + - - +
462E LEU* 3.9 6.7 - - - +
464E ASN* 1.3 73.0 - - - +
466E VAL* 1.3 63.3 + - - +
468E VAL* 3.3 3.8 + - - +
469E VAL* 3.0 30.6 + - - +
480E PHE* 4.1 14.8 - - + -
484E ARG* 3.3 34.5 - - - -
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Residues in contact with VAL 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E LEU 3.3 17.8 + - - +
463E LYS* 4.2 4.0 - - - +
464E ASN 3.2 0.2 - - - -
465E TYR* 1.3 77.0 - - - +
467E ARG* 1.3 55.7 + - - +
469E VAL* 3.7 5.6 - - - -
470E GLU* 2.8 31.2 + - + +
480E PHE* 3.8 23.1 - - + -
481E TYR* 3.5 21.5 - - - +
487E SER* 4.1 24.9 - - - +
490E LEU* 4.4 9.4 - - + +
492E TYR* 3.4 32.3 - - + -
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Residues in contact with ARG 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E ASP* 3.0 44.8 + - - +
408E GLY* 3.3 26.8 - - - +
409E LEU* 4.4 2.2 - - + +
463E LYS* 3.3 31.4 + - - +
464E ASN* 3.1 12.4 + - - +
466E VAL* 1.3 81.0 - - - +
468E VAL* 1.3 62.5 + - - +
470E GLU* 3.3 1.7 + - - -
471E VAL* 2.9 25.6 + - - +
492E TYR* 2.6 47.9 + - + +
493E GLY* 3.8 7.1 - - - -
494E ASP 3.4 28.2 + - - +
495E ILE* 3.3 15.6 - - + +
498E LEU* 4.0 8.9 - - - +
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Residues in contact with VAL 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360E MET* 4.2 10.5 - - + -
406E ASP* 6.0 0.2 - - - -
409E LEU* 4.2 9.6 - - + -
414E GLY* 3.6 22.2 - - - +
417E PHE* 4.5 0.9 - - + -
418E GLU* 3.8 31.2 - - + +
421E TYR* 3.7 34.3 - - + -
464E ASN 3.1 16.5 + - - +
465E TYR* 3.7 6.5 - - - +
467E ARG* 1.3 76.1 - - - +
469E VAL* 1.3 62.5 + - - +
471E VAL* 3.3 6.0 - - - +
472E TRP* 3.1 24.8 + - + +
473E TRP* 4.5 0.2 - - - -
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Residues in contact with VAL 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E MET* 3.7 23.3 - - + -
465E TYR 3.0 18.2 + - - +
466E VAL* 3.7 5.8 - - + +
468E VAL* 1.3 77.0 - - - +
470E GLU* 1.3 65.8 + - + +
473E TRP* 2.9 47.1 + - + +
474E ASP 4.1 1.7 + - - -
477E LYS* 3.4 33.2 - - + +
480E PHE* 3.9 29.2 - - + -
481E TYR* 5.3 1.1 - - + -
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Residues in contact with GLU 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466E VAL* 2.8 22.1 + - + +
467E ARG* 4.1 3.8 - - - +
469E VAL* 1.3 75.5 - - + +
471E VAL* 1.3 61.5 + - - +
474E ASP* 4.9 4.5 + - - +
477E LYS* 3.2 42.5 + - - +
481E TYR* 2.9 26.2 + - - +
492E TYR* 3.8 38.5 + - + +
495E ILE* 4.8 7.2 - - + -
499E LYS* 3.7 22.9 + - - -
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Residues in contact with VAL 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E GLU* 5.8 1.3 - - + -
467E ARG 2.9 22.0 + - - +
468E VAL* 3.3 2.2 - - - +
470E GLU* 1.3 77.7 - - - +
472E TRP* 1.3 86.8 + - + +
474E ASP* 4.4 1.0 - - - +
495E ILE* 3.3 22.1 - - + +
498E LEU* 4.0 33.2 - - + +
499E LYS* 4.1 16.6 - - + +
502E ARG* 2.7 34.2 + - - -
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Residues in contact with TRP 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E GLU* 4.2 13.7 + - + +
421E TYR* 4.0 27.6 - + + -
422E LYS* 3.3 38.0 - - + +
425E GLN* 3.6 37.3 - - + +
426E CYS* 3.6 29.8 - - - -
468E VAL* 3.1 23.1 + - + +
471E VAL* 1.3 114.6 - - + +
473E TRP* 1.3 67.7 + - - +
474E ASP 3.2 3.6 + - - -
498E LEU* 5.2 3.4 - - + +
501E PHE* 4.4 9.6 - + - -
502E ARG* 3.4 40.3 + - + +
507E CYS* 4.0 0.2 - - - -
510E PHE* 3.2 19.8 - - - +
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Residues in contact with TRP 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TRP* 4.0 17.0 - + - -
357E ASP 4.6 1.3 - - - -
358E TRP* 3.4 42.2 - + - -
360E MET* 3.3 30.1 - - + +
421E TYR* 3.4 30.1 + + - -
468E VAL 4.5 1.6 - - - -
469E VAL* 2.9 44.6 + - + +
472E TRP* 1.3 76.6 - - - +
474E ASP* 1.3 71.4 + - - +
476E TYR* 3.2 35.9 + - + +
477E LYS 3.9 5.2 - - - +
480E PHE* 3.5 25.8 - + + -
510E PHE* 3.4 33.2 - + - +
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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