Contacts of the helix formed by residues 460 - 473 (chain D) 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 PRO 460 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D GLN* 3.2 38.4 - - + +
411D ILE* 3.8 28.9 - - + +
452D PRO* 6.2 0.4 - - + -
454D ILE* 3.5 31.6 - - + -
459D SER* 1.3 87.3 - - - +
461D THR* 1.3 64.2 + - - +
462D LEU 3.4 1.1 - - - -
463D LYS* 2.8 28.8 + - - +
464D ASN* 3.2 7.8 + - - +
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Residues in contact with THR 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ILE 4.3 3.3 + - - +
412D TRP* 2.5 52.4 - - + +
413D GLY* 3.5 9.2 - - - -
458D SER 4.5 0.2 + - - -
459D SER 3.7 1.1 - - - -
460D PRO* 1.3 79.5 - - - +
462D LEU* 1.3 59.6 + - - +
464D ASN* 2.6 28.5 + - - +
465D TYR* 2.9 25.4 + - + +
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Residues in contact with LEU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D SER* 3.3 24.4 + - - +
460D PRO 3.4 0.8 - - - -
461D THR* 1.3 78.8 - - - +
463D LYS* 1.3 62.3 - - - +
465D TYR* 3.3 16.1 + - + +
466D VAL* 3.1 28.0 + - - +
480D PHE* 4.4 2.0 - - + -
484D ARG* 3.8 36.6 - - - +
486D GLU* 4.5 12.3 - - + +
487D SER* 3.3 35.7 - - - +
490D LEU* 3.4 21.1 - - + -
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Residues in contact with LYS 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D GLN* 5.0 9.4 - - + +
456D VAL* 3.2 38.4 - - - +
458D SER 4.5 1.0 + - - -
459D SER* 3.4 17.9 - - - +
460D PRO* 2.8 16.9 + - + +
462D LEU* 1.3 79.7 - - - +
464D ASN* 1.3 62.6 + - - +
466D VAL* 3.4 7.2 + - - +
467D ARG* 3.1 27.2 + - - +
490D LEU* 4.1 25.6 - - - +
491D PRO* 3.6 31.0 - - - +
492D TYR* 4.1 13.8 - - - +
657D VAL 3.4 8.9 + - - -
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Residues in contact with ASN 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D GLY 4.0 2.1 - - - +
409D LEU* 3.7 21.0 - - + +
410D GLN* 2.7 54.1 + - - +
411D ILE 4.1 0.4 + - - -
413D GLY* 3.1 28.1 - - - +
414D GLY 4.2 1.3 - - - +
460D PRO 3.4 10.0 - - - +
461D THR* 2.6 19.8 + - - +
463D LYS* 1.3 72.2 - - - +
465D TYR* 1.3 64.9 + - - +
467D ARG* 3.2 6.1 + - - +
468D VAL* 3.1 26.8 + - - +
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Residues in contact with TYR 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D SER 4.1 8.1 - - - -
360D MET* 3.8 37.1 + - + -
361D LEU* 4.6 10.1 - - + +
412D TRP* 3.8 24.3 - - - -
413D GLY 4.1 2.9 - - - -
414D GLY* 3.4 31.4 - - - -
417D PHE* 5.5 1.1 - + - -
461D THR* 2.9 23.5 + - + +
462D LEU* 3.7 17.5 - - + +
464D ASN* 1.3 78.8 - - - +
466D VAL* 1.3 62.2 + - - +
468D VAL* 3.3 3.7 + - - +
469D VAL* 3.0 29.0 + - - +
480D PHE* 3.8 15.0 - + + -
484D ARG* 3.6 30.5 - - - -
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Residues in contact with VAL 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D LEU 3.1 15.8 + - - +
463D LYS* 3.8 6.7 - - - +
464D ASN 3.2 0.2 - - - -
465D TYR* 1.3 74.4 - - - +
467D ARG* 1.3 62.5 + - - +
469D VAL* 3.8 2.2 - - + +
470D GLU* 2.9 25.4 + - + +
480D PHE* 3.9 12.1 - - + -
481D TYR* 3.6 21.8 - - + +
487D SER* 2.7 38.8 - - - +
488D GLN 5.9 0.4 - - - +
490D LEU* 4.9 6.7 - - + +
492D TYR* 3.5 35.9 - - + -
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Residues in contact with ARG 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D ASP* 3.0 44.3 + - - +
408D GLY* 3.5 32.7 - - - +
409D LEU* 4.5 5.8 - - + -
463D LYS* 3.1 19.4 + - - +
464D ASN* 3.2 10.7 + - - +
466D VAL* 1.3 79.3 - - - +
468D VAL* 1.3 63.9 + - - +
470D GLU* 4.1 2.8 - - - +
471D VAL* 2.9 25.3 + - - +
492D TYR* 2.9 35.0 + - + +
493D GLY* 3.7 6.1 - - - -
494D ASP 3.3 27.1 + - - +
495D ILE* 3.5 23.0 - - + +
498D LEU* 3.8 9.7 - - - +
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Residues in contact with VAL 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D MET* 3.5 13.2 - - + -
409D LEU* 4.5 7.2 - - + -
414D GLY* 3.5 24.0 - - - +
417D PHE* 4.4 0.7 - - + -
418D GLU* 4.0 26.9 - - + +
421D TYR* 3.5 37.5 - - + -
464D ASN 3.1 17.1 + - - +
465D TYR* 3.7 7.0 - - - +
467D ARG* 1.3 76.4 - - - +
469D VAL* 1.3 63.1 + - - +
471D VAL* 3.3 7.1 - - - +
472D TRP* 3.0 26.5 + - + +
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Residues in contact with VAL 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D MET* 3.7 18.6 - - + -
465D TYR 3.0 21.6 + - - +
466D VAL* 3.3 4.5 + - + +
468D VAL* 1.3 74.8 - - - +
470D GLU* 1.3 68.8 + - + +
473D TRP* 2.8 47.1 + - + +
474D ASP 4.1 1.2 + - - -
477D LYS* 3.5 36.6 - - + +
480D PHE* 3.7 35.4 - - + -
481D TYR* 5.4 1.6 - - + -
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Residues in contact with GLU 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 5.9 3.0 - - - +
466D VAL* 2.9 26.1 + - + +
467D ARG 4.1 1.6 - - - +
469D VAL* 1.3 78.7 - - + +
471D VAL* 1.3 60.2 + - - +
474D ASP* 4.8 2.4 + - - +
477D LYS* 3.2 42.7 + - - +
481D TYR* 2.4 46.1 + - - +
492D TYR* 4.0 23.7 + - + -
495D ILE* 4.1 18.2 - - + -
499D LYS* 2.9 23.4 + - - +
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Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D ASP* 6.1 0.2 - - - +
418D GLU* 5.8 1.1 - - + -
467D ARG 2.9 21.3 - - - +
468D VAL* 3.3 9.2 - - - +
470D GLU* 1.3 81.2 - - - +
472D TRP* 1.3 81.3 + - + +
474D ASP* 4.5 0.2 - - - +
495D ILE* 4.6 12.1 - - + -
498D LEU* 3.9 40.6 - - + +
499D LYS* 4.1 18.8 + - + +
502D ARG* 2.6 33.3 + - - -
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Residues in contact with TRP 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D GLU* 4.1 16.9 + - + +
421D TYR* 4.0 29.2 - + + -
422D LYS* 3.2 37.7 - - + +
425D GLN* 3.7 29.8 - - + +
426D CYS* 3.8 27.8 - - - -
468D VAL* 3.0 23.0 + - + +
471D VAL* 1.3 112.5 - - + +
473D TRP* 1.3 66.4 + - + +
474D ASP 3.3 2.2 - - - -
498D LEU* 4.9 5.0 - - + +
501D PHE* 4.5 8.3 - + - -
502D ARG* 3.2 51.5 + - + -
507D CYS* 4.4 0.7 - - + -
510D PHE* 3.3 17.1 - - - +
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Residues in contact with TRP 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TRP* 4.0 16.8 - + - -
357D ASP 4.6 1.1 - - - -
358D TRP* 3.4 40.4 - + - -
360D MET* 3.8 20.2 - - + +
421D TYR* 3.3 40.3 + + - -
469D VAL* 2.8 43.2 + - + +
472D TRP* 1.3 70.5 - - + +
474D ASP* 1.3 69.4 + - - +
475D GLU 3.2 0.2 + - - -
476D TYR* 3.2 29.9 + - + +
477D LYS 4.1 4.9 - - - +
480D PHE* 3.5 37.5 - + + -
510D PHE* 3.4 37.3 - + - +
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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