Contacts of the helix formed by residues 458 - 473 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C ILE* 4.0 4.7 - - - -
457C GLY* 1.3 64.6 + - - -
459C SER* 1.3 67.0 + - - +
460C PRO* 3.2 8.5 - - - +
461C THR* 4.2 13.9 + - - -
462C LEU* 3.3 24.4 + - - +
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Residues in contact with SER 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C GLN* 5.1 2.4 + - - -
456C VAL* 2.5 39.8 - - - +
457C GLY* 2.7 11.1 - - - -
458C SER* 1.3 72.5 - - - +
460C PRO* 1.4 54.3 - - - +
462C LEU* 4.8 1.6 - - - -
463C LYS* 2.5 62.1 + - - +
490C LEU* 5.0 10.4 - - - +
491C PRO* 5.4 3.8 + - - +
657C VAL 4.6 8.6 + - - -
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Residues in contact with PRO 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C GLN* 4.5 24.0 - - + +
411C ILE* 4.3 26.9 - - + -
454C ILE* 3.2 43.7 - - + -
456C VAL* 4.6 2.2 - - + +
458C SER* 3.3 6.7 - - - +
459C SER* 1.4 90.5 - - - +
461C THR* 1.3 61.9 + - - +
463C LYS* 3.7 3.1 - - + +
464C ASN* 2.9 31.6 + - - +
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Residues in contact with THR 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C ILE* 4.8 3.6 + - - +
412C TRP* 2.8 51.3 - - + +
413C GLY* 4.5 1.1 - - - -
458C SER* 3.9 10.4 + - - -
460C PRO* 1.3 77.9 - - - +
462C LEU* 1.3 67.0 + - - +
464C ASN* 2.9 17.6 + - - +
465C TYR* 3.0 38.8 + - + +
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Residues in contact with LEU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C SER* 3.3 22.5 + - - +
459C SER 4.1 0.2 - - - +
461C THR* 1.3 77.4 - - - +
463C LYS* 1.3 61.2 + - - +
465C TYR* 3.3 11.5 + - + -
466C VAL* 3.1 26.2 + - - +
480C PHE* 4.3 6.5 - - + -
484C ARG* 3.3 44.6 - - - +
486C GLU* 4.2 16.6 - - + +
487C SER* 3.4 29.8 - - - -
490C LEU* 3.6 18.4 - - + -
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Residues in contact with LYS 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLY 5.8 2.0 - - - +
410C GLN* 4.0 23.5 - - + +
459C SER* 2.5 41.7 + - - +
460C PRO 3.7 3.4 - - - +
462C LEU* 1.3 71.8 - - - +
464C ASN* 1.3 64.0 + - - +
466C VAL* 3.3 5.4 + - - +
467C ARG* 3.1 28.0 + - - +
490C LEU* 4.1 12.9 - - + +
491C PRO* 2.9 26.3 + - - +
492C TYR* 3.1 32.1 - - - +
493C GLY* 4.3 6.4 - - - +
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Residues in contact with ASN 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLY 4.0 3.3 - - - +
409C LEU* 3.6 28.4 - - + +
410C GLN* 3.4 26.7 + - - +
411C ILE 3.2 25.9 + - - +
413C GLY* 3.7 21.5 - - - -
414C GLY* 4.5 2.0 - - - -
460C PRO 2.9 15.7 + - - +
461C THR* 2.9 7.6 + - - +
463C LYS* 1.3 77.8 - - - +
465C TYR* 1.3 66.0 + - - +
467C ARG* 3.2 6.5 + - - +
468C VAL* 3.1 26.8 + - - +
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Residues in contact with TYR 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C SER 4.1 9.6 - - - -
360C MET* 3.8 38.6 + - + +
361C LEU* 4.6 10.7 - - + +
412C TRP* 5.5 4.3 + - - -
413C GLY 5.0 1.4 + - - -
414C GLY* 3.8 29.3 + - - -
417C PHE* 5.5 2.2 - + - -
461C THR* 3.0 35.1 + - + +
462C LEU* 3.3 18.4 + - + +
464C ASN* 1.3 76.3 - - - +
466C VAL* 1.3 63.6 + - - +
468C VAL* 3.3 3.6 + - - +
469C VAL* 3.0 29.0 + - - +
480C PHE* 3.8 15.3 - + + -
484C ARG* 3.7 30.5 - - - -
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Residues in contact with VAL 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C LEU 3.1 14.9 + - - +
463C LYS* 3.8 7.0 - - - +
464C ASN 3.2 0.4 - - - -
465C TYR* 1.3 74.6 - - - +
467C ARG* 1.3 63.4 + - - +
469C VAL* 3.8 2.0 - - - +
470C GLU* 2.9 25.8 + - + +
480C PHE* 3.9 14.6 - - + -
481C TYR* 3.5 23.6 - - + +
487C SER* 3.7 36.8 - - - +
490C LEU* 4.4 7.6 - - + +
492C TYR* 3.5 32.8 - - + -
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Residues in contact with ARG 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C ASP* 3.0 43.8 + - - +
408C GLY* 3.5 34.1 - - - +
409C LEU* 4.5 5.8 - - + -
463C LYS* 3.1 21.7 + - - +
464C ASN* 3.2 10.7 + - - +
466C VAL* 1.3 78.8 - - - +
468C VAL* 1.3 63.7 + - - +
470C GLU* 4.1 1.9 - - - +
471C VAL* 2.9 25.4 + - - +
492C TYR* 2.9 37.2 + - + +
493C GLY* 3.7 4.4 - - - -
494C ASP 2.8 33.7 + - - +
495C ILE* 3.6 23.5 - - + +
498C LEU* 3.8 4.6 - - - +
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Residues in contact with VAL 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C MET* 3.5 13.5 - - + -
409C LEU* 4.3 6.5 - - + -
414C GLY* 3.3 27.4 - - - +
417C PHE* 4.3 0.7 - - + -
418C GLU* 4.0 26.2 - - + +
421C TYR* 3.5 37.7 - - + -
464C ASN 3.1 16.2 + - - +
465C TYR* 3.7 6.1 - - - +
467C ARG* 1.3 75.4 - - - +
469C VAL* 1.3 64.7 + - - +
471C VAL* 3.3 7.2 - - - +
472C TRP* 3.0 25.7 + - + +
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C MET* 3.7 18.4 - - + -
465C TYR 3.0 21.2 + - - +
466C VAL* 3.8 4.5 - - + +
468C VAL* 1.3 74.8 - - - +
470C GLU* 1.3 68.0 + - + +
473C TRP* 2.8 46.3 + - + +
474C ASP 4.0 1.7 + - - -
477C LYS* 3.5 37.0 - - + +
480C PHE* 3.7 35.9 - - + -
481C TYR* 5.5 1.3 - - + -
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Residues in contact with GLU 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C VAL* 2.9 25.7 + - + +
467C ARG* 4.1 2.9 - - - +
469C VAL* 1.3 78.8 - - - +
471C VAL* 1.3 59.5 + - - +
474C ASP* 4.8 2.9 + - - +
477C LYS* 3.2 42.5 + - - +
481C TYR* 2.5 44.3 + - + +
492C TYR* 4.0 32.6 + - + +
495C ILE* 5.2 6.3 - - + -
499C LYS* 2.9 25.1 + - - +
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Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C ASP* 6.1 0.2 - - - +
418C GLU* 5.8 0.9 - - + -
467C ARG 2.9 20.9 - - - +
468C VAL* 3.3 9.6 - - - +
470C GLU* 1.3 81.4 - - - +
472C TRP* 1.3 80.7 + - + +
474C ASP 5.2 0.2 - - - -
495C ILE* 4.3 19.9 - - + +
498C LEU* 3.9 34.1 - - + +
499C LYS* 4.1 19.1 + - + +
502C ARG* 2.6 34.3 + - - -
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Residues in contact with TRP 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C GLU* 4.1 17.1 + - + +
421C TYR* 4.0 29.4 - + + -
422C LYS* 3.2 37.0 - - + +
425C GLN* 3.7 31.2 - - + +
426C CYS* 3.8 29.2 - - - -
468C VAL* 3.0 23.9 + - + +
471C VAL* 1.3 111.7 - - + +
473C TRP* 1.3 65.1 + - + +
474C ASP 3.3 2.2 - - - -
498C LEU* 4.9 5.0 - - + +
501C PHE* 4.5 8.1 - + - -
502C ARG* 3.2 50.1 + - + -
507C CYS* 4.4 0.4 - - + -
510C PHE* 3.2 17.8 - - - +
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Residues in contact with TRP 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C TRP* 4.0 17.7 - + - -
357C ASP 4.6 1.1 - - - -
358C TRP* 3.4 40.4 - + - -
360C MET* 3.8 20.8 - - + +
421C TYR* 3.3 40.9 + + - -
469C VAL* 2.8 42.7 + - + +
472C TRP* 1.3 70.4 - - + +
474C ASP* 1.3 69.2 + - - +
475C GLU 3.3 0.2 + - - -
476C TYR* 3.3 31.4 + - + +
477C LYS 4.1 5.2 - - - +
480C PHE* 3.5 35.9 - + + -
510C PHE* 3.4 37.5 - + - +
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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