Contacts of the helix formed by residues 547 - 564 (chain C) in PDB entry 1V40
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 THR 547 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C ASP 4.9 1.3 - - - +
477C LEU* 3.2 23.1 - - - +
479C GLY* 4.4 12.8 - - - +
480C ASN* 5.6 2.5 - - - +
488C VAL* 3.8 23.0 - - + +
542C ILE* 4.0 18.4 - - + +
545C SER* 3.6 12.3 - - - +
546C VAL* 1.3 84.3 - - - +
548C TRP* 1.3 59.2 + - - +
549C ALA* 3.0 21.2 + - - +
550C ASP* 2.9 33.1 + - - +
551C PHE* 3.5 2.3 + - - -
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Residues in contact with TRP 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE* 3.7 16.0 - - + +
421C ILE* 4.4 4.9 - - + -
465C LEU* 3.8 25.4 - - + -
468C ALA* 3.5 25.6 - - + -
469C ARG* 4.0 24.5 - - + +
472C THR* 3.6 36.6 + - + -
477C LEU* 3.1 32.2 + - + +
478C ALA* 4.4 5.1 + - - +
488C VAL* 3.4 18.5 - - + +
489C ASP* 3.9 19.6 + - - -
492C VAL* 3.8 35.7 - - + -
547C THR* 1.3 71.2 - - - +
549C ALA* 1.3 60.2 + - - +
550C ASP 3.2 0.2 - - - -
551C PHE* 3.4 23.5 - - + +
552C TYR* 2.9 28.4 + + + +
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Residues in contact with ALA 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C VAL* 3.9 15.9 - - + +
491C ILE* 4.3 8.7 - - + -
492C VAL* 3.9 19.1 - - + -
495C LEU* 4.5 2.8 - - - +
541C LEU* 3.9 5.2 - - + +
542C ILE* 3.7 23.8 - - + -
547C THR* 3.0 13.6 + - - +
548C TRP* 1.3 78.0 - - - +
550C ASP* 1.3 60.8 + - - +
552C TYR* 3.3 2.6 + - - +
553C TRP* 3.0 27.4 + - - +
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Residues in contact with ASP 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C TRP* 3.5 17.5 - - - +
541C LEU* 3.0 40.4 + - - +
542C ILE 4.9 0.3 + - - -
545C SER 4.2 0.2 - - - +
546C VAL* 3.5 13.2 - - + -
547C THR* 2.9 36.3 + - - +
549C ALA* 1.3 75.6 - - - +
551C PHE* 1.3 65.5 + - - +
553C TRP* 3.2 4.7 + - - +
554C GLU* 3.0 22.7 + - - +
577C LEU* 3.7 9.2 - - + +
581C VAL* 3.8 21.5 - - + +
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Residues in contact with PHE 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE* 3.6 11.9 - - + -
420C TYR* 3.9 29.6 - + + -
421C ILE* 4.4 6.5 - - + -
424C TYR* 3.6 36.1 - + + -
477C LEU* 3.7 28.9 - - + -
546C VAL* 3.7 19.1 - - + -
547C THR 4.2 3.1 - - - -
548C TRP* 3.2 23.1 + - + +
550C ASP* 1.3 80.3 - - - +
552C TYR* 1.3 57.9 + - - +
554C GLU* 3.2 3.8 + - - +
555C ILE* 2.9 32.6 + - - +
581C VAL* 3.7 18.6 - - + -
584C ILE* 4.1 8.1 - - + -
587C VAL* 4.0 17.3 - - + -
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Residues in contact with TYR 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 4.2 4.4 + - - +
417C ILE* 3.8 34.0 - - + +
464C SER* 5.2 0.9 + - - -
465C LEU* 4.0 15.3 - - + +
492C VAL* 3.6 41.5 - - + -
495C LEU* 3.9 11.2 - - + -
496C ASP* 2.8 34.1 + - + -
548C TRP* 2.9 16.7 + + - +
549C ALA* 3.6 8.7 - - - +
550C ASP 3.2 0.4 - - - -
551C PHE* 1.3 78.1 - - - +
553C TRP* 1.3 56.7 + - - +
555C ILE* 3.8 6.4 - - + +
556C CYS* 2.9 52.2 + - - -
3601C O16 3.1 29.6 - + - -
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Residues in contact with TRP 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C LEU* 3.6 20.1 - - + +
528C MET* 3.5 33.4 - - + -
531C LEU* 3.6 27.6 - - + -
541C LEU* 4.0 15.0 - - + -
549C ALA 3.0 14.2 + - - +
550C ASP* 3.2 8.3 + - - +
552C TYR* 1.3 75.2 - - - +
554C GLU* 1.3 54.1 + - - +
556C CYS* 4.7 1.8 - - + -
557C SER* 2.6 65.8 + - - -
560C LEU* 5.5 3.1 - - + -
567C LEU* 5.1 1.3 - - + -
568C LEU* 3.8 20.2 - - + -
574C LEU* 3.3 41.0 + - + +
577C LEU* 3.7 27.9 - - + +
578C ARG* 3.6 11.0 - - + +
581C VAL* 6.0 0.2 - - + -
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Residues in contact with GLU 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C TYR* 2.6 36.8 + - - -
550C ASP 3.0 12.0 + - - +
551C PHE 3.2 6.3 + - - +
553C TRP* 1.3 79.4 - - + +
555C ILE* 1.3 57.0 + - - +
557C SER* 3.5 5.4 - - - -
558C THR* 2.9 44.2 + - - -
578C ARG* 3.2 26.3 + - + +
581C VAL* 4.0 18.2 - - + -
582C GLN* 2.9 39.6 + - + +
591C ILE* 4.0 4.9 - - - +
594C ARG* 5.4 1.9 + - - -
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Residues in contact with ILE 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ARG* 5.4 5.9 + - + +
413C GLY 4.5 2.9 - - - +
416C GLU* 3.7 23.3 - - + -
417C ILE* 3.4 42.0 - - + +
420C TYR* 3.5 38.4 - - + +
551C PHE 2.9 20.5 + - - +
552C TYR* 3.8 9.2 - - + +
554C GLU* 1.3 76.5 - - - +
556C CYS* 1.3 67.1 + - - +
558C THR* 3.3 13.3 + - - -
559C THR* 3.4 14.5 + - - +
3601C O16 4.4 19.1 - - + -
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Residues in contact with CYS 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C LEU* 4.2 14.4 - - + -
499C MET* 3.6 28.4 - - - +
552C TYR* 2.9 46.1 + - - +
553C TRP* 4.1 5.4 - - + +
555C ILE* 1.3 72.9 - - - +
557C SER* 1.3 63.2 + - - +
559C THR* 3.2 6.4 + - - -
560C LEU* 3.0 29.0 + - + +
3601C O16 3.5 28.5 - - - -
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Residues in contact with SER 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C TRP* 2.6 55.3 + - - -
554C GLU 3.3 0.9 + - - -
556C CYS* 1.3 74.0 - - - +
558C THR* 1.3 64.8 + - - +
560C LEU* 4.4 8.5 - - - +
561C LEU* 2.9 32.7 + - - +
567C LEU* 5.0 3.4 - - - -
568C LEU* 4.8 2.2 - - - -
578C ARG* 2.9 38.0 + - - +
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Residues in contact with THR 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ARG* 4.0 27.4 - - - +
420C TYR* 5.2 1.0 + - - -
554C GLU* 2.9 36.2 + - - -
555C ILE* 3.6 7.2 - - - -
556C CYS 3.2 0.4 - - - -
557C SER* 1.3 78.8 + - - +
559C THR* 1.3 63.4 + - - +
561C LEU* 3.6 4.9 + - - +
562C VAL* 3.5 19.0 + - + +
578C ARG* 3.1 20.6 + - - +
582C GLN* 4.4 0.2 + - - -
594C ARG* 4.8 11.2 + - - +
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Residues in contact with THR 559 (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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412C ARG* 3.2 21.5 + - - +
413C GLY* 6.1 0.2 - - - -
499C MET* 4.3 9.6 - - + -
504C TRP* 3.8 28.7 - - + -
555C ILE* 3.4 10.1 + - - +
556C CYS 3.2 8.3 + - - -
558C THR* 1.3 77.0 - - - +
560C LEU* 1.3 66.3 + - - +
561C LEU 3.2 0.4 - - - -
562C VAL* 3.0 24.3 + - - +
563C PHE* 3.4 8.5 - - + -
599C LEU* 4.0 25.0 + - + -
3601C O16 5.1 10.5 - - + +
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Residues in contact with LEU 560 (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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498C PHE* 4.1 18.8 - - + -
499C MET* 3.8 30.5 - - + -
502C PHE* 3.8 32.3 - - + -
504C TRP* 5.4 2.5 - - + -
520C LEU* 4.1 10.8 - - + +
527C LEU* 6.0 0.2 - - + -
528C MET* 4.9 9.9 - - + -
553C TRP* 5.5 2.7 - - + -
556C CYS* 3.0 22.6 + - + +
557C SER* 4.1 4.3 - - - +
559C THR* 1.3 78.5 - - + +
561C LEU* 1.3 58.0 + - - +
563C PHE* 3.1 9.7 + - + +
564C LYS* 2.9 29.3 + - - +
567C LEU* 3.7 25.8 - - + -
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Residues in contact with LEU 561 (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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557C SER 2.9 25.3 + - - +
558C THR* 3.8 6.3 - - - +
559C THR 3.2 0.2 - - - -
560C LEU* 1.3 74.8 - - - +
562C VAL* 1.3 66.6 + - - +
564C LYS 3.7 8.3 - - - +
565C PRO* 3.3 49.2 - - + +
567C LEU* 4.0 0.9 - - + -
568C LEU* 3.4 33.4 - - + +
578C ARG* 3.5 38.1 - - - +
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Residues in contact with VAL 562 (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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412C ARG* 4.7 2.7 - - - +
558C THR* 3.5 17.5 - - + +
559C THR* 3.0 15.5 + - - +
561C LEU* 1.3 81.0 - - + +
563C PHE* 1.3 78.9 + - + +
565C PRO* 4.5 6.6 - - - +
598C LYS* 3.9 49.6 - - + +
599C LEU* 5.3 0.4 - - + -
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Residues in contact with PHE 563 (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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502C PHE* 6.4 0.2 - + - -
504C TRP* 4.3 3.4 - + - -
512C LYS* 6.1 2.2 - - - -
516C PHE* 3.7 45.3 - + + -
517C ASN* 4.8 9.7 - - - +
520C LEU* 4.6 12.3 - - + +
559C THR* 3.4 23.6 - - + -
560C LEU* 3.1 9.0 + - + +
562C VAL* 1.3 90.7 - - + +
564C LYS* 1.3 62.0 + - - +
565C PRO* 3.7 6.0 - - - +
598C LYS* 5.8 3.1 - - + -
599C LEU* 3.6 38.1 - - + -
793D ARG* 5.8 9.2 + - - +
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Residues in contact with LYS 564 (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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517C ASN* 6.1 1.3 - - - +
520C LEU* 3.7 48.7 - - + +
521C THR* 3.2 27.1 + - - +
560C LEU 2.9 8.0 + - - +
561C LEU* 3.5 9.2 - - - -
563C PHE* 1.3 83.0 - - - +
565C PRO* 1.3 67.7 - - + +
566C ASP* 3.2 28.6 + - - +
567C LEU* 3.0 31.5 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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