Contacts of the helix formed by residues 463 - 480 (chain C) in PDB entry 2XYN
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 463 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ILE* 3.3 17.8 - - - +
434C MET* 4.1 1.3 - - - -
437C ASP 3.8 18.6 - - - -
438C THR* 4.1 9.2 - - - -
455C GLU* 4.3 5.2 + - - -
461C THR* 4.4 1.5 + - - -
462C PHE* 1.3 77.0 - - - +
464C ILE* 1.3 63.7 + - - +
465C LYS* 2.9 21.8 + - - +
466C SER* 3.0 22.8 + - - -
467C ASP* 3.2 9.0 + - - +
526C PRO* 5.1 1.4 - - - +
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Residues in contact with ILE 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C GLU* 4.8 25.6 - - + +
404C ASN* 6.0 2.0 - - - +
405C PHE 5.1 6.7 - - - +
406C ILE* 3.6 13.0 - - + +
434C MET* 4.0 9.3 - - + +
437C ASP 4.7 0.4 + - - -
463C SER* 1.3 74.5 - - - +
465C LYS* 1.3 58.0 + - - +
467C ASP* 3.2 10.3 + - + +
468C VAL* 3.0 24.8 + - - +
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Residues in contact with LYS 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C SER* 2.9 12.6 + - - +
464C ILE* 1.3 76.5 - - - +
466C SER* 1.3 60.9 + - - +
468C VAL* 3.4 11.3 + - - +
469C TRP 3.2 12.5 + - - -
526C PRO* 3.7 37.2 - - + +
529C ARG* 2.9 22.1 + - + +
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Residues in contact with SER 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C TRP 5.1 0.2 - - - +
453C ALA* 4.1 8.3 + - - +
455C GLU* 4.0 12.3 - - - -
456C SER* 3.8 22.2 - - - -
462C PHE* 4.2 10.5 - - - -
463C SER* 3.0 27.3 + - - -
465C LYS* 1.3 73.0 - - - +
467C ASP* 1.3 68.4 + - - +
468C VAL 3.1 0.2 - - - -
469C TRP* 3.0 13.5 + - - +
470C ALA* 3.1 13.5 + - - +
529C ARG* 4.0 3.1 - - - +
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Residues in contact with ASP 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C MET* 6.5 1.3 - - + -
400C LEU* 5.8 1.2 - - - +
405C PHE 4.7 1.0 - - - +
406C ILE* 3.4 17.0 - - - +
407C HIS* 2.6 34.9 + - - +
408C ARG* 3.1 24.8 + - - -
409C ASP 4.8 0.2 + - - -
410C LEU* 3.6 16.0 - - + +
462C PHE* 6.0 0.7 - - - -
463C SER 3.2 4.4 + - - +
464C ILE* 3.2 12.8 + - - +
466C SER* 1.3 79.6 - - - +
468C VAL* 1.3 54.6 + - - +
470C ALA* 3.4 8.7 + - - +
471C PHE* 2.9 27.9 + - - +
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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
----------------------------------------------------------
464C ILE 3.0 13.7 + - - +
465C LYS* 3.5 14.4 - - - +
466C SER 3.1 0.4 - - - -
467C ASP* 1.3 73.7 - - - +
469C TRP* 1.3 66.9 + - - +
471C PHE* 3.2 10.9 + - - +
472C GLY 3.2 14.2 + - - -
521C CYS* 3.4 17.3 - - + +
529C ARG* 4.6 10.3 - - + -
530C PRO 4.0 20.4 - - - +
532C PHE 5.9 2.5 - - - +
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Residues in contact with TRP 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C LYS 4.6 4.6 + - - -
451C TRP* 3.7 19.2 + - - -
452C THR 3.8 8.3 + - - -
453C ALA* 3.7 18.4 - - + -
454C PRO* 3.5 27.8 - - + -
465C LYS 3.2 8.0 + - - +
466C SER 3.0 10.6 + - - +
468C VAL* 1.3 77.2 - - - +
470C ALA* 1.3 60.3 + - - +
472C GLY* 2.9 19.6 + - - -
473C VAL* 3.3 10.0 + - + +
486C TYR* 4.4 9.5 + - - -
498C LEU* 3.8 40.6 - - + +
521C CYS 3.4 24.4 + - - +
522C TRP* 3.3 51.8 + + + +
523C LYS 3.7 8.3 - - - -
524C TRP* 4.8 1.3 - - - -
529C ARG* 3.5 18.4 - - - +
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Residues in contact with ALA 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.7 32.5 - - + +
451C TRP* 3.6 24.9 - - + +
466C SER 3.1 8.0 + - - +
467C ASP* 3.6 11.4 - - - +
469C TRP* 1.3 76.8 - - - +
471C PHE* 1.3 66.0 + - - +
473C VAL* 2.9 8.2 + - - +
474C LEU* 2.8 23.4 + - - +
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Residues in contact with PHE 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ILE* 6.2 2.5 - - + -
410C LEU* 4.0 15.0 - - + +
467C ASP 2.9 14.2 + - - +
468C VAL* 3.2 14.1 + - - +
470C ALA* 1.3 75.7 - - - +
472C GLY* 1.3 51.8 + - - +
474C LEU* 3.0 13.0 + - + +
475C LEU* 2.7 40.7 + - + +
521C CYS* 5.2 3.8 - - - -
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Residues in contact with GLY 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C VAL 3.2 4.0 + - - -
469C TRP 2.9 10.1 + - - -
471C PHE* 1.3 77.4 - - - +
473C VAL* 1.3 61.0 + - - +
475C LEU* 3.2 10.4 + - - +
476C TRP 3.0 17.0 + - - -
518C MET* 3.5 5.4 - - - +
521C CYS* 3.9 18.3 - - - +
522C TRP* 3.4 23.2 - - - -
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Residues in contact with VAL 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C LYS 4.4 14.1 - - - +
451C TRP* 3.7 25.8 - - + +
469C TRP* 3.3 10.3 + - + +
470C ALA 2.9 10.5 + - - +
472C GLY* 1.3 73.7 - - - +
474C LEU* 1.3 58.6 + - - +
476C TRP* 2.9 9.3 + - - +
477C GLU* 2.9 31.1 + - - +
485C PRO* 5.2 3.8 - - + +
486C TYR* 5.8 0.7 - - + +
504C MET* 4.7 10.5 - - + +
522C TRP* 3.4 13.7 - - - +
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Residues in contact with LEU 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 4.6 4.7 - - + -
393C ILE* 4.0 32.3 - - + -
410C LEU* 4.2 18.4 - - + -
411C ALA* 4.6 8.7 - - - -
412C ALA* 3.5 35.7 - - + +
415C CYS* 4.2 11.7 - - - -
451C TRP* 4.6 0.8 - - - +
470C ALA 2.8 12.1 + - - +
471C PHE* 3.2 11.0 - - - +
473C VAL* 1.3 75.8 - - - +
475C LEU* 1.3 63.0 + - + +
477C GLU* 3.0 11.2 + - - +
478C ILE* 2.9 39.2 + - + +
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Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ALA* 5.1 15.7 - - + -
471C PHE* 2.7 22.2 + - + +
472C GLY* 3.2 11.4 + - - +
474C LEU* 1.3 73.9 - - + +
476C TRP* 1.3 57.7 + - - +
478C ILE* 3.4 10.1 + - + +
479C ALA* 2.9 28.9 + - - +
514C VAL* 5.3 10.7 - - + +
517C LEU* 5.9 7.6 - - + -
518C MET* 4.0 22.6 - - + +
521C CYS* 6.0 3.1 - - - -
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Residues in contact with TRP 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY 5.0 0.2 - - - -
296B GLY* 5.6 2.2 - - - -
297B GLY* 5.3 3.1 - - - -
472C GLY 3.0 8.0 + - - +
473C VAL 2.9 10.4 + - - +
475C LEU* 1.3 73.2 - - - +
477C GLU* 1.3 70.8 + - - +
479C ALA* 3.3 1.8 + - - +
480C THR* 2.9 45.6 + - + +
483C MET* 3.4 38.1 - - + -
484C SER 3.4 26.5 - - - -
485C PRO* 3.7 8.5 - - + -
487C PRO* 4.4 5.2 - - + -
504C MET* 3.6 44.1 - - + +
505C GLU* 3.1 38.4 + - - -
507C PRO* 3.7 17.4 - - + +
518C MET* 3.7 24.8 - - - -
522C TRP* 4.2 1.3 - + + -
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Residues in contact with GLU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 3.6 25.4 - - + +
373C LEU* 4.1 2.4 - - - +
411C ALA* 3.7 0.9 - - - -
412C ALA* 2.9 40.9 + - + +
413C ARG 5.1 0.9 + - - -
451C TRP* 3.0 40.1 + - + +
473C VAL 2.9 19.1 + - - +
474C LEU* 3.3 10.0 - - - +
476C TRP* 1.3 79.9 - - + +
478C ILE* 1.3 59.8 + - - +
480C THR* 3.0 10.8 + - - -
482C GLY* 2.9 29.1 + - - -
483C MET 4.3 13.7 - - - +
485C PRO* 4.5 6.9 - - + +
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Residues in contact with ILE 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 4.2 7.6 - - + -
373C LEU* 3.9 19.0 - - + +
386C LEU* 3.6 50.3 - - + +
389C MET* 4.3 8.5 - - + -
390C ALA* 4.5 19.3 - - + +
393C ILE* 4.0 26.5 - - + -
474C LEU* 2.9 30.9 + - + +
475C LEU* 3.7 9.6 - - + +
477C GLU* 1.3 76.3 - - + +
479C ALA* 1.3 62.7 + - - +
481C TYR* 3.1 13.9 + - - -
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Residues in contact with ALA 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C LEU* 4.3 12.2 - - - +
475C LEU 2.9 17.8 + - - +
476C TRP 3.3 2.4 + - - +
478C ILE* 1.3 75.9 - - - +
480C THR* 1.3 60.1 + - - +
481C TYR* 3.7 10.0 + - - -
507C PRO* 3.7 31.6 - - + +
508C GLU 4.4 7.4 - - - +
510C CYS* 4.3 16.6 + - + +
514C VAL* 6.0 1.3 - - + -
518C MET* 4.3 7.4 - - + -
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Residues in contact with THR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY 5.4 0.7 - - - -
378C ARG* 4.4 5.4 + - - -
476C TRP* 2.9 43.2 + - + +
477C GLU* 3.0 10.0 + - - -
478C ILE 3.1 0.2 - - - -
479C ALA* 1.3 74.8 - - - +
481C TYR* 1.3 71.7 + - - +
482C GLY 3.3 0.3 + - - -
483C MET* 3.1 33.7 + - + +
507C PRO* 3.8 26.0 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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