Contacts of the helix formed by residues 405 - 421 (chain C) in PDB entry 4WCX
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 PHE 405 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C ARG* 6.3 0.4 - - - -
396C PHE* 3.6 38.8 - + + -
401C GLN* 3.3 47.6 - - + +
402C ILE 3.2 3.6 + - - +
403C HIS 3.4 0.2 - - - -
404C ASN* 1.3 83.9 - - + +
406C CYS* 1.3 61.9 + - - +
407C LEU 3.4 1.1 - - - -
408C PRO* 3.5 2.9 - - - +
409C ASN* 2.9 39.5 + - - +
466C PHE* 3.8 39.9 - + + -
502C SF4 5.2 0.2 - - - -
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Residues in contact with CYS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.7 22.4 - - - +
396C PHE* 4.2 4.3 - - - -
402C ILE* 2.8 43.6 + - - +
405C PHE* 1.3 72.4 - - - +
407C LEU* 1.3 60.9 + - - +
409C ASN* 3.7 1.6 - - - +
410C ALA* 2.8 31.9 + - - +
502C SF4 2.2 59.2 - - - -
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASN* 4.6 5.2 - - - +
77C ARG* 4.0 20.8 - - + +
376C LEU* 3.8 22.9 - - + -
402C ILE 3.9 2.0 + - - -
403C HIS* 3.4 19.5 - - + +
406C CYS* 1.3 76.0 - - - +
408C PRO* 1.3 72.8 - - + +
410C ALA* 3.2 1.9 + - - +
411C ILE* 2.9 36.8 + - + +
437C ASN* 3.9 14.1 - - + +
440C LYS* 3.8 41.5 - - + +
441C ILE* 3.8 16.4 - - + +
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Residues in contact with PRO 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C HIS 3.1 18.4 - - - +
404C ASN 3.5 17.5 - - - +
405C PHE 3.5 9.2 - - - +
407C LEU* 1.3 91.1 - - + +
409C ASN* 1.3 57.9 + - - +
411C ILE* 3.2 4.4 + - + +
412C LEU* 2.8 35.6 + - - +
441C ILE* 3.9 9.0 - - + -
446C VAL* 3.7 15.7 - - + -
450C THR* 3.5 26.2 - - + +
466C PHE* 3.5 19.3 - - + -
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Residues in contact with ASN 409 (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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380C CYS* 3.5 18.4 - - - -
382C ALA* 4.1 7.3 - - - +
405C PHE* 2.9 27.4 + - - +
406C CYS* 3.8 3.6 - - - +
408C PRO* 1.3 75.2 - - - +
410C ALA* 1.3 59.3 + - - +
412C LEU* 3.9 4.5 - - - +
413C THR* 2.9 36.7 + - - +
465C TYR* 3.4 14.1 - - + -
466C PHE* 2.8 51.4 + - - -
502C SF4 3.6 20.6 - - - -
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Residues in contact with ALA 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.1 9.2 - - + -
376C LEU* 3.8 19.1 - - + -
377C PRO 4.3 2.9 - - - +
378C SER* 3.7 30.3 - - - +
380C CYS* 4.5 2.2 - - + +
406C CYS 2.8 22.1 + - - +
407C LEU 3.7 3.4 - - - +
409C ASN* 1.3 72.9 - - - +
411C ILE* 1.3 57.8 + - - +
413C THR* 2.9 19.8 + - - -
414C PHE* 2.9 20.3 + - - +
502C SF4 5.4 0.2 - - - -
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Residues in contact with ILE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C LEU* 3.9 19.1 - - + -
407C LEU* 2.9 30.3 + - + +
408C PRO* 3.4 7.6 - - + +
410C ALA* 1.3 76.3 - - - +
412C LEU* 1.3 62.8 + - - +
414C PHE* 3.2 6.9 + - - +
415C LYS* 3.0 21.3 + - - +
434C ILE* 3.9 28.3 - - + +
437C ASN* 3.8 5.4 - - + +
438C LEU* 3.7 35.7 - - + +
441C ILE* 4.0 14.4 - - + -
450C THR* 4.2 8.3 - - + -
454C LEU* 4.1 16.8 - - + -
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PRO 2.8 24.3 + - - +
409C ASN* 4.0 6.1 - - - +
411C ILE* 1.3 71.4 - - - +
413C THR* 1.3 63.6 + - - +
415C LYS* 3.2 5.7 + - - +
416C GLU* 3.1 27.0 + - - +
450C THR* 3.8 22.9 - - + +
453C ARG* 3.9 12.3 - - + -
454C LEU* 3.7 22.9 - - + -
457C ILE* 3.9 19.8 - - + +
464C LEU* 3.4 29.8 - - + +
465C TYR* 4.5 10.1 - - + -
466C PHE* 4.0 22.2 - - + -
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Residues in contact with THR 413 (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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379C TYR* 4.0 16.5 + - - +
380C CYS* 3.7 33.1 + - + -
381C THR 5.2 0.4 - - - +
409C ASN 2.9 15.9 + - - +
410C ALA* 2.9 23.7 + - - -
412C LEU* 1.3 74.4 - - - +
414C PHE* 1.3 56.4 + - - +
416C GLU* 3.4 6.5 + - - +
417C PHE* 3.0 25.8 + - - +
465C TYR* 3.1 36.8 - - + +
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Residues in contact with PHE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 4.9 5.6 - - + -
371C CYS* 3.9 25.1 - - - -
376C LEU* 3.8 18.6 - - + -
377C PRO* 3.9 34.5 - - + +
379C TYR* 4.5 9.2 - + - -
410C ALA 2.9 19.5 + - - +
411C ILE 3.6 5.2 - - - +
412C LEU 3.1 0.6 - - - -
413C THR* 1.3 75.5 + - - +
415C LYS* 1.3 61.5 + - - +
417C PHE* 3.2 30.9 + + - +
418C LEU* 2.9 40.6 + - + +
426C THR* 5.6 2.0 - - + -
430C GLY* 3.6 31.0 - - - -
433C ALA* 4.3 3.6 - - + -
434C ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ILE 3.0 7.6 + - - +
412C LEU 3.2 6.9 + - - +
414C PHE* 1.3 78.4 - - - +
416C GLU* 1.3 63.9 + - - +
418C LEU* 3.1 9.2 + - + +
419C ILE* 3.1 37.1 + - + +
431C GLU* 4.1 22.1 + - + +
434C ILE* 3.9 19.9 - - + +
454C LEU* 3.5 35.0 - - + -
457C ILE* 3.8 17.3 - - + -
458C GLU* 3.0 41.7 + - - +
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Residues in contact with GLU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ARG* 5.4 2.9 + - - -
412C LEU 3.1 14.7 + - - +
413C THR* 3.4 7.4 + - - +
415C LYS* 1.3 75.9 - - - +
417C PHE* 1.3 56.8 + - - +
419C ILE* 3.9 1.7 - - - -
420C ASP* 2.8 41.4 + - - +
421C TYR* 5.4 0.2 - - - -
457C ILE* 4.0 24.4 - - + +
462C ARG* 3.3 34.1 - - - +
463C ASP* 2.8 32.7 + - - +
464C LEU 4.5 0.5 + - - -
465C TYR* 3.2 24.0 + - - -
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Residues in contact with PHE 417 (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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125C MET 3.4 24.7 - - - -
126C GLY* 3.9 19.7 - - - +
128C LYS* 5.8 2.2 - - - +
364C ASN* 4.5 8.3 - - - -
367C LEU* 3.4 31.6 - - + -
379C TYR* 3.9 24.7 - + + -
413C THR 3.0 15.4 + - - +
414C PHE* 3.4 29.2 - + - +
416C GLU* 1.3 78.3 - - - +
418C LEU* 1.3 75.5 + - + +
421C TYR* 2.7 45.6 + + + -
422C GLY* 3.0 12.2 + - - -
426C THR* 4.2 7.4 - - + -
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Residues in contact with LEU 418 (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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414C PHE* 2.9 32.4 + - + +
415C LYS* 3.1 8.0 + - + +
417C PHE* 1.3 93.8 - - + +
419C ILE* 1.3 60.1 + - + +
422C GLY* 3.1 15.9 + - - +
426C THR* 3.6 34.5 - - + +
427C LYS* 3.1 38.3 - - + +
430C GLY* 3.6 29.2 - - - +
431C GLU* 3.8 11.2 - - + +
434C ILE* 4.1 15.9 - - + -
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Residues in contact with ILE 419 (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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415C LYS* 3.1 36.3 + - + +
416C GLU 4.0 2.5 - - - +
418C LEU* 1.3 79.6 - - + +
420C ASP* 1.3 65.3 + - - +
422C GLY 4.7 1.2 + - - +
427C LYS* 4.3 14.4 + - - +
457C ILE* 3.7 38.1 - - + +
458C GLU* 4.6 6.5 - - + -
462C ARG* 3.4 23.1 - - - +
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Residues in contact with ASP 420 (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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160C ASN* 4.0 25.7 + - + +
416C GLU* 2.8 24.8 + - - +
419C ILE* 1.3 78.0 - - - +
421C TYR* 1.3 87.5 + - + +
462C ARG* 3.0 44.5 + - - -
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Residues in contact with TYR 421 (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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123C GLU 3.0 21.5 + - - -
124C GLU* 3.5 24.9 - - - +
125C MET* 4.5 2.0 - - - -
126C GLY* 3.6 14.4 - - - +
128C LYS* 3.9 18.2 - - - -
158C LEU* 4.8 10.6 - - + +
159C LYS 4.1 4.2 + - - -
160C ASN 3.0 10.7 + - - -
161C GLY* 2.9 35.2 + - - -
364C ASN* 5.7 2.6 + - - +
417C PHE* 2.7 43.1 + + + +
420C ASP* 1.3 97.3 - - + +
422C GLY* 1.3 64.3 + - - +
423C ASP* 3.6 1.6 + - - +
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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