Contacts of the helix formed by residues 411 - 425 (chain C) in PDB entry 4CFE
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 LYS 411 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C SER* 1.3 75.4 - - - +
412C PRO* 1.3 77.7 - - + +
413C TYR* 3.2 4.9 - - + +
414C ASP* 3.1 39.2 + - + +
415C ILE* 3.1 17.2 + - - +
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Residues in contact with PRO 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C SER 3.6 0.2 - - - -
411C LYS* 1.3 92.2 - - + +
413C TYR* 1.3 62.1 + - - +
415C ILE* 3.4 13.3 + - + +
416C MET* 3.3 27.2 + - - +
436C TYR* 3.7 29.8 - - + +
457C LEU* 4.2 5.0 - - + +
465C TYR* 3.2 39.3 - - + +
203D PRO* 4.9 6.7 - - + -
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Residues in contact with TYR 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LYS* 3.2 4.9 - - + -
412C PRO* 1.3 78.8 - - - +
414C ASP* 1.3 76.1 + - - +
416C MET* 3.4 5.9 + - + +
417C ALA* 2.9 43.0 + - + +
436C TYR* 5.1 1.7 + - - -
194D CYS 5.4 7.4 - - - -
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Residues in contact with ASP 414 (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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410C SER* 4.4 10.1 - - - +
411C LYS* 3.1 39.1 + - + +
413C TYR* 1.3 91.9 - - - +
415C ILE* 1.3 58.2 + - - +
417C ALA* 3.4 6.1 + - - +
418C GLU* 2.8 30.1 + - - +
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Residues in contact with ILE 415 (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 SER* 3.7 29.2 - - - +
410C SER* 3.5 15.5 - - - +
411C LYS 3.1 15.2 + - - +
412C PRO* 3.7 6.1 - - + +
413C TYR 3.3 0.2 - - - -
414C ASP* 1.3 76.1 - - - +
416C MET* 1.3 70.3 + - + +
418C GLU* 3.0 6.9 + - + +
419C VAL* 2.8 43.3 + - + +
457C LEU* 4.2 18.6 - - + -
465C TYR* 3.9 27.1 - - + -
467C LEU* 5.5 6.5 - - + -
550C LEU* 6.3 0.4 - - + -
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Residues in contact with MET 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C PRO 3.3 15.9 + - - +
413C TYR* 3.8 8.3 - - + +
415C ILE* 1.3 87.8 - - + +
417C ALA* 1.3 61.3 + - - +
419C VAL* 3.2 12.9 - - + +
420C TYR* 3.0 45.2 + - + -
435C ALA 3.7 25.1 - - - +
436C TYR* 4.1 13.9 - - + -
438C LEU* 4.0 24.0 - - + -
457C LEU* 3.7 34.8 - - + +
467C LEU* 4.5 11.2 - - + -
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Residues in contact with ALA 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C TYR* 2.9 39.4 + - + +
414C ASP* 3.7 8.3 - - - +
415C ILE 3.2 0.2 - - - -
416C MET* 1.3 76.8 - - - +
418C GLU* 1.3 61.1 + - - +
420C TYR* 3.8 10.1 + - - +
421C ARG* 3.6 20.4 + - - +
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Residues in contact with GLU 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 ASP 2.8 18.2 + - - +
415C ILE* 3.0 9.4 + - + +
417C ALA* 1.3 76.0 - - - +
419C VAL* 1.3 63.3 + - + +
420C TYR 3.2 2.0 - - - -
421C ARG* 2.8 63.8 + - - +
422C ALA* 3.2 8.7 + - - +
549C THR 4.8 1.7 - - - +
550C LEU* 3.6 24.1 - - + +
551C ALA* 4.6 15.2 + - + +
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Residues in contact with VAL 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 ILE* 2.8 30.8 + - + +
416C MET* 3.2 32.8 - - + +
418C GLU* 1.3 72.1 - - + +
420C TYR* 1.3 71.6 + - + +
422C ALA* 3.5 4.0 + - - +
423C MET* 3.1 40.7 + - + +
438C LEU* 5.0 2.2 - - + -
455C LEU* 5.5 2.7 - - + -
467C LEU* 4.0 20.0 - - + -
546C LEU* 4.7 4.2 - - + +
550C LEU* 3.9 32.1 - - + -
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Residues in contact with TYR 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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416C MET* 3.0 35.1 + - + +
417C ALA* 3.9 9.2 - - - +
418C GLU 3.2 0.2 - - - -
419C VAL* 1.3 84.1 - - + +
421C ARG* 1.3 64.0 + - - +
422C ALA 3.4 0.5 + - - -
423C MET* 3.4 14.9 + - + +
424C LYS* 3.6 20.4 + - - +
430C TRP* 3.4 39.7 - + + -
432C VAL* 5.1 5.0 - - - +
434C ASN 5.2 0.9 + - - -
435C ALA* 4.6 9.4 + - - -
438C LEU* 3.6 37.7 - - + +
192D TYR 4.7 5.4 - - - +
193D VAL* 3.9 11.2 - - + +
194D CYS 3.4 34.7 + - - -
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Residues in contact with ARG 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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417C ALA 3.6 11.0 + - - +
418C GLU* 2.8 48.5 + - - +
420C TYR* 1.3 77.3 - - - +
422C ALA* 1.3 62.6 + - - +
424C LYS* 3.5 29.9 + - + +
425C GLN* 3.7 31.7 + - - +
549C THR 5.6 3.2 + - - -
551C ALA* 5.4 4.6 - - - +
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Residues in contact with ALA 422 (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* 3.2 17.6 + - - +
419C VAL 3.6 6.7 - - - +
420C TYR 3.1 0.4 - - - -
421C ARG* 1.3 82.3 - - + +
423C MET* 1.3 61.2 + - - +
424C LYS 3.6 0.2 + - - -
425C GLN* 3.7 11.2 + - - +
426C LEU* 3.6 23.9 - - - +
546C LEU* 3.8 13.7 - - + -
549C THR* 3.5 26.1 + - - +
550C LEU* 3.8 13.7 - - + -
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Residues in contact with MET 423 (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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419C VAL* 3.1 32.9 + - + +
420C TYR* 3.4 11.2 + - + +
421C ARG 3.3 0.4 - - - -
422C ALA* 1.3 76.2 - - - +
424C LYS* 1.3 60.5 + - - +
425C GLN 3.4 0.2 - - - -
426C LEU 3.4 1.2 + - - +
427C ASP* 3.0 8.7 + - - -
428C PHE* 2.9 56.2 + - + +
430C TRP* 3.3 41.5 - - - +
438C LEU* 4.6 7.9 - - + -
440C VAL* 3.6 15.5 - - + -
455C LEU* 3.6 31.0 - - + -
546C LEU* 4.4 7.4 - - + -
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Residues in contact with LYS 424 (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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420C TYR* 3.6 21.1 + - - +
421C ARG* 3.5 18.2 + - + +
423C MET* 1.3 79.0 - - - +
425C GLN* 1.3 61.9 + - + +
426C LEU 3.1 1.3 + - - -
427C ASP* 3.3 19.4 + - - +
430C TRP* 5.8 0.4 - - - -
192D TYR* 4.1 31.0 + - + +
193D VAL 5.0 3.0 + - - -
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Residues in contact with GLN 425 (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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421C ARG* 3.7 37.5 + - - +
422C ALA* 3.7 10.6 + - - +
423C MET 3.4 0.6 - - - -
424C LYS* 1.3 78.4 - - + +
426C LEU* 1.3 69.0 + - + +
427C ASP* 3.5 1.5 - - - +
549C THR* 4.4 19.6 - - + +
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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
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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