Contacts of the strand formed by residues 406 - 414 (chain C) in PDB entry 1CZY
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 HIS 406 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C ASN 3.3 2.6 - - - -
398C GLY* 2.8 32.6 + - - -
402C GLY 2.8 7.6 + - - +
405C THR* 1.3 114.6 + - - +
407C LEU* 1.3 62.8 + - - +
408C SER 3.6 0.2 - - - -
470C PRO 3.7 17.9 - - - +
471C LEU* 3.7 43.8 + - + +
473C CYS 3.3 6.9 - - - +
474C PRO* 3.6 32.5 - - + +
475C VAL* 3.8 6.4 - - - +
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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
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394C ILE* 3.3 38.6 - - + -
395C TYR 3.7 2.0 - - - +
396C LEU* 3.5 33.7 - - + -
406C HIS* 1.3 72.7 - - - +
408C SER* 1.3 58.9 + - - +
409C LEU* 5.6 0.2 - - + -
434C LEU* 4.3 24.0 - - + -
472C PHE* 3.2 34.5 + - + +
473C CYS* 2.5 28.2 + - + +
475C VAL* 4.2 2.0 - - + +
478C MET* 3.2 34.8 - - + -
490C ILE* 5.1 0.4 - - + -
492C ILE* 4.8 1.3 - - + -
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Residues in contact with SER 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ILE* 3.3 5.9 - - - +
395C TYR* 2.8 40.0 + - - -
398C GLY* 3.1 6.6 - - - -
399C ASP* 2.7 33.8 + - - -
402C GLY* 4.2 0.3 - - - -
406C HIS 3.5 0.4 + - - -
407C LEU* 1.3 71.7 - - - +
409C LEU* 1.3 59.7 + - - +
410C PHE* 3.5 20.0 - - - -
469C CYS 3.6 4.7 - - - -
470C PRO* 2.6 24.7 + - - -
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Residues in contact with LEU 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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356C TRP* 5.2 0.7 - - + -
392C LEU* 4.2 19.5 - - + -
393C ARG 3.7 8.7 - - - +
394C ILE* 4.3 16.8 - - + -
407C LEU 4.0 0.6 + - - -
408C SER* 1.3 73.2 - - - +
410C PHE* 1.3 86.6 + - - +
432C LEU* 3.9 29.6 - - + +
433C MET 4.8 0.2 - - - +
468C GLY* 3.9 0.5 - - - -
469C CYS* 2.9 33.3 + - - +
472C PHE* 3.9 38.3 - - + +
492C ILE* 3.8 27.6 - - + -
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Residues in contact with PHE 410 (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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392C LEU* 3.4 6.8 - - - +
393C ARG* 2.7 45.5 + - + +
395C TYR* 3.6 24.9 - + - -
399C ASP* 3.7 19.5 - - + -
408C SER* 3.5 23.8 - - - -
409C LEU* 1.3 81.0 - - - +
411C PHE* 1.3 60.1 + - - +
432C LEU* 4.9 2.2 - - - -
466C ALA* 3.6 17.5 - - + -
467C SER* 3.6 6.3 - - - +
468C GLY* 3.3 21.5 - - - -
470C PRO* 4.0 30.5 - - + -
205E GLN 3.4 17.0 - - - -
206E GLN 3.9 2.5 - - - -
207E ALA* 3.7 22.0 - - + -
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Residues in contact with PHE 411 (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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381C PHE* 4.4 4.3 - + - -
390C MET* 3.3 48.9 - - + -
391C CYS 3.9 2.5 - - - -
392C LEU* 4.1 16.4 - - + -
410C PHE* 1.3 73.4 - - - +
412C VAL* 1.3 64.4 + - - +
413C VAL* 3.7 20.4 + - + -
426C PHE* 3.6 29.6 - + - -
430C VAL* 4.0 26.2 - - + -
432C LEU* 5.0 2.0 - - + +
447C PHE* 3.7 17.5 - + + -
456C PHE* 4.2 16.1 - + - -
465C ILE 4.7 0.5 - - - +
466C ALA* 3.4 3.3 - - - -
467C SER* 2.8 36.2 + - - +
468C GLY* 4.6 0.4 - - - -
496C VAL* 4.1 8.3 - - + -
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Residues in contact with VAL 412 (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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377C PHE* 4.2 6.3 - - + -
390C MET* 3.2 9.5 - - - +
391C CYS* 2.8 58.9 + - - +
393C ARG* 4.0 18.6 - - + +
411C PHE* 1.3 83.3 - - - +
413C VAL* 1.3 75.8 + - - +
414C MET* 3.6 1.5 + - + -
463C MET* 4.0 16.8 - - + -
464C ASN 3.8 16.4 - - - +
465C ILE 5.4 0.9 - - - -
466C ALA* 3.6 22.7 - - + +
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Residues in contact with VAL 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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388C TYR* 5.3 2.7 - - + -
389C LYS 3.9 6.7 - - - +
390C MET* 4.8 0.9 - - + +
411C PHE* 3.7 24.9 - - + -
412C VAL* 1.3 73.5 - - - +
414C MET* 1.3 64.0 + - - +
424C TRP* 3.9 22.7 - - + -
426C PHE* 4.2 14.4 - - + -
455C SER 3.6 25.3 + - - +
456C PHE* 4.2 11.7 - - + -
457C GLN 4.7 0.2 - - - +
459C PRO* 3.7 19.9 - - + +
464C ASN* 3.0 32.9 + - - +
465C ILE 5.5 0.8 + - - -
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Residues in contact with MET 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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380C ALA* 3.0 25.6 - - + -
389C LYS* 2.9 46.0 + - + +
390C MET 2.9 33.0 - - - +
391C CYS* 3.5 27.1 - - + -
412C VAL* 4.1 2.9 - - + +
413C VAL* 1.3 79.2 - - - +
415C LYS* 1.3 66.1 + - - +
416C GLY 3.1 4.0 + - - -
419C ASP* 3.9 2.6 - - - +
424C TRP* 5.1 0.9 - - - -
459C PRO* 3.5 11.4 - - - +
462C ASP* 3.5 11.4 - - - +
463C MET* 4.0 24.9 - - + -
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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