Contacts of the strand formed by residues 467 - 474 (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 SER 467 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C PHE* 3.6 4.9 - - - -
411C PHE* 2.8 35.6 + - - +
447C PHE* 4.0 2.5 - - - -
453C SER* 5.3 0.3 + - - -
455C SER* 3.6 25.1 - - - -
456C PHE* 3.9 13.5 - - - -
465C ILE 3.7 0.2 + - - -
466C ALA* 1.3 75.8 - - - +
468C GLY* 1.3 60.5 + - - +
204E PRO* 3.2 27.7 - - - +
205E GLN 3.3 11.2 + - - -
206E GLN* 4.2 5.2 + - - +
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Residues in contact with GLY 468 (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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409C LEU 3.9 4.9 - - - -
410C PHE* 3.3 5.8 - - - -
447C PHE* 4.0 17.5 - - - -
467C SER* 1.3 78.4 + - - +
469C CYS* 1.3 65.8 + - - -
470C PRO* 3.5 6.0 - - - +
204E PRO* 3.8 8.6 - - - +
205E GLN* 2.7 33.0 + - - +
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Residues in contact with CYS 469 (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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409C LEU 2.9 34.2 + - - +
410C PHE* 4.3 2.0 - - - -
432C LEU* 4.2 18.8 - - - -
445C ASP* 3.3 37.9 - - - +
446C ALA 5.1 2.5 - - - -
447C PHE* 4.5 11.4 - - - -
468C GLY* 1.3 77.5 - - - -
470C PRO* 1.3 67.6 - - - +
471C LEU 3.1 2.4 + - - +
472C PHE* 3.3 23.0 + - + +
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Residues in contact with PRO 470 (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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399C ASP* 3.7 15.5 - - - +
400C GLY* 5.4 0.7 - - - -
401C THR* 3.4 21.8 - - - +
402C GLY* 3.6 10.4 - - - -
406C HIS* 3.7 3.3 - - - +
408C SER* 2.6 31.7 + - - +
410C PHE* 4.0 14.1 - - + -
468C GLY 3.5 8.5 - - - +
469C CYS* 1.3 83.6 - - - +
471C LEU* 1.3 59.8 + - + +
472C PHE 3.4 2.0 + - - -
205E GLN* 3.4 40.6 - - + +
206E GLN 5.3 1.3 - - - +
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Residues in contact with LEU 471 (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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401C THR* 3.5 25.8 - - - +
402C GLY* 3.5 28.7 - - - -
406C HIS* 3.7 34.6 + - + +
445C ASP* 5.6 0.9 - - - +
469C CYS* 3.1 3.2 - - - +
470C PRO* 1.3 79.9 - - + +
472C PHE* 1.3 64.6 + - - +
473C CYS 3.5 2.8 + - - -
474C PRO* 5.5 0.3 - - - +
205E GLN* 5.6 2.2 - - - +
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Residues in contact with PHE 472 (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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407C LEU* 3.2 22.4 + - + +
409C LEU* 3.9 30.3 - - + +
432C LEU* 3.5 41.7 - - + -
433C MET* 3.7 8.1 - - - -
434C LEU* 3.8 25.4 - - + -
443C VAL* 3.7 24.4 - - + +
444C ILE 4.5 1.3 - - - -
445C ASP* 3.8 29.5 - - + +
469C CYS* 3.3 28.1 + - + +
471C LEU* 1.3 78.3 - - - +
473C CYS* 1.3 68.4 + - + +
474C PRO* 4.7 1.3 - - - +
492C ILE* 5.0 1.6 - - + -
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Residues in contact with CYS 473 (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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406C HIS* 3.3 4.0 - - - -
407C LEU* 2.5 46.1 + - + +
434C LEU* 3.8 23.3 - - + -
443C VAL* 4.1 8.5 - - + -
471C LEU 3.5 0.6 - - - -
472C PHE* 1.3 93.5 - - + +
474C PRO* 1.3 84.2 - - - +
477C LYS* 3.8 21.8 - - - -
478C MET* 3.9 8.1 - - - -
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Residues in contact with PRO 474 (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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405C THR 3.6 9.0 - - - +
406C HIS* 3.7 23.6 - - + +
472C PHE 4.7 1.1 - - - +
473C CYS* 1.3 90.7 - - - +
475C VAL* 1.3 60.3 + - - +
476C SER* 3.8 16.8 - - - +
477C LYS* 2.9 34.8 + - + +
478C MET* 3.2 10.0 + - - +
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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
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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