Contacts of the strand formed by residues 467 - 474 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B PHE* 3.5 9.0 - - - -
411B PHE* 2.9 30.8 + - - +
447B PHE* 3.9 4.2 - - - -
453B SER* 5.6 1.1 - - - -
455B SER* 3.8 14.2 - - - -
456B PHE* 3.0 34.4 - - - -
465B ILE 3.9 0.4 + - - -
466B ALA* 1.3 77.0 - - - +
468B GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B LEU 3.9 4.3 - - - -
410B PHE* 3.3 10.7 - - - -
432B LEU* 5.2 0.2 - - - -
447B PHE* 4.0 21.7 - - - +
467B SER* 1.3 77.6 - - - +
469B CYS* 1.3 66.0 + - - -
470B PRO* 3.5 10.6 - - - +
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Residues in contact with CYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B LEU 2.9 31.7 + - - +
410B PHE* 4.2 1.7 - - - -
432B LEU* 4.2 20.9 - - - -
445B ASP* 3.6 35.2 - - - +
446B ALA 5.3 0.7 - - - -
447B PHE* 4.4 12.1 - - - -
468B GLY* 1.3 78.6 - - - -
470B PRO* 1.3 68.0 - - - +
471B LEU 3.1 3.2 + - - +
472B PHE* 3.3 23.2 + - + +
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Residues in contact with PRO 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B ASP* 4.0 13.0 - - - +
400B GLY* 5.6 0.4 - - - -
401B THR* 3.4 25.4 - - + +
402B GLY* 3.6 12.0 - - - -
406B HIS* 3.9 2.3 - - - +
408B SER* 2.6 31.9 + - - +
410B PHE* 3.9 17.4 - - + -
468B GLY 3.5 10.5 - - - +
469B CYS* 1.3 83.3 - - - +
471B LEU* 1.3 61.7 + - + +
472B PHE 3.5 0.6 + - - -
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B THR* 3.6 21.1 - - - +
402B GLY* 3.4 35.7 - - - +
406B HIS* 3.5 34.2 + - + +
445B ASP* 5.4 1.8 - - - +
469B CYS* 3.1 2.8 - - - -
470B PRO* 1.3 81.5 - - + +
472B PHE* 1.3 63.0 + - - +
473B CYS 3.4 2.9 + - - -
474B PRO* 5.7 0.3 - - - +
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Residues in contact with PHE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B LEU* 3.2 24.3 + - + +
409B LEU* 3.9 31.0 - - + +
432B LEU* 3.5 34.5 - - + -
433B MET* 3.7 14.1 - - - -
434B LEU* 3.8 25.8 - - + -
443B VAL* 3.6 24.4 - - + +
445B ASP* 3.8 29.1 - - + +
469B CYS* 3.3 26.1 + - + +
471B LEU* 1.3 77.4 - - - +
473B CYS* 1.3 68.2 + - + +
474B PRO* 4.8 0.5 - - - +
492B ILE* 5.0 1.8 - - + -
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Residues in contact with CYS 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B HIS* 3.2 4.7 - - - -
407B LEU* 2.6 44.5 + - + +
434B LEU* 4.0 14.4 - - + -
443B VAL* 4.0 24.5 - - + -
471B LEU 3.4 1.2 - - - -
472B PHE* 1.3 94.8 - - + +
474B PRO* 1.3 87.0 - - - +
477B LYS* 4.0 13.5 - - - -
478B MET* 4.0 8.1 - - - -
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Residues in contact with PRO 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B THR 3.6 4.9 - - - +
406B HIS* 3.5 27.6 - - + +
471B LEU 5.7 0.2 - - - +
472B PHE 4.8 0.9 - - - +
473B CYS* 1.3 91.7 - - - +
475B VAL* 1.3 66.8 + - - +
476B SER* 3.7 17.0 - - - +
477B LYS* 2.9 27.5 + - + +
478B MET* 3.2 9.7 + - - +
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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