Contacts of the strand formed by residues 406 - 414 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A ASN* 3.3 2.9 - - - -
398A GLY* 2.8 35.2 + - - -
402A GLY 2.9 9.4 + - - +
405A THR* 1.3 110.8 + - - +
407A LEU* 1.3 56.7 + - - +
408A SER 3.7 0.2 - - - -
470A PRO 3.8 15.7 - - - +
471A LEU* 3.7 42.9 + - + +
473A CYS 3.3 7.3 - - - +
474A PRO* 3.4 37.0 - - + +
475A VAL* 3.8 6.5 - - - -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE* 3.5 35.0 - - + -
395A TYR 3.5 11.9 - - - +
396A LEU* 3.5 26.0 - - + -
398A GLY 4.5 0.2 - - - +
406A HIS* 1.3 73.2 - - - +
408A SER* 1.3 59.9 + - - +
409A LEU* 5.5 0.4 - - + -
434A LEU* 4.0 25.1 - - + -
472A PHE* 3.3 20.9 + - + +
473A CYS* 2.6 40.7 + - + +
475A VAL* 4.3 1.6 - - - +
478A MET* 3.3 33.7 - - + -
490A ILE* 5.2 0.4 - - + -
492A ILE* 4.8 2.0 - - + -
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE* 3.4 6.2 - - - +
395A TYR* 2.8 37.9 + - - -
398A GLY* 3.2 5.7 - - - -
399A ASP 2.9 28.9 + - - -
406A HIS 3.6 0.6 + - - -
407A LEU* 1.3 72.5 - - - +
409A LEU* 1.3 60.5 + - - +
410A PHE* 3.6 21.8 - - - -
469A CYS 3.5 4.5 - - - -
470A PRO* 2.6 25.5 + - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A TRP* 5.3 0.7 - - + -
392A LEU* 4.3 15.7 - - + -
393A ARG 3.7 9.4 - - - +
394A ILE* 4.4 16.2 - - + -
407A LEU* 5.5 0.4 - - + -
408A SER* 1.3 73.2 - - - +
410A PHE* 1.3 85.2 + - - +
432A LEU* 3.9 28.2 - - + +
433A MET 4.6 0.7 - - - +
469A CYS* 2.9 34.2 + - - +
472A PHE* 3.9 39.8 - - + +
492A ILE* 3.6 33.2 - - + -
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.4 6.8 - - - +
393A ARG* 2.7 43.3 + - + +
395A TYR* 3.6 26.9 - + - -
399A ASP* 3.7 18.8 - - + -
408A SER* 3.6 23.6 - - - -
409A LEU* 1.3 81.7 - - - +
411A PHE* 1.3 61.2 + - - +
432A LEU* 4.7 3.8 - - - -
466A ALA* 3.7 18.2 - - + -
467A SER* 3.6 4.3 - - - +
468A GLY* 3.3 22.4 - - - -
470A PRO* 4.0 30.1 - - + -
205D GLN 3.3 17.3 - - - -
206D GLN 3.8 2.9 - - - -
207D ALA* 3.6 20.4 - - + -
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Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A PHE* 4.4 4.3 - + - -
390A MET* 3.4 48.7 - - + -
391A CYS 4.0 1.6 - - - -
392A LEU* 4.1 16.6 - - + -
410A PHE* 1.3 71.4 - - - +
412A VAL* 1.3 70.5 + - - +
413A VAL* 3.8 19.1 - - + -
426A PHE* 3.6 30.5 - + - -
430A VAL* 4.0 25.6 - - + -
432A LEU* 4.8 1.8 - - + +
447A PHE* 3.7 15.0 - + + -
456A PHE* 4.1 17.0 - + - -
465A ILE 4.6 0.5 - - - +
466A ALA* 3.4 0.3 - - - -
467A SER* 2.8 37.4 + - - +
468A GLY* 4.6 0.4 - - - -
494A ALA* 5.7 0.2 - - + -
496A VAL* 4.1 12.8 - - + -
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A PHE* 4.3 5.8 - - + -
390A MET* 3.1 9.5 - - - +
391A CYS* 2.8 60.8 + - - +
393A ARG* 4.0 18.4 - - + +
411A PHE* 1.3 83.9 - - - +
413A VAL* 1.3 75.1 + - - +
414A MET* 3.7 1.7 + - + -
463A MET* 4.0 17.5 - - + -
464A ASN 3.8 16.6 - - - +
465A ILE 5.3 0.7 - - - -
466A ALA* 3.5 23.1 - - + +
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A TYR* 5.3 2.2 - - + -
389A LYS 3.9 6.5 - - - +
390A MET* 4.6 2.9 - - + +
411A PHE* 3.8 24.2 - - + -
412A VAL* 1.3 74.5 - - - +
414A MET* 1.3 64.3 + - - +
424A TRP* 3.9 24.0 - - + -
426A PHE* 4.3 14.1 - - + -
455A SER 3.5 24.4 + - - +
456A PHE* 4.2 12.6 - - + -
459A PRO* 3.8 19.3 - - + -
464A ASN* 3.0 35.1 + - - +
465A ILE 5.4 0.6 + - - -
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Residues in contact with MET 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A SER 5.6 0.2 - - - +
380A ALA* 3.0 26.5 - - + -
389A LYS* 2.9 42.9 + - + +
390A MET 2.9 31.0 - - - +
391A CYS* 3.6 26.5 - - - -
412A VAL* 4.2 2.7 - - + +
413A VAL* 1.3 79.7 - - - +
415A LYS* 1.3 65.8 + - - +
416A GLY 3.1 4.3 + - - -
419A ASP* 3.9 3.1 - - - +
424A TRP* 5.1 0.7 - - - -
459A PRO* 3.6 12.4 - - - +
462A ASP* 3.3 17.7 - - - +
463A MET* 4.0 22.0 - - + -
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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