Contacts of the strand formed by residues 389 - 395 (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 LYS 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ALA* 3.5 19.7 - - + -
381A PHE 3.6 2.9 - - - +
382A TYR* 3.4 39.4 + - + +
387A GLY 3.7 1.4 + - - -
388A TYR* 1.3 70.7 - - - +
390A MET* 1.3 65.9 + - - +
413A VAL* 3.8 4.0 - - - +
414A MET* 2.9 51.2 + - + +
415A LYS 3.5 20.6 + - - +
416A GLY* 3.8 20.6 - - - -
417A PRO* 4.7 4.5 - - + +
419A ASP* 4.9 0.6 + - - -
424A TRP* 6.2 0.2 - - - -
462A ASP* 5.0 8.3 + - - -
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Residues in contact with MET 390 (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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352A GLY* 5.0 0.2 - - - -
380A ALA* 3.1 0.9 - - - -
381A PHE* 2.9 59.6 + - + +
382A TYR* 3.6 6.3 - - - -
383A THR* 3.5 43.5 - - + +
388A TYR* 3.7 8.7 - - + +
389A LYS* 1.3 80.3 - - - +
391A CYS* 1.3 59.9 + - - +
411A PHE* 3.4 38.8 - - + -
412A VAL 3.1 12.3 - - - +
413A VAL* 4.8 3.1 - - + -
414A MET* 2.9 18.8 - - - +
426A PHE* 4.3 8.5 - - + -
496A VAL* 3.8 11.7 - - + -
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Residues in contact with CYS 391 (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* 3.9 23.6 - - - -
378A SER* 3.5 24.9 - - - +
379A PRO 3.7 6.7 - - - +
381A PHE* 4.0 5.4 - - - -
390A MET* 1.3 77.9 - - - +
392A LEU* 1.3 70.2 + - - +
411A PHE* 4.4 0.9 - - - -
412A VAL* 2.8 49.5 + - - +
414A MET* 3.6 23.3 - - + -
463A MET* 4.1 5.6 - - - -
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Residues in contact with LEU 392 (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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354A PHE* 4.2 13.7 - - + -
356A TRP* 4.0 16.8 - - + -
377A PHE* 3.4 3.6 - - - -
378A SER* 2.8 39.8 + - - +
381A PHE* 4.3 9.0 - - + -
391A CYS* 1.3 86.7 - - - +
393A ARG* 1.3 61.6 + - - +
409A LEU* 4.3 6.1 - - + -
410A PHE 3.4 13.5 - - - +
411A PHE* 4.1 13.0 - - + -
412A VAL* 4.5 0.4 - - - -
432A LEU* 4.1 12.1 - - + -
492A ILE* 3.8 27.1 - - + +
494A ALA* 3.8 33.4 - - + +
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Residues in contact with ARG 393 (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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374A PRO* 5.9 0.6 - - - +
375A ALA* 3.5 18.6 - - + +
376A ILE 3.4 9.0 - - - +
377A PHE* 2.6 52.1 - - + -
392A LEU* 1.3 75.2 - - - +
394A ILE* 1.3 62.6 + - - +
395A TYR* 2.8 28.3 + - + -
409A LEU* 3.6 2.6 - - - +
410A PHE* 2.7 42.5 + - + +
412A VAL* 4.0 14.8 - - + +
466A ALA* 4.1 19.3 - - + -
209D ASP* 2.8 31.3 + - - -
210D ASP* 2.8 29.6 + - - +
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Residues in contact with ILE 394 (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* 3.6 26.4 - - + -
358A ILE* 4.1 11.7 - - + -
375A ALA* 3.2 5.7 - - - +
376A ILE* 3.0 44.8 + - + +
392A LEU 4.3 0.2 - - - -
393A ARG* 1.3 74.4 - - - +
395A TYR* 1.3 67.2 + - - +
396A LEU* 3.8 17.6 + - + -
407A LEU* 3.5 29.6 - - + -
408A SER 3.4 12.1 - - - +
409A LEU* 4.4 9.6 - - + -
490A ILE* 4.4 1.6 - - + -
492A ILE* 4.1 31.0 - - + -
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Residues in contact with TYR 395 (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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374A PRO* 3.3 26.5 - - + +
375A ALA* 3.5 9.2 - - + -
393A ARG* 2.8 32.8 + - + -
394A ILE* 1.3 76.5 - - - +
396A LEU* 1.3 63.0 + - - +
397A ASN 3.0 3.6 - - - +
398A GLY* 3.1 32.2 + - - +
399A ASP* 3.6 24.6 + - + -
407A LEU* 3.5 4.4 - - - +
408A SER* 2.8 26.5 + - - +
410A PHE* 3.6 37.0 - + - -
207D ALA* 3.6 12.7 - - + +
209D ASP* 2.6 39.2 + - - -
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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