Contacts of the strand formed by residues 489 - 496 (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 ALA 489 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B LYS* 4.2 24.7 - - + -
358B ILE 3.2 13.2 - - - +
359B SER* 4.1 8.5 - - - +
361B PHE* 4.1 3.4 - - - +
437B GLN* 2.9 20.9 + - - -
484B TYR 3.5 1.2 - - - +
485B VAL* 4.1 1.6 - - - +
486B ARG 3.1 18.1 + - - +
487B ASP* 4.0 4.5 - - + +
488B ASP* 1.3 80.5 - - - +
490B ILE* 1.3 65.3 + - - +
491B PHE* 5.0 3.8 - - + -
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Residues in contact with ILE 490 (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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357B LYS* 3.5 4.5 - - - +
358B ILE* 2.8 61.4 + - + +
361B PHE* 3.9 27.6 - - + -
394B ILE* 4.9 2.5 - - + -
396B LEU* 4.6 7.9 - - + -
407B LEU* 5.1 0.9 - - + -
434B LEU* 4.3 9.6 - - + -
437B GLN* 4.1 0.9 - - - +
478B MET* 4.1 13.2 - - + -
484B TYR 3.7 11.4 - - - +
485B VAL* 3.5 30.3 - - + -
489B ALA* 1.3 79.2 - - - +
491B PHE* 1.3 65.7 + - - +
492B ILE* 4.3 17.0 - - + -
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Residues in contact with PHE 491 (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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417A PRO 4.0 5.8 - - - -
418A ASN* 3.4 22.4 - - - -
420A ALA* 4.2 10.5 - - + -
421A LEU* 3.6 31.2 - - + -
355B ILE* 3.9 13.9 - - + -
356B TRP 3.4 3.1 - - - -
357B LYS* 3.7 43.3 - - + -
434B LEU* 3.6 6.7 - - - +
435B LEU* 2.9 51.4 + - + +
437B GLN* 3.6 35.8 - - + +
484B TYR 4.8 1.2 + - - -
486B ARG 5.8 0.2 - - - -
489B ALA* 5.0 4.7 - - + -
490B ILE* 1.3 80.3 - - - +
492B ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 492 (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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354B PHE 3.9 0.3 - - - +
355B ILE* 3.4 3.1 - - - +
356B TRP* 2.6 54.6 + - + +
358B ILE* 4.3 20.4 - - + -
392B LEU* 4.0 20.7 - - + +
394B ILE* 4.2 20.0 - - + -
407B LEU* 4.8 3.4 - - + -
409B LEU* 3.7 27.4 - - + -
432B LEU* 5.6 0.2 - - + -
433B MET 3.2 10.3 - - - +
434B LEU* 3.6 30.7 - - + -
472B PHE* 5.0 0.2 - - + -
490B ILE* 4.3 6.1 - - + -
491B PHE* 1.3 74.3 - - - +
493B LYS* 1.3 65.8 + - - +
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Residues in contact with LYS 493 (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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353B VAL* 4.0 18.2 - - - +
354B PHE 3.3 10.1 - - - +
355B ILE* 4.0 22.1 - - + +
431B THR 3.9 0.3 - - - +
432B LEU* 3.5 3.1 - - - -
433B MET* 2.8 54.8 + - + +
435B LEU* 4.1 29.4 - - + -
491B PHE 4.2 0.4 - - - -
492B ILE* 1.3 80.3 - - - +
494B ALA* 1.3 65.9 + - - +
495B ILE* 3.8 28.9 - - + +
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Residues in contact with ALA 494 (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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352B GLY 3.6 1.6 - - - +
353B VAL* 3.4 5.0 - - - +
354B PHE* 2.8 34.3 + - + +
381B PHE* 4.2 15.9 - - + -
392B LEU* 3.9 24.2 - - + +
411B PHE* 5.9 0.4 - - + -
430B VAL* 5.4 2.7 - - + -
431B THR 3.3 3.6 - - - +
432B LEU* 3.9 19.5 - - + -
493B LYS* 1.3 75.4 - - - +
495B ILE* 1.3 65.6 + - - +
496B VAL* 4.2 1.3 - - + -
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Residues in contact with ILE 495 (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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352B GLY 3.5 2.0 - - - -
353B VAL* 4.5 17.3 - - + +
429B LYS 3.9 0.2 - - - +
430B VAL* 3.7 0.4 - - - -
431B THR* 2.9 54.2 + - + +
433B MET* 4.5 14.6 - - - -
493B LYS* 3.8 32.1 - - + +
494B ALA* 1.3 80.4 - - - +
496B VAL* 1.3 70.7 + - - +
497B ASP* 3.7 4.5 + - - +
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Residues in contact with VAL 496 (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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351B ASP 4.9 0.3 - - - +
352B GLY* 2.8 29.1 + - - +
381B PHE* 3.9 13.5 - - + -
383B THR* 3.9 20.4 - - + -
390B MET* 3.7 22.0 - - + -
411B PHE* 4.0 13.0 - - + -
426B PHE* 4.0 8.7 - - + -
428B GLN* 3.8 17.9 - - + -
429B LYS 3.6 5.6 - - - +
430B VAL* 4.5 6.7 - - + +
494B ALA* 5.5 0.4 - - + -
495B ILE* 1.3 80.1 - - - +
497B ASP* 1.3 73.6 + - - +
498B LEU* 3.3 14.8 + - + +
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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