Contacts of the strand formed by residues 399 - 406 (chain B) in PDB entry 2ZZ0
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 ILE 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B GLU* 5.3 1.3 - - + +
390B ALA* 4.0 27.6 - - + +
391B VAL* 4.1 22.4 - - + -
394B PHE* 3.6 32.8 - - + -
395B GLY 3.5 3.8 + - - +
396B GLU 3.4 8.5 + - - +
397B GLU 3.4 1.0 - - - -
398B ASN* 1.3 91.0 - - - +
400B GLU* 1.3 62.9 + - - +
401B VAL* 4.1 22.4 + - + +
426B ILE* 4.1 8.1 - - + -
427B CYS 3.5 11.7 - - - +
428B ASN* 3.9 8.7 - - + +
429B THR* 4.4 0.4 - - - -
436B VAL* 5.3 1.1 - - + -
487B ARG* 3.3 21.6 + - - -
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Residues in contact with GLU 400 (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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398B ASN 4.1 1.0 + - - -
399B ILE* 1.3 79.1 - - - +
401B VAL* 1.3 63.8 + - - +
402B TYR* 4.1 27.6 + - + +
427B CYS* 2.7 40.8 + - + +
429B THR* 3.9 16.6 + - + +
433B GLU* 6.2 0.7 - - + -
485B THR* 2.9 33.5 + - - +
487B ARG* 3.5 24.8 + - - +
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU* 3.6 32.5 - - + +
399B ILE* 4.1 13.8 + - + -
400B GLU* 1.3 83.7 + - - +
402B TYR* 1.3 64.7 + - - +
403B HIS* 3.9 1.2 + - + -
424B LYS* 4.3 15.7 - - + -
425B ILE 3.7 7.2 - - - +
426B ILE* 3.8 8.7 - - + -
485B THR* 3.2 3.0 + - - -
486B LYS* 2.6 70.1 + - + +
487B ARG 5.5 0.2 - - - +
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Residues in contact with TYR 402 (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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400B GLU* 4.1 20.9 - - + +
401B VAL* 1.3 73.2 - - - +
403B HIS* 1.3 60.2 + - - +
424B LYS* 3.3 2.9 - - - +
425B ILE* 3.0 37.8 + - + +
427B CYS* 3.6 36.3 - - + -
433B GLU* 3.3 23.6 + - - +
462B LYS* 3.9 31.4 - - + +
482B LEU* 3.9 27.4 - - + +
483B SER* 4.4 11.2 - - - -
484B VAL 3.4 17.5 - - - +
485B THR* 4.5 10.5 - - - -
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Residues in contact with HIS 403 (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 VAL* 4.7 1.3 - - + -
402B TYR* 1.3 76.8 - - - +
404B SER* 1.3 66.1 - - - +
422B TYR* 2.4 33.1 + + - +
423B ALA 3.2 11.9 - - - +
424B LYS* 3.6 7.4 - - + -
482B LEU* 3.9 6.2 - - - +
483B SER 5.4 0.3 + - - -
484B VAL* 3.3 24.1 + - + +
485B THR 4.1 3.4 + - - -
486B LYS* 3.1 47.4 - - + +
490B ALA 5.1 3.5 + - - -
492B ILE* 2.7 44.9 - - + +
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Residues in contact with SER 404 (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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403B HIS* 1.3 82.2 - - - +
405B TYR* 1.3 71.9 + - - +
406B PHE* 4.3 0.2 - - - -
422B TYR* 3.7 2.8 - - - -
423B ALA* 2.9 30.6 + - - +
478B VAL* 4.1 10.4 - - - +
482B LEU* 3.5 20.2 - - - -
492B ILE* 3.8 17.7 + - - +
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Residues in contact with TYR 405 (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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235B LYS* 3.2 24.6 - - + -
404B SER* 1.3 88.6 + - - +
406B PHE* 1.3 64.5 + - - +
419B ASN* 2.8 48.7 - - - +
420B LYS* 4.3 7.2 - - - -
421B CYS 3.2 17.5 - - - -
422B TYR* 3.7 24.1 - + - -
478B VAL* 4.2 1.2 - - - +
492B ILE* 3.4 40.9 + - + +
493B LEU* 4.1 26.2 - - + +
242D GLU* 4.6 12.6 + - + +
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Residues in contact with PHE 406 (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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404B SER 4.3 0.4 - - - -
405B TYR* 1.3 83.1 - - - +
407B TRP* 1.3 63.5 + - - +
408B PRO* 4.0 4.4 - - + +
417B ASP 5.3 0.2 - - - +
419B ASN* 4.1 10.9 + - - -
421B CYS* 3.2 52.7 + - + +
422B TYR* 3.2 35.0 - - - -
423B ALA* 4.1 6.7 - - + -
440B VAL* 4.2 13.9 - - + -
441B LEU 3.6 8.7 - - - -
442B GLY* 4.3 4.3 - - - -
443B PRO* 4.7 0.7 - - + -
475B CYS* 3.7 45.8 - - + -
478B VAL* 4.2 24.5 - - + -
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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