Contacts of the strand formed by residues 251 - 255 (chain K) in PDB entry 4ZZ7
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 ASN 251 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249K ALA* 3.3 25.2 - - - +
250K LYS* 1.3 73.3 + - - +
252K HIS* 1.3 60.0 + - - +
281K MET* 3.3 27.4 - - - +
282K ALA 3.4 18.3 + - - +
283K LEU* 3.6 11.7 - - + +
284K SER* 3.3 11.1 + - - -
285K VAL* 3.2 24.3 + - - +
410K ASN* 3.7 2.6 - - - +
411K GLY* 2.8 46.7 + - - +
412K THR* 5.1 0.4 - - - -
439K PRO 5.5 2.2 - - - +
441K PRO* 5.5 0.7 - - - +
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Residues in contact with HIS 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K LYS* 2.8 30.8 + - + -
251K ASN* 1.3 76.7 + - - +
253K ALA* 1.3 59.2 + - - +
254K ILE 4.2 0.2 - - - -
283K LEU* 3.9 3.0 - - - +
285K VAL* 3.2 34.9 - - + +
287K VAL* 3.8 13.5 - - + -
379K TYR* 3.0 33.7 + + - -
402K LEU* 4.7 3.2 + - + -
403K ILE* 3.5 43.7 - - + +
406K HIS* 4.2 21.3 - + + -
411K GLY 3.7 3.6 + - - -
412K THR* 2.7 27.9 + - - +
413K CYS* 3.0 8.3 + - - +
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Residues in contact with ALA 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K HIS* 1.3 72.2 - - - +
254K ILE* 1.3 63.9 + - - +
255K VAL* 3.4 3.5 + - - +
268K LEU* 4.4 4.5 - - + -
283K LEU* 3.2 33.4 - - + -
285K VAL 2.9 9.0 + - - +
286K ALA* 3.6 4.7 - - + -
287K VAL* 2.9 25.0 + - - +
413K CYS* 3.2 8.1 - - + +
415K PHE* 3.8 22.2 - - + -
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Residues in contact with ILE 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253K ALA* 1.3 71.3 - - - +
255K VAL* 1.3 59.5 + - - +
256K MET* 3.5 30.2 + - + -
287K VAL* 3.4 9.0 - - + +
289K VAL* 4.2 9.2 - - + -
396K MET* 4.5 5.2 - - + +
399K ALA* 3.7 31.4 - - + -
400K MET* 3.9 11.0 - - + -
403K ILE* 3.9 19.7 - - + -
413K CYS 2.9 10.9 + - - +
414K ILE* 3.6 8.0 - - + -
415K PHE* 3.0 26.5 + - - +
425K PHE* 3.3 34.3 - - + -
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Residues in contact with VAL 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253K ALA 4.1 8.1 - - - +
254K ILE* 1.3 70.2 - - - +
256K MET* 1.3 66.1 + - - +
259K ALA* 4.4 8.3 - - + -
261K MET* 3.5 37.9 - - + -
264K ALA* 4.9 5.6 - - + -
268K LEU* 4.7 7.4 - - + -
286K ALA* 4.8 1.8 - - + -
287K VAL 2.9 14.8 + - - +
288K ALA* 4.5 6.3 - - + -
289K VAL* 3.3 20.2 + - - +
293K ALA* 3.9 7.9 - - + +
297K LEU* 4.3 26.9 - - + -
415K PHE* 4.1 18.8 - - + -
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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