Contacts of the strand formed by residues 242 - 246 (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 ARG 242 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J TYR* 4.5 8.7 - - - -
458J GLY* 4.4 15.0 + - - +
459J ASP* 3.6 39.8 + - + +
461J HIS* 5.0 6.3 + - - -
139K MET* 3.2 20.2 - - + +
218K LYS 3.5 15.2 + - - +
219K ALA* 3.4 9.6 - - + -
220K VAL* 3.1 21.8 + - - -
240K GLY 3.9 1.6 + - - -
241K LYS* 1.3 79.1 - - - +
243K CYS* 1.3 60.5 + - - +
469K ARG* 3.1 9.9 + - - +
470K PHE* 2.7 46.7 + - + +
472K THR 2.7 28.5 + - - -
473K LYS* 3.6 19.0 - - - +
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Residues in contact with CYS 243 (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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233J TYR* 4.9 3.7 + - - -
459J ASP* 4.4 6.5 + - - +
220K VAL* 3.4 16.4 - - + +
232K ILE* 4.2 17.0 - - - -
233K TYR* 3.4 55.2 - - + +
236K ALA* 3.9 19.7 - - + -
237K SER* 5.2 1.8 - - - +
241K LYS 3.8 1.3 + - - +
242K ARG* 1.3 78.9 - - - +
244K GLN* 1.3 76.9 + - - +
245K ALA* 4.3 1.3 - - - -
457K PHE 4.3 0.5 - - - +
458K GLY* 4.3 4.7 - - - -
459K ASP 5.3 0.5 + - - -
470K PHE* 3.7 10.4 - - - -
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Residues in contact with GLN 244 (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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158K MET* 5.7 0.2 - - - +
220K VAL 3.2 4.8 + - - +
221K SER* 2.6 32.7 + - - +
222K PHE 2.9 25.4 + - - +
243K CYS* 1.3 76.4 - - - +
245K ALA* 1.3 62.4 + - - +
246K LEU* 4.3 11.0 - - + +
456K LEU* 6.0 0.7 - - + -
457K PHE 3.5 7.2 - - - +
458K GLY* 5.1 0.7 - - - -
460K LEU 2.8 30.7 + - - +
461K HIS 3.3 20.2 + - - -
462K ALA* 4.5 10.1 - - - +
463K TYR 5.2 1.2 + - - -
467K ALA* 5.6 1.6 - - - +
470K PHE* 3.7 30.1 - - + +
471K TYR* 4.0 5.4 + - - -
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Residues in contact with ALA 245 (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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222K PHE* 3.3 13.5 - - + -
229K ALA* 3.7 33.9 - - + +
233K TYR* 4.3 1.3 - - + +
243K CYS* 4.3 10.3 - - - -
244K GLN* 1.3 76.0 - - - +
246K LEU* 1.3 63.9 - - - +
456K LEU* 3.5 0.3 - - - -
457K PHE* 2.8 52.1 + - + -
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Residues in contact with LEU 246 (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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157K TRP* 4.3 6.5 - - + -
222K PHE* 2.8 23.0 + - - +
223K VAL* 3.6 15.6 - - + -
224K GLY 2.9 27.7 + - - +
229K ALA* 4.2 0.9 - - - -
244K GLN* 4.6 12.3 - - + +
245K ALA* 1.3 83.0 - - - +
247K GLY* 1.3 60.9 + - - +
410K ASN* 5.7 1.3 - - - +
449K PHE* 3.5 42.2 - - + +
450K GLY* 4.4 4.3 - - - -
451K GLY 5.2 1.3 - - - +
455K SER 3.6 4.9 - - - +
456K LEU* 3.9 22.7 - - + +
461K HIS* 5.5 0.2 - - - -
462K ALA* 3.8 26.7 - - + +
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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