Contacts of the strand formed by residues 210 - 218 (chain B) in PDB entry 3ZZY
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 VAL 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A THR* 5.5 3.1 - - - +
201B HIS* 4.0 18.4 + - + +
204B PHE* 3.9 9.6 - - + -
205B SER* 3.6 36.1 + - - +
208B GLY 3.3 0.6 + - - -
209B THR* 1.3 75.7 - - - +
211B LEU* 1.3 64.7 + - - +
212B LYS 4.1 3.4 - - - +
213B ILE* 3.8 33.7 - - + -
226B LEU* 3.9 14.6 - - + -
227B GLN 3.7 5.2 - - - +
228B TYR* 3.9 17.5 - - + -
275B TYR* 3.5 17.8 - - + +
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Residues in contact with LEU 211 (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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193A TYR* 4.9 0.2 - - - +
209B THR* 3.9 20.6 - - + -
210B VAL* 1.3 73.2 - - - +
212B LYS* 1.3 70.0 + - + +
227B GLN* 2.8 33.7 + - + +
228B TYR 3.8 7.0 - - - +
229B ALA* 3.7 34.5 - - + +
274B ASP* 3.6 2.4 - - - +
275B TYR* 2.8 29.8 + - - +
276B THR* 3.6 27.3 + - + -
505C PRO* 4.6 22.0 - - + -
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Residues in contact with LYS 212 (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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210B VAL* 3.7 0.8 - - - +
211B LEU* 1.3 91.1 - - + +
213B ILE* 1.3 71.0 + - - +
226B LEU* 3.4 1.0 - - - +
227B GLN* 2.9 43.5 + - - +
262B SER* 4.5 7.3 + - - -
263B LEU* 3.0 36.9 + - + +
264B ASN* 4.9 2.4 - - - +
265B VAL* 4.0 18.9 - - + +
273B ARG 3.3 7.4 - - - +
274B ASP* 3.6 34.4 + - - +
275B TYR* 4.3 1.6 - - - -
276B THR* 4.6 5.8 - - - -
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Residues in contact with ILE 213 (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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197B LEU* 3.9 28.0 - - + +
200B LEU* 4.3 10.8 - - + -
201B HIS* 3.8 41.1 - - + +
210B VAL* 3.8 11.4 - - + -
212B LYS* 1.3 80.7 - - - +
214B ILE* 1.3 72.6 + - - +
215B THR* 4.2 11.7 - - + -
224B ALA* 4.7 2.5 - - + -
225B LEU 3.3 10.8 - - - +
226B LEU* 3.9 20.2 - - + -
263B LEU* 4.9 0.2 - - - -
272B SER* 3.3 2.9 - - - -
273B ARG 2.9 32.9 + - - +
275B TYR* 4.0 10.3 - - + -
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Residues in contact with ILE 214 (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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213B ILE* 1.3 80.1 - - - +
215B THR* 1.3 71.6 + - - +
216B PHE* 4.3 13.6 - - + -
224B ALA* 3.1 4.7 - - - +
225B LEU* 2.8 42.9 + - + +
263B LEU* 4.6 19.1 - - + -
264B ASN 3.3 26.9 - - - +
265B VAL* 3.8 16.2 - - + -
271B LYS 3.5 7.9 - - - +
272B SER* 4.0 9.6 - - - -
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Residues in contact with THR 215 (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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197B LEU* 4.4 14.1 - - + +
200B LEU* 4.0 17.7 - - + -
213B ILE* 4.2 8.3 - - + -
214B ILE* 1.3 83.9 - - - +
216B PHE* 1.3 67.2 + - - +
222B PHE* 4.1 16.0 - - + -
223B GLN 3.4 9.0 - - - -
224B ALA* 3.9 13.5 - - + -
270B ASP 4.0 2.9 + - - -
271B LYS* 2.8 54.9 + - - +
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Residues in contact with PHE 216 (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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214B ILE* 4.3 11.7 - - + -
215B THR* 1.3 83.1 - - - +
217B THR* 1.3 63.3 + - - +
218B LYS* 4.0 16.6 - - + -
221B GLN 3.7 0.2 - - - +
222B PHE* 3.8 2.3 - - - -
223B GLN* 2.8 68.0 + - + +
224B ALA* 4.4 9.4 - - - -
225B LEU* 4.2 31.6 - - + -
271B LYS* 3.7 11.6 - - - +
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Residues in contact with THR 217 (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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216B PHE* 1.3 75.3 + - - +
218B LYS* 1.3 61.5 + - - +
220B ASN* 4.5 9.0 - - - +
221B GLN 3.3 22.6 + - - +
222B PHE* 4.3 14.0 - - - +
271B LYS* 4.7 4.9 + - - +
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Residues in contact with LYS 218 (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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216B PHE* 4.0 15.0 - - + -
217B THR* 1.3 74.3 - - - +
219B ASN* 1.3 71.5 + - + +
220B ASN 3.1 1.6 - - - -
221B GLN* 3.0 15.2 + - - +
223B GLN* 3.0 31.4 + - - +
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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