Contacts of the helix formed by residues 196 - 205 (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 THR 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B PRO* 3.9 11.8 + - + +
195B VAL* 1.3 77.3 - - - +
197B LEU* 1.3 64.8 + - - +
198B ASP* 3.6 10.5 + - - +
199B VAL* 3.1 32.9 + - + +
200B LEU* 3.2 23.3 + - - +
222B PHE* 5.5 0.9 - - - -
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Residues in contact with LEU 197 (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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196B THR* 1.3 71.2 - - - +
198B ASP* 1.3 66.7 + - - +
200B LEU* 3.1 13.3 + - - +
201B HIS* 3.0 18.5 + - - +
213B ILE* 3.9 27.6 - - + +
215B THR* 4.4 9.0 - - + +
222B PHE* 5.8 0.2 - - - -
269B ASN 4.1 3.4 - - - +
270B ASP* 3.8 16.4 + - - +
271B LYS 3.6 8.1 - - - +
272B SER* 3.5 42.8 - - - +
273B ARG* 3.8 25.1 - - + +
275B TYR* 3.0 28.5 - - - +
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR* 3.2 10.0 + - - +
197B LEU* 1.3 79.4 - - - +
199B VAL* 1.3 57.4 + - + +
201B HIS* 3.3 9.1 + - - +
202B GLN* 2.9 30.1 + - - +
273B ARG* 3.1 30.6 + - - -
275B TYR* 4.5 4.5 + - - -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 4.3 9.2 - - + -
196B THR* 3.1 30.1 + - + +
197B LEU 3.2 0.2 - - - -
198B ASP* 1.3 75.8 - - + +
200B LEU* 1.3 65.3 + - - +
202B GLN* 3.3 12.8 + - - +
203B ILE* 3.0 33.7 + - + +
246B ILE* 4.0 10.5 - - + -
247B TYR* 3.6 19.3 - - - +
501D LEU* 3.5 28.5 - - + -
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Residues in contact with LEU 200 (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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186B ILE* 5.2 5.8 - - + -
188B VAL* 4.8 6.1 - - + -
195B VAL* 4.0 17.0 - - + -
196B THR 3.2 12.5 + - - +
197B LEU* 3.1 8.8 + - - +
199B VAL* 1.3 76.8 - - - +
201B HIS* 1.3 57.7 + - - +
203B ILE* 4.8 1.8 - - + -
204B PHE* 2.9 58.3 + - + +
213B ILE* 4.3 13.5 - - + -
215B THR* 4.0 17.3 - - + -
222B PHE* 4.6 10.3 - - + -
224B ALA* 4.0 27.6 - - + -
226B LEU* 5.1 2.7 - - + -
246B ILE* 4.4 12.3 - - + -
253B LEU* 4.6 6.7 - - + -
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Residues in contact with HIS 201 (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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270A ASP* 3.6 27.7 + - + -
197B LEU 3.0 7.9 + - - +
198B ASP* 3.5 9.3 + - - +
200B LEU* 1.3 78.0 - - - +
202B GLN* 1.3 61.9 + - - +
204B PHE* 5.2 1.3 - - - -
205B SER* 2.7 52.2 + - - +
210B VAL* 4.0 16.1 + - + +
213B ILE* 3.8 9.3 - - + +
275B TYR* 3.2 61.0 - + - +
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Residues in contact with GLN 202 (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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269A ASN* 3.2 38.2 - - + +
270A ASP* 3.8 18.8 + - - +
282A SER 2.8 27.9 + - - +
283A GLY* 3.7 6.3 - - - -
284A ASP* 5.8 0.2 + - - -
198B ASP 2.9 15.6 + - - +
199B VAL* 3.5 16.1 - - - +
201B HIS* 1.3 79.1 + - - +
203B ILE* 1.3 63.2 + - - +
205B SER 3.9 1.0 + - - -
501D LEU* 3.4 26.9 - - + +
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Residues in contact with ILE 203 (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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282A SER* 3.9 19.7 - - - +
199B VAL* 3.0 23.9 + - + +
200B LEU* 3.9 5.4 - - + +
202B GLN* 1.3 74.1 - - + +
204B PHE* 1.3 74.2 + - + +
205B SER 3.1 1.6 - - - -
206B LYS* 3.0 35.9 + - + +
241B LEU* 4.0 20.4 - - + -
246B ILE* 3.7 37.7 - - + -
253B LEU* 5.0 0.9 - - + -
500D LEU* 3.7 33.7 - - + -
501D LEU* 4.3 8.1 - - + -
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Residues in contact with PHE 204 (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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184B LEU* 4.1 10.3 - - + -
186B ILE* 3.4 29.4 - - + -
200B LEU* 2.9 36.1 + - + +
203B ILE* 1.3 82.1 - - + +
205B SER* 1.3 60.7 - - - +
206B LYS* 3.0 2.2 + - - -
207B PHE* 3.2 7.8 + - - +
210B VAL* 3.9 4.9 - - + -
226B LEU* 3.6 26.9 - - + -
228B TYR* 2.6 44.7 + + + +
237B ALA* 4.2 3.4 - - + -
241B LEU* 3.8 22.9 - - + -
253B LEU* 4.2 25.4 - - + -
255B ILE* 3.9 25.8 - - + -
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Residues in contact with SER 205 (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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198A ASP* 3.6 0.8 - - - +
269A ASN 4.2 0.4 - - - -
270A ASP* 3.4 29.3 - - - +
273A ARG* 2.9 21.1 + - - -
201B HIS* 2.7 47.3 + - - -
202B GLN 4.0 0.4 - - - -
203B ILE 3.1 0.4 + - - -
204B PHE* 1.3 71.5 - - - +
206B LYS* 1.3 56.5 + - - +
207B PHE 3.0 10.7 + - - -
208B GLY 3.2 21.8 + - - +
210B VAL* 3.6 8.6 + - - +
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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