Contacts of the helix formed by residues 196 - 205 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PRO* 4.0 9.3 + - + +
195A VAL* 1.3 77.9 - - - +
197A LEU* 1.3 66.2 + - - +
198A ASP* 3.7 5.1 + - - -
199A VAL* 3.1 29.5 + - + +
200A LEU* 3.2 15.0 + - - +
222A PHE* 5.5 0.4 - - - -
209B THR* 2.7 45.1 + - + -
210B VAL 5.5 2.9 - - - +
275B TYR* 6.5 0.7 - - + -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A VAL 4.2 0.2 + - - -
196A THR* 1.3 74.7 - - - +
198A ASP* 1.3 57.7 + - - +
200A LEU* 3.1 15.0 + - - +
201A HIS* 3.0 23.2 + - - +
213A ILE* 3.8 29.0 - - + +
215A THR* 4.4 9.2 - - + +
222A PHE* 5.6 0.6 - - - -
270A ASP 3.8 15.7 + - - +
271A LYS* 3.6 8.3 - - - +
272A SER* 3.5 42.6 - - - +
273A ARG* 3.7 28.5 - - + +
275A TYR* 3.1 27.6 - - - +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 3.1 3.4 + - - -
197A LEU* 1.3 79.3 + - - +
199A VAL* 1.3 57.4 + - - +
201A HIS* 3.2 9.6 + - - +
202A GLN* 3.0 26.9 + - - +
273A ARG* 3.0 37.5 + - - -
275A TYR* 4.4 2.8 + - - -
205B SER* 3.6 1.4 - - - +
207B PHE 4.3 0.7 - - - -
208B GLY* 3.1 38.2 + - - +
209B THR* 3.4 20.2 + - - +
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 4.4 9.4 - - + -
196A THR* 3.1 30.4 + - + +
198A ASP* 1.3 73.9 - - - +
200A LEU* 1.3 66.2 + - - +
202A GLN* 3.2 12.9 + - - +
203A ILE* 3.0 32.3 + - + +
246A ILE* 4.1 7.4 - - + -
247A TYR* 3.5 26.9 - - + +
209B THR* 4.1 8.7 - - + +
501C LEU* 3.9 19.7 - - + -
505C PRO* 5.8 3.1 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 5.1 5.2 - - + -
188A VAL* 4.6 6.1 - - + -
195A VAL* 4.0 17.5 - - + -
196A THR 3.2 13.0 + - - +
197A LEU* 3.1 8.8 + - - +
199A VAL* 1.3 75.9 - - - +
201A HIS* 1.3 63.2 + - - +
203A ILE* 3.4 2.4 + - + -
204A PHE* 3.0 52.5 + - + +
213A ILE* 4.5 13.9 - - + -
215A THR* 4.2 15.0 - - + -
222A PHE* 4.5 11.4 - - + -
224A ALA* 4.0 26.9 - - + -
226A LEU* 5.0 2.0 - - + -
246A ILE* 4.4 13.7 - - + -
253A LEU* 4.5 7.9 - - + -
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Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU 3.0 9.8 + - - +
198A ASP* 3.4 11.4 + - - +
199A VAL 3.2 0.2 - - - -
200A LEU* 1.3 77.0 - - - +
202A GLN* 1.3 58.4 + - - +
205A SER* 2.7 59.4 + - - +
210A VAL* 3.8 21.6 + - + +
213A ILE* 3.9 8.0 - - + +
275A TYR* 3.2 56.4 - + - +
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Residues in contact with GLN 202 (chain A).
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 3.0 12.5 + - - +
199A VAL* 3.2 15.8 + - - +
201A HIS* 1.3 82.5 + - - +
203A ILE* 1.3 63.6 + - + +
205A SER* 3.6 11.2 + - - -
206A LYS* 3.9 11.6 + - - +
501C LEU* 3.5 38.0 - - - +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A VAL* 3.0 19.5 + - + +
200A LEU* 3.9 5.6 - - + +
202A GLN* 1.3 79.0 - - + +
204A PHE* 1.3 70.3 + - + +
206A LYS* 3.5 19.5 + - - +
207A PHE* 4.0 7.4 - - - -
241A LEU* 3.7 24.5 - - + -
246A ILE* 3.6 47.3 - - + -
253A LEU* 4.7 1.8 - - + -
500C LEU* 3.8 23.3 - - + -
501C LEU* 4.2 21.3 - - + -
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.9 20.4 - - + -
186A ILE* 3.5 25.1 - - + -
200A LEU* 3.0 36.5 + - + +
203A ILE* 1.3 82.9 - - + +
205A SER* 1.3 61.6 + - - +
206A LYS 3.1 5.2 - - - -
207A PHE* 3.1 11.0 + - - -
210A VAL* 4.0 5.8 - - + -
226A LEU* 3.7 26.0 - - + -
228A TYR* 2.7 47.8 + + + +
237A ALA* 4.0 4.3 - - + -
241A LEU* 3.8 21.8 - - + -
253A LEU* 4.2 18.4 - - + -
255A ILE* 3.9 22.7 - - + -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A HIS* 2.7 50.3 + - - -
202A GLN* 3.9 6.7 - - - -
203A ILE 3.3 0.8 - - - -
204A PHE* 1.3 75.7 - - - +
206A LYS* 1.3 61.7 + - - +
207A PHE 3.1 0.4 - - - -
208A GLY 3.2 22.4 + - - +
210A VAL* 3.7 9.6 + - - +
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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