Contacts of the helix formed by residues 220 - 225 (chain C) in PDB entry 1ZVM
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 SER 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C SER* 3.7 19.4 + - - -
127C ARG* 3.3 25.8 - - - +
217C ASP* 2.5 26.1 + - - +
219C ASP* 1.3 81.2 - - - +
221C THR* 1.3 63.8 + - - +
222C PHE* 3.4 4.0 + - - +
223C GLY 3.1 12.0 + - - -
224C SER* 2.9 26.4 + - - -
305C SO4 3.5 10.3 - - - -
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Residues in contact with THR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C TRP* 5.2 3.4 - - + +
190C LYS* 5.5 2.9 - - - -
193C SER* 4.1 26.9 - - - +
220C SER* 1.3 72.4 - - - +
222C PHE* 1.3 64.5 + - - +
224C SER* 4.1 4.7 - - - -
225C VAL* 3.0 36.5 + - + +
226C GLU* 3.1 16.3 + - - +
305C SO4 2.8 29.1 + - - -
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Residues in contact with PHE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 4.0 20.4 - - + -
125C TRP 4.9 0.9 - - - +
126C SER* 3.8 24.8 + - - -
206C VAL* 3.6 39.5 - - + -
208C LEU* 4.4 9.6 - - + -
216C PHE* 3.8 26.7 - + - -
220C SER* 3.2 4.8 + - - +
221C THR* 1.3 80.4 - - - +
223C GLY* 1.3 59.9 + - - +
226C GLU* 3.0 30.6 + - + +
227C VAL* 2.8 61.4 + - + +
230C LEU* 5.3 0.2 - - + -
238C LEU* 4.3 8.1 - - + -
262C LEU* 3.9 13.0 - - + -
305C SO4 4.5 0.4 + - - -
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Residues in contact with GLY 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C PHE* 3.8 25.2 - - - -
217C ASP 3.8 4.9 - - - -
218C LYS* 3.4 23.9 - - - +
220C SER* 3.1 8.9 + - - -
222C PHE* 1.3 78.6 - - - +
224C SER* 1.3 58.3 + - - +
227C VAL* 3.3 6.1 - - - +
228C HIS* 3.2 21.3 - - - -
265C ILE* 5.6 0.7 - - - +
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASP* 5.1 4.9 - - - +
250A SER* 3.0 35.2 - - - -
251A ARG* 4.9 3.6 - - - -
218C LYS 3.9 8.1 - - - -
219C ASP* 4.9 2.9 + - - -
220C SER 2.9 17.6 + - - -
221C THR* 3.8 1.6 + - - -
222C PHE 3.3 0.6 - - - -
223C GLY* 1.3 79.5 - - - +
225C VAL* 1.3 80.1 + - - +
226C GLU 3.6 0.4 - - - -
228C HIS* 3.0 24.0 + - - +
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASP* 4.9 12.6 - - + -
250A SER* 4.9 3.1 - - - +
190C LYS* 3.8 31.4 - - + +
193C SER* 4.5 4.7 - - - -
194C ARG* 3.6 37.4 - - + +
221C THR* 3.0 23.0 + - + +
224C SER* 1.3 89.8 + - - +
226C GLU* 1.3 63.3 + - - +
229C ASN* 2.5 35.8 + - - +
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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