Contacts of the helix formed by residues 226 - 230 (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 GLU 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C LEU* 3.6 27.8 - - + +
125C TRP 4.4 9.5 + - - +
145C LEU* 5.9 2.3 - - - +
193C SER* 4.2 25.1 + - - +
196C PHE* 5.3 2.4 - - - -
197C ALA* 3.7 25.9 - - + +
221C THR* 3.1 14.8 + - + +
222C PHE* 3.0 46.4 + - + +
224C SER 3.6 0.2 - - - -
225C VAL* 1.3 74.7 - - - +
227C VAL* 1.3 67.9 + - - +
228C HIS 3.1 1.6 - - - -
229C ASN* 2.8 15.9 + - - -
230C LEU* 3.6 8.1 + - - +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 4.6 3.6 - - + -
222C PHE* 2.8 62.5 + - + +
223C GLY* 3.3 24.5 - - - +
226C GLU* 1.3 73.4 - - - +
228C HIS* 1.3 73.9 + - + +
229C ASN 3.2 0.7 + - - -
230C LEU* 3.4 19.2 + - + +
262C LEU* 4.0 15.3 - - + -
265C ILE* 4.8 8.5 - - + -
266C ILE* 4.5 13.9 - - + +
269C ARG* 3.2 21.7 + - - -
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Residues in contact with HIS 228 (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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250A SER* 3.8 24.6 - - - -
279A TYR* 4.1 36.6 + + + +
280A ARG* 5.8 4.0 - - - +
223C GLY 3.2 23.0 + - - -
224C SER* 3.0 26.3 + - - +
225C VAL 4.6 0.7 - - - +
226C GLU 3.1 1.2 - - - -
227C VAL* 1.3 82.2 - - + +
229C ASN* 1.3 63.6 + - - +
231C GLN* 5.0 0.5 - - - +
265C ILE* 3.9 25.1 - - + +
269C ARG* 3.1 35.7 + - + +
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Residues in contact with ASN 229 (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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250A SER* 5.5 3.0 - - - -
280A ARG* 5.4 8.0 + - - -
194C ARG* 3.9 43.2 + - - +
197C ALA* 4.3 3.4 - - + -
198C GLU* 3.2 34.7 - - - +
225C VAL* 2.5 31.7 + - - +
226C GLU 2.8 7.4 + - - +
228C HIS* 1.3 85.8 - - - +
230C LEU* 1.3 59.7 + - - +
231C GLN* 3.2 18.3 + - - +
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Residues in contact with LEU 230 (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* 4.3 13.2 - - + -
197C ALA* 3.9 17.9 - - + +
200C ALA* 4.4 0.9 - - + -
204C VAL* 4.3 24.2 - - + -
222C PHE* 5.3 0.2 - - + -
226C GLU 3.8 7.9 - - - +
227C VAL* 3.6 26.9 - - + +
229C ASN* 1.3 75.5 - - - +
231C GLN* 1.3 64.1 + - - +
232C PRO* 3.4 4.2 - - - +
235C VAL* 4.3 15.3 - - + -
238C LEU* 4.0 26.7 - - + -
266C ILE* 4.2 14.6 - - + -
269C ARG* 2.4 26.8 + - - +
271C ILE* 3.6 16.3 - - + +
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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