Contacts of the helix formed by residues 220 - 225 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B SER* 3.6 21.3 + - - -
127B ARG* 3.5 20.9 - - - +
217B ASP* 2.6 31.1 + - - +
219B ASP* 1.3 79.3 - - - +
221B THR* 1.3 54.4 + - - +
222B PHE* 3.4 3.6 + - - +
223B GLY 2.9 13.3 + - - -
224B SER* 2.7 35.0 + - - -
303B SO4 3.4 11.4 - - - -
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Residues in contact with THR 221 (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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189B TRP* 4.9 7.3 - - + +
190B LYS* 5.2 4.0 - - + -
193B SER* 3.8 26.2 - - - +
220B SER* 1.3 75.0 - - - +
222B PHE* 1.3 57.3 + - - +
224B SER* 4.1 4.0 - - - -
225B VAL* 3.0 34.4 + - + -
226B GLU* 3.1 20.3 + - - +
303B SO4 3.1 26.1 + - - -
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Residues in contact with PHE 222 (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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124B LEU* 3.8 16.2 - - + -
125B TRP 4.4 3.1 - - - +
126B SER* 3.9 16.8 + - - -
206B VAL* 3.4 46.4 - - + -
208B LEU* 4.5 8.7 - - + -
216B PHE* 3.8 26.2 - + - -
220B SER* 3.2 6.8 + - - +
221B THR* 1.3 80.5 - - - +
223B GLY* 1.3 60.8 + - - +
226B GLU* 3.3 33.2 + - + +
227B VAL* 3.0 56.8 + - + +
230B LEU* 5.5 0.2 - - + -
238B LEU* 4.1 11.9 - - + -
262B LEU* 4.1 9.0 - - + -
303B SO4 4.5 1.0 + - - -
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Residues in contact with GLY 223 (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* 3.7 20.9 - - - -
217B ASP 3.5 18.8 - - - -
218B LYS* 3.1 12.0 - - - +
220B SER* 2.9 10.7 + - - -
222B PHE* 1.3 79.9 - - - +
224B SER* 1.3 55.5 + - - +
227B VAL* 3.3 7.0 - - - +
228B HIS* 3.2 21.8 - - - -
265B ILE* 5.1 0.5 - - - +
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Residues in contact with SER 224 (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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218B LYS 3.1 12.3 + - - -
219B ASP* 3.8 8.7 + - - -
220B SER 2.7 25.3 + - - -
221B THR* 4.1 2.8 - - - -
223B GLY* 1.3 73.7 - - - +
225B VAL* 1.3 68.3 + - - +
228B HIS* 3.6 18.6 + - - +
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Residues in contact with VAL 225 (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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190B LYS* 4.0 29.6 - - + +
193B SER* 4.5 3.4 - - - -
194B ARG* 3.9 37.0 - - + +
221B THR* 3.0 23.6 + - + +
223B GLY 3.7 0.2 - - - -
224B SER* 1.3 91.3 - - - +
226B GLU* 1.3 66.9 + - - +
227B VAL 3.6 0.9 - - - -
228B HIS* 3.4 8.6 + - - +
229B ASN* 2.7 30.6 + - - +
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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