Contacts of the helix formed by residues 226 - 230 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.9 26.6 - - + +
125D TRP 4.3 7.9 + - - +
145D LEU* 5.3 4.0 - - - +
193D SER* 3.8 38.2 + - - +
196D PHE* 5.2 3.3 - - - -
197D ALA* 3.5 25.7 - - + +
221D THR* 3.1 11.0 + - - +
222D PHE* 3.2 42.9 + - + +
225D VAL* 1.3 73.8 - - - +
227D VAL* 1.3 67.4 + - - +
229D ASN 3.2 9.2 + - - -
230D LEU* 3.6 7.1 + - - +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D PHE* 4.6 3.6 - - + -
222D PHE* 3.0 49.0 + - + +
223D GLY* 3.2 28.5 - - - +
226D GLU* 1.3 72.3 - - - +
228D HIS* 1.3 80.4 + - + +
229D ASN 3.0 5.5 + - - -
230D LEU* 3.3 22.9 + - - +
238D LEU* 4.7 1.3 - - + -
262D LEU* 3.9 18.2 - - + -
265D ILE* 4.4 12.3 - - + -
266D ILE* 4.5 8.9 - - + +
269D ARG* 3.5 14.9 + - - -
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Residues in contact with HIS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D LYS* 6.3 0.4 - - + -
223D GLY 3.1 23.9 + - - -
224D SER* 3.8 18.1 + - - +
225D VAL 3.7 6.1 + - - +
226D GLU 3.3 0.6 - - - -
227D VAL* 1.3 83.5 - - + +
229D ASN* 1.3 65.6 + - - +
231D GLN* 5.0 1.0 - - - +
265D ILE* 3.7 30.6 - - + +
269D ARG* 3.0 33.6 + - - +
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Residues in contact with ASN 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ARG* 3.8 39.0 + - - +
197D ALA* 4.2 3.4 - - + -
198D GLU* 3.2 44.2 - - - +
225D VAL* 2.7 30.5 + - - +
226D GLU 3.2 5.7 + - - +
227D VAL 3.0 1.2 - - - -
228D HIS* 1.3 83.9 + - - +
230D LEU* 1.3 65.2 + - - +
231D GLN* 3.4 15.4 + - - +
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 4.3 13.0 - - + -
197D ALA* 3.9 18.2 - - + +
200D ALA* 4.0 17.3 - - + -
204D VAL* 4.3 12.8 - - + -
222D PHE* 5.5 0.2 - - + -
226D GLU 3.6 13.0 - - - +
227D VAL* 3.3 19.7 + - + +
229D ASN* 1.3 76.6 - - - +
231D GLN* 1.3 62.6 + - - +
232D PRO* 3.6 1.6 - - - +
235D VAL* 4.1 11.4 - - + -
238D LEU* 4.4 24.9 - - + -
266D ILE* 4.3 18.4 - - + -
269D ARG* 2.2 32.4 + - - -
271D ILE* 4.0 15.3 - - + +
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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