Contacts of the helix formed by residues 220 - 225 (chain D) in PDB entry 1I2M
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 LEU 220 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE* 3.7 33.7 - - + +
158D PRO* 4.1 21.8 - - + -
159D MET* 3.9 22.0 - - + -
214D ARG* 3.4 52.5 - - + +
218D GLN 4.7 3.4 - - - +
219D GLY* 1.3 71.0 - - - -
221D GLU* 1.3 68.6 + - - +
222D ARG 3.2 3.4 - - - -
223D LEU* 3.0 28.3 + - + +
224D LEU* 3.1 19.2 + - + +
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Residues in contact with GLU 221 (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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158D PRO* 3.7 26.3 - - + +
219D GLY* 2.9 22.6 - - - -
220D LEU* 1.3 95.8 + - - +
222D ARG* 1.3 57.5 + - - +
224D LEU* 4.6 1.6 - - - +
225D VAL* 3.0 46.9 + - + +
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Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LYS* 4.2 27.5 - - - +
206D ARG* 2.9 60.2 + - - +
207D VAL* 3.8 20.9 - - + +
208D PRO* 3.4 26.4 - - - +
211D PHE* 4.3 19.5 - - - +
215D GLY* 6.4 1.6 - - - -
219D GLY 4.7 5.1 + - - +
220D LEU 3.2 1.3 - - - -
221D GLU* 1.3 80.1 + - - +
223D LEU* 1.3 60.0 + - + +
225D VAL* 3.7 4.6 - - - +
227D LYS* 4.4 7.8 - - + +
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Residues in contact with LEU 223 (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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148D ASP* 6.5 0.7 - - + -
153D ILE* 5.0 7.6 - - + -
196D LEU* 3.3 10.7 - - - -
197D GLY 3.0 33.4 + - - +
198D CYS* 5.1 1.1 - - - -
199D GLY* 4.4 11.7 - - - +
200D GLU* 6.2 0.7 - - + -
204D LEU* 3.6 21.7 - - + +
206D ARG* 3.3 8.0 + - - +
207D VAL* 4.0 24.7 - - + -
211D PHE 5.2 1.1 - - - +
212D ALA* 4.5 8.7 - - - +
214D ARG* 3.9 34.1 - - + +
215D GLY* 4.7 2.2 - - - +
220D LEU* 3.0 22.5 + - + +
222D ARG* 1.3 80.8 - - + +
224D LEU* 1.3 63.2 + - + +
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Residues in contact with LEU 224 (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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146D PHE* 3.8 18.2 - - + -
153D ILE* 3.4 42.8 - - + +
154D GLY 4.1 3.1 - - - +
155D LEU 3.5 23.5 - - - +
156D LEU* 4.1 17.6 - - - +
157D GLU* 3.6 7.4 - - - +
158D PRO* 3.6 28.0 - - + -
196D LEU* 3.6 16.3 - - - +
197D GLY* 4.3 4.5 - - - -
220D LEU* 3.1 17.6 + - + +
221D GLU* 4.6 2.9 - - - +
223D LEU* 1.3 79.7 - - + +
225D VAL* 1.3 61.6 + - + +
226D PRO* 3.5 8.3 - - - +
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Residues in contact with VAL 225 (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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156D LEU 5.2 6.7 - - - +
196D LEU* 4.5 0.7 - - - -
206D ARG* 3.1 18.3 + - - -
221D GLU* 3.0 35.8 + - + +
222D ARG* 3.7 0.7 - - - +
224D LEU* 1.3 78.6 - - + +
226D PRO* 1.3 77.1 - - + +
227D LYS* 3.1 34.6 + - - +
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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