Contacts of the helix formed by residues 197 - 207 (chain D) in PDB entry 3PII
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 GLY 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D ASP* 2.9 10.5 + - - +
196D ILE* 1.3 80.9 - - - +
198D ASP* 1.3 62.1 + - - -
199D GLU* 3.0 10.3 + - - -
200D LYS* 3.2 20.1 + - - +
201D LEU* 3.3 14.6 + - - +
214D ASN* 3.9 0.9 - - - -
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Residues in contact with ASP 198 (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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196D ILE 3.4 1.4 + - - +
197D GLY* 1.3 69.8 - - - -
199D GLU* 1.3 61.5 + - + +
201D LEU* 3.6 11.2 - - - +
202D GLU* 3.2 25.7 + - - +
214D ASN* 2.7 29.9 + - - +
217D LYS* 3.2 25.5 + - - +
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Residues in contact with GLU 199 (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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197D GLY* 3.0 2.9 - - - -
198D ASP* 1.3 75.9 - - + +
200D LYS* 1.3 66.1 + - + +
202D GLU* 2.9 24.3 + - - +
203D LEU* 3.0 12.2 + - - +
329D ASN* 6.0 0.3 + - - -
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Residues in contact with LYS 200 (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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173D ILE* 2.9 40.8 - - + +
174D GLY* 4.1 10.9 - - - -
195D ASP* 3.6 30.2 + - - +
197D GLY* 3.2 12.1 + - - +
199D GLU* 1.3 78.7 - - + +
201D LEU* 1.3 53.8 + - - +
203D LEU* 3.0 18.0 + - + +
204D ALA* 2.7 35.3 + - - +
329D ASN* 4.3 25.0 + - + +
330D GLY 6.0 0.7 - - - +
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Residues in contact with LEU 201 (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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173D ILE* 4.5 3.8 - - + -
193D ALA* 3.9 16.8 - - + +
194D VAL 4.1 1.1 - - - -
195D ASP* 3.5 34.1 - - + +
197D GLY 3.3 9.6 + - - +
198D ASP* 3.6 11.7 - - - +
199D GLU 3.3 0.2 - - - -
200D LYS* 1.3 77.0 - - - +
202D GLU* 1.3 59.3 + - - +
204D ALA* 3.7 3.8 - - - +
205D LYS* 3.3 20.1 + - - +
212D VAL* 3.5 35.2 - - + +
213D VAL* 3.4 28.5 - - - +
214D ASN* 3.7 24.0 - - + +
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Residues in contact with GLU 202 (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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198D ASP* 3.2 16.5 + - + +
199D GLU* 2.9 12.5 + - - +
201D LEU* 1.3 74.6 - - - +
203D LEU* 1.3 66.6 + - - +
205D LYS* 2.9 45.3 + - - +
206D GLU* 3.1 21.7 + - - +
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Residues in contact with LEU 203 (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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173D ILE* 4.7 10.3 - - + +
178D HIS* 4.3 22.9 - - + -
199D GLU 3.0 10.9 + - - +
200D LYS* 3.2 19.1 - - + +
202D GLU* 1.3 73.3 - - - +
204D ALA* 1.3 65.5 + - - +
206D GLU* 3.1 25.4 + - - +
207D LEU* 3.0 45.6 + - + +
307D ILE* 5.0 14.4 - - + -
329D ASN* 6.5 0.9 - - + -
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Residues in contact with ALA 204 (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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173D ILE* 4.0 16.7 - - + +
181D VAL* 4.1 4.0 - - + +
193D ALA* 3.5 32.1 - - + -
200D LYS 2.7 18.6 + - - +
201D LEU* 3.7 8.3 - - - +
203D LEU* 1.3 73.6 - - - +
205D LYS* 1.3 62.7 + - - +
207D LEU* 3.1 15.6 + - - +
208D GLY 3.4 0.7 + - - -
209D ALA* 3.0 25.3 + - + +
212D VAL* 4.7 0.4 - - + -
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Residues in contact with LYS 205 (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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201D LEU 3.3 12.5 + - - +
202D GLU* 2.9 38.6 + - - +
204D ALA* 1.3 78.9 - - - +
206D GLU* 1.3 63.5 + - - +
208D GLY* 3.2 13.0 + - - -
209D ALA* 3.9 19.8 + - - +
210D ASP 5.8 2.7 - - - +
211D LEU* 6.2 0.2 - - - -
212D VAL* 4.6 19.8 - - + +
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Residues in contact with GLU 206 (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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202D GLU* 3.1 21.1 + - - +
203D LEU* 3.1 25.5 + - + +
205D LYS* 1.3 77.6 - - - +
207D LEU* 1.3 62.1 + - + +
208D GLY* 3.2 5.4 + - - -
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Residues in contact with LEU 207 (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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178D HIS* 3.5 45.8 - - + +
181D VAL* 4.2 12.1 - - + +
182D GLN* 3.8 42.4 - - + +
185D LYS* 4.5 2.9 - - - +
203D LEU* 3.0 36.3 + - + +
204D ALA* 3.1 11.8 + - - +
206D GLU* 1.3 79.5 - - + +
208D GLY* 1.3 55.4 + - - +
209D ALA 3.6 1.1 - - - -
305D LYS 5.1 1.6 - - - +
307D ILE* 5.3 7.6 - - + -
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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