Contacts of the helix formed by residues 192 - 204 (chain Y) in PDB entry 3D29
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 VAL 192 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192I ARG* 4.0 4.0 - - - +
193I GLN 4.8 4.9 + - - +
194I ASP* 3.9 27.4 - - + +
160Y LEU* 3.9 24.5 - - + -
163Y ALA* 4.0 22.2 - - + -
164Y HIS* 6.2 0.4 - - + -
170Y GLY 4.8 0.2 - - - -
171Y GLY 2.9 28.0 + - - +
172Y SER* 4.2 5.4 - - - -
173Y VAL* 4.5 10.3 - - + -
190Y HIS 3.2 3.1 + - - +
191Y ASP* 1.3 69.1 - - - +
193Y GLY* 1.3 65.4 + - - +
194Y GLU 3.0 1.1 + - - -
195Y LEU* 3.7 7.9 - - - -
196Y PHE* 3.1 27.2 + - + +
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Residues in contact with GLY 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I MET 6.0 0.2 - - - -
192I ARG* 3.6 30.8 - - - +
191Y ASP* 2.4 26.9 + - - -
192Y VAL* 1.3 70.6 - - - +
194Y GLU* 1.3 63.9 + - - +
197Y TRP* 3.3 23.9 + - - -
14Z TYR* 5.6 1.7 - - - -
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Residues in contact with GLU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Y ASP* 3.1 32.9 + - - +
193Y GLY* 1.3 80.7 - - - +
195Y LEU* 1.3 68.6 + - - +
196Y PHE 3.3 2.2 + - - -
197Y TRP* 3.5 6.8 + - - +
198Y LYS* 3.0 25.4 + - - +
14Z LYS* 2.9 42.2 - - + +
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Residues in contact with LEU 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Y LYS* 3.7 48.0 - - + +
160Y LEU* 4.0 20.9 - - + -
173Y VAL* 3.9 20.6 - - + -
190Y HIS* 4.0 15.9 - - + +
191Y ASP 2.9 18.4 + - - +
192Y VAL* 3.9 5.4 - - - -
194Y GLU* 1.3 77.9 - - - +
196Y PHE* 1.3 57.4 + - - +
198Y LYS* 3.4 15.9 + - + +
199Y VAL* 2.9 49.1 + - + +
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Residues in contact with PHE 196 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193I GLN* 3.4 34.3 - - + +
160Y LEU* 4.1 14.1 - - + +
164Y HIS* 3.8 15.7 - + + -
192Y VAL* 3.1 28.7 + - + +
195Y LEU* 1.3 78.5 - - - +
197Y TRP* 1.3 83.1 + + + +
199Y VAL* 3.2 1.9 + - - +
200Y LYS* 2.7 41.3 + - + +
206Y PHE* 3.4 57.4 - + + -
209Y VAL* 3.8 23.3 - - + -
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Residues in contact with TRP 197 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H LEU* 4.2 19.5 - - + -
190I LYS* 3.6 47.9 - - + +
191I MET 3.6 28.6 + - - -
192I ARG* 5.2 1.0 - - - +
193I GLN* 3.8 11.5 - - + +
193Y GLY 3.3 26.3 + - - -
194Y GLU* 3.5 5.5 + - - +
195Y LEU 3.5 0.4 - - - -
196Y PHE* 1.3 94.2 - + + +
198Y LYS* 1.3 67.6 + - - +
200Y LYS* 3.5 16.3 - - + +
201Y GLU* 3.0 27.1 + - - +
209Y VAL* 4.2 19.1 - - + -
210Y ILE 4.2 0.4 - - - -
211Y GLY* 3.9 20.4 - - - -
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Residues in contact with LYS 198 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156Y LYS* 5.5 6.3 - - - +
194Y GLU 3.0 19.7 + - - +
195Y LEU* 3.6 18.2 - - + +
197Y TRP* 1.3 77.7 - - - +
199Y VAL* 1.3 65.1 + - + +
201Y GLU* 3.8 6.0 - - - +
202Y GLU* 2.8 70.6 + - - +
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Residues in contact with VAL 199 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Y TYR* 3.6 28.7 - - + +
156Y LYS* 5.5 1.6 - - + -
157Y ARG* 3.4 30.1 - - - +
160Y LEU* 3.7 17.7 - - + -
195Y LEU* 2.9 36.6 + - + +
196Y PHE 3.7 3.4 - - - +
198Y LYS* 1.3 78.8 - - + +
200Y LYS* 1.3 58.1 + - - +
202Y GLU* 4.7 2.9 - - - -
203Y GLU* 2.7 44.8 + - + +
205Y SER* 4.0 4.0 - - - +
206Y PHE* 4.4 2.5 - - + -
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Residues in contact with LYS 200 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196Y PHE* 2.7 28.4 + - + +
197Y TRP* 3.2 27.8 + - + +
199Y VAL* 1.3 74.2 - - - +
201Y GLU* 1.3 57.9 + - - +
204Y GLY* 2.7 33.8 + - - -
205Y SER 3.3 20.0 - - - +
206Y PHE* 3.3 32.7 - - + +
207Y ASN* 4.8 4.7 + - - +
209Y VAL* 2.8 21.9 + - - -
210Y ILE* 3.9 0.6 - - - +
211Y GLY* 3.3 24.4 - - - +
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Residues in contact with GLU 201 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197Y TRP 3.0 15.8 + - - +
198Y LYS* 3.8 5.2 - - - +
200Y LYS* 1.3 81.0 - - - +
202Y GLU* 1.3 73.5 + - + +
203Y GLU 3.4 0.2 + - - -
204Y GLY* 3.6 5.9 + - - -
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Residues in contact with GLU 202 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198Y LYS* 2.8 62.0 + - - +
199Y VAL* 4.3 2.2 - - - +
201Y GLU* 1.3 86.8 - - + +
203Y GLU* 1.3 60.1 + - + +
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Residues in contact with GLU 203 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140J HIS* 3.0 28.2 + - - -
143J ARG* 2.9 21.9 + - - +
153Y TYR* 2.6 32.2 + - - +
157Y ARG* 2.9 17.2 + - - -
199Y VAL* 2.7 25.0 + - + +
202Y GLU* 1.3 75.3 - - + +
204Y GLY* 1.3 54.9 + - - +
205Y SER* 2.6 27.1 + - - +
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Residues in contact with GLY 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J ARG* 2.9 31.1 + - - -
200Y LYS 2.7 22.7 + - - -
201Y GLU 3.6 4.6 + - - -
202Y GLU 3.5 1.6 - - - -
203Y GLU* 1.3 69.9 - - - +
205Y SER* 1.3 60.7 + - - +
207Y ASN* 4.4 8.3 - - - +
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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