Contacts of the helix formed by residues 189 - 201 (chain J) in PDB entry 3Q2K
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 ALA 189 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160J VAL* 4.2 12.6 - - + -
184J ALA 3.1 19.0 + - - +
185J PHE* 3.4 10.2 + - - +
188J GLN* 1.3 70.3 - - - +
190J SER* 1.3 51.7 + - - +
191J HIS 3.1 3.4 - - - -
192J TYR* 2.6 14.7 + - + -
193J VAL* 2.6 39.4 + - + +
237J ILE* 4.9 0.7 - - + -
239J VAL* 3.8 32.8 - - + -
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Residues in contact with SER 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J LYS* 3.2 17.7 - - - -
104J PRO* 4.9 3.6 - - - -
130J LYS* 3.3 14.7 + - - -
185J PHE 3.0 10.1 + - - -
186J MET 3.2 20.0 + - - -
187J ASN 3.0 16.1 + - - -
188J GLN 3.2 0.4 - - - -
189J ALA* 1.3 79.2 - - - +
191J HIS* 1.3 56.9 + - - +
193J VAL* 3.8 8.3 - - - +
194J ASP* 2.8 28.6 + - - +
328J SER* 4.6 2.1 + - - -
332J LEU* 4.2 14.1 - - - -
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Residues in contact with HIS 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J LYS* 3.7 27.5 - - + +
129J VAL 4.6 1.8 - - - -
130J LYS* 4.5 7.8 - - - +
131J GLN* 3.5 29.5 + - - -
132J ASN* 3.5 33.4 + - + +
188J GLN 3.9 11.0 - - - -
189J ALA 3.1 0.4 - - - -
190J SER* 1.3 78.9 + - - +
192J TYR* 1.3 66.9 + - + +
194J ASP* 3.4 18.8 - - - +
195J LEU* 3.6 16.1 - - - +
500J NAI 3.6 5.1 + - - -
550J HP7 3.0 52.6 + - + -
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Residues in contact with TYR 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J ASN* 4.3 8.6 + - - -
158J VAL* 3.9 18.8 - - + +
159J ASN 4.6 1.3 - - - -
160J VAL* 3.5 28.3 - - + -
162J TRP* 3.4 34.9 - + - -
188J GLN 4.4 1.1 - - - -
189J ALA* 2.6 22.3 + - - +
191J HIS* 1.3 86.7 - - + +
193J VAL* 1.3 65.9 + - - +
194J ASP 3.0 0.9 - - - -
195J LEU* 2.8 34.9 + - + +
196J LEU* 3.8 7.4 + - - +
237J ILE* 4.2 5.1 - - + +
250J GLY* 4.2 12.1 - - - -
251J SER 4.8 0.9 - - - -
266J VAL 4.1 0.2 + - - -
267J ALA* 3.3 30.0 - - - +
268J VAL* 3.7 29.7 - - + +
550J HP7 4.8 0.8 + - - -
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Residues in contact with VAL 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J PHE* 4.0 16.4 - - + -
189J ALA 2.6 22.6 + - - +
190J SER* 3.8 7.0 - - - +
192J TYR* 1.3 72.4 - - - +
194J ASP* 1.3 62.1 + - - +
196J LEU* 3.1 26.1 + - + +
197J ASP* 4.3 0.5 + - - +
237J ILE* 3.9 20.9 - - + +
328J SER* 4.0 14.8 - - - +
331J LEU* 3.8 34.5 - - + +
332J LEU* 3.8 25.6 - - + +
335J ILE* 4.6 7.4 - - + -
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Residues in contact with ASP 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J LYS* 3.7 26.2 - - - +
132J ASN* 6.0 1.0 - - - +
133J ARG* 2.7 54.0 + - - +
190J SER 2.8 20.2 + - - +
191J HIS* 3.4 12.0 - - - +
192J TYR 3.0 0.4 - - - -
193J VAL* 1.3 76.4 - - - +
195J LEU* 1.3 66.4 + - - +
196J LEU 3.2 0.7 + - - -
197J ASP* 3.7 4.1 + - - +
198J TRP* 3.3 17.0 + - - +
324J GLU 4.9 0.9 - - - +
328J SER* 4.0 15.4 - - - -
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Residues in contact with LEU 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J ASN* 5.4 3.8 - - + -
133J ARG* 5.7 1.1 - - + -
138J LEU* 3.7 30.7 - - + -
158J VAL* 5.3 3.8 - - + -
191J HIS 3.6 16.2 - - - +
192J TYR* 2.8 39.3 + - + +
194J ASP* 1.3 76.8 - - - +
196J LEU* 1.3 65.2 + - + +
198J TRP* 3.8 20.4 - - + +
199J LEU* 3.0 37.8 + - + +
200J VAL* 3.8 2.1 + - - +
252J ILE* 4.3 32.9 - - + +
268J VAL* 4.4 4.9 - - + -
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Residues in contact with LEU 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J VAL* 4.8 4.5 - - + -
158J VAL* 4.1 26.9 - - + -
192J TYR 3.9 4.5 - - - +
193J VAL* 3.3 26.2 - - + +
194J ASP 3.1 0.6 - - - -
195J LEU* 1.3 77.5 - - + +
197J ASP* 1.3 58.3 + - - +
200J VAL* 3.2 22.2 + - - +
201J GLY 3.4 1.5 - - - +
203J VAL* 4.3 2.9 - - + -
227J LEU* 3.9 29.2 - - + -
229J TRP* 3.3 44.5 + - + -
236J SER 5.7 0.4 - - - +
237J ILE* 4.6 11.9 - - + -
252J ILE* 5.8 0.7 - - + -
331J LEU* 3.7 21.3 - - + -
335J ILE* 5.4 1.8 - - + -
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Residues in contact with ASP 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J VAL 4.3 1.2 + - - +
194J ASP* 3.7 4.7 + - - +
196J LEU* 1.3 80.4 - - - +
198J TRP* 1.3 67.3 + - - +
201J GLY* 3.0 23.8 + - - -
202J PRO* 3.1 34.3 - - - +
203J VAL* 4.1 4.0 + - + +
324J GLU* 5.3 5.4 - - - +
327J GLN* 2.9 42.8 + - + +
328J SER* 6.2 0.7 - - - -
331J LEU* 4.7 9.9 - - + +
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Residues in contact with TRP 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ARG* 3.3 84.2 - - + +
138J LEU* 4.0 20.2 - - + -
139J GLN* 3.6 19.3 - - - -
142J LYS* 3.1 57.9 + - + +
194J ASP 3.3 17.9 + - - +
195J LEU* 4.1 10.1 - - + -
197J ASP* 1.3 83.7 - - - +
199J LEU* 1.3 85.0 + - + +
201J GLY* 5.5 0.2 - - - -
319J GLU* 5.0 5.0 + - - -
324J GLU* 4.7 4.3 - - - -
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Residues in contact with LEU 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J LEU* 4.1 11.0 - - + +
141J VAL* 4.1 15.7 - - + -
142J LYS* 3.8 39.7 + - + +
145J ILE* 3.6 32.1 - - + +
195J LEU* 3.0 27.6 + - + +
198J TRP* 1.3 104.6 - - + +
200J VAL* 1.3 68.9 + - + +
201J GLY 3.7 0.2 + - - -
252J ILE* 3.7 32.1 - - + -
254J ILE* 4.5 0.2 - - + -
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Residues in contact with VAL 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ILE* 4.9 5.0 - - + +
153J ILE* 4.2 20.1 - - + +
156J VAL* 4.0 24.0 - - + -
195J LEU 4.6 2.2 - - - +
196J LEU* 3.2 9.1 + - - +
199J LEU* 1.3 89.1 - - + +
201J GLY* 1.3 59.7 + - - +
229J TRP* 3.4 28.9 - - + +
231J HIS* 3.0 38.9 + - + +
252J ILE* 4.9 2.0 - - + -
254J ILE* 4.4 15.5 - - + -
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Residues in contact with GLY 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196J LEU 3.4 0.4 + - - -
197J ASP* 3.0 30.5 + - - +
198J TRP 5.5 0.2 - - - -
199J LEU 3.5 0.4 - - - -
200J VAL* 1.3 82.3 - - - +
202J PRO* 1.3 75.6 - - - +
203J VAL 3.5 0.3 + - - -
229J TRP* 3.1 14.1 + - - -
231J HIS* 4.9 0.7 - - - -
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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