Contacts of the helix formed by residues 184 - 194 (chain I) in PDB entry 2B4X
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 184 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180I GLU* 3.7 15.7 - - - +
181I GLN* 4.1 9.2 - - - +
182I SER 2.2 18.8 + - - -
183I ARG* 1.3 71.8 - - - +
185I ALA* 1.3 52.8 + - - +
186I ILE 3.1 2.7 - - - +
187I ASN* 4.2 11.3 - - - +
188I LYS* 2.7 37.3 + - - +
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Residues in contact with ALA 185 (chain I).
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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147I PHE* 5.5 1.5 - - - -
173I LEU* 4.0 18.4 - - + -
181I GLN 3.2 18.0 + - - +
182I SER* 2.4 25.1 + - - +
184I ALA* 1.3 72.0 - - - +
186I ILE* 1.3 59.0 + - - +
188I LYS* 3.8 3.9 - - - +
189I TRP* 3.3 20.4 + - - +
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Residues in contact with ILE 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I PHE* 3.4 62.1 - - + -
173I LEU* 4.1 10.5 - - + -
175I PHE* 5.4 1.8 - - + -
182I SER 2.8 10.2 + - - +
183I ARG* 4.7 0.2 - - - -
184I ALA 4.5 0.4 - - - +
185I ALA* 1.3 73.0 - - - +
187I ASN* 1.3 59.7 + - - +
188I LYS 2.6 4.5 + - - -
189I TRP* 2.5 29.0 + - - +
190I VAL* 3.2 10.3 + - + +
201I VAL* 4.7 2.2 - - + -
202I ILE* 3.5 26.7 - - + -
207I ILE* 3.7 27.6 - - + -
214I VAL* 5.2 4.3 - - + -
216I VAL* 4.1 13.9 - - + -
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Residues in contact with ASN 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I ARG* 4.5 17.9 + - - +
184I ALA* 4.0 10.0 - - - -
186I ILE* 1.3 72.6 - - - +
188I LYS* 1.3 56.6 + - - +
191I SER* 3.1 30.8 + - - -
199I THR 3.5 8.5 - - - +
200I ASP* 3.6 8.7 - - - +
201I VAL* 3.5 18.0 - - - +
202I ILE* 2.7 63.2 + - - +
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Residues in contact with LYS 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I ALA 2.7 23.2 + - - +
185I ALA* 3.8 7.0 - - - +
186I ILE 2.6 4.9 + - - -
187I ASN* 1.3 72.9 - - - +
189I TRP* 1.3 65.7 + - - +
191I SER* 4.1 2.6 - - - -
192I ASN* 3.3 20.3 + - - +
861I NAG 5.7 0.7 - - - +
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Residues in contact with TRP 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I SER 5.3 1.8 - - - -
143I ALA* 4.2 14.6 - - + -
144I ASN 3.7 21.5 - - - -
145I ARG* 3.4 69.4 - - + +
147I PHE* 4.6 10.8 - + + -
168I ALA* 5.1 1.6 - - + -
185I ALA 3.3 11.2 + - - +
186I ILE* 2.5 22.1 + - - +
188I LYS* 1.3 71.3 - - - +
190I VAL* 1.3 91.9 + - + +
192I ASN* 2.9 22.5 + - - +
193I LYS* 3.1 16.7 + - + +
216I VAL* 4.4 3.6 - - + -
861I NAG 4.6 23.2 + - + -
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Residues in contact with VAL 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ALA* 5.1 0.4 - - - -
186I ILE* 3.2 7.1 + - + +
189I TRP* 1.3 96.6 - - + +
191I SER* 1.3 56.2 + - - +
192I ASN 2.6 16.7 + - - -
193I LYS* 2.8 17.1 + - - +
194I THR* 2.9 16.2 + - + +
198I ILE* 3.5 18.6 - - + -
201I VAL* 3.1 42.0 - - + -
216I VAL* 3.7 14.8 - - + -
218I THR* 3.6 24.7 - - + -
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Residues in contact with SER 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I ASN 3.1 21.2 + - - -
188I LYS* 4.1 3.6 - - - -
190I VAL* 1.3 78.4 - - - +
192I ASN* 1.3 55.8 + - - +
194I THR* 3.8 3.4 - - - -
196I GLY* 3.2 26.0 + - - -
198I ILE 2.8 25.2 + - - -
199I THR* 3.2 25.6 - - - +
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Residues in contact with ASN 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I LYS 3.3 12.8 + - - +
189I TRP* 2.9 14.8 + - - +
190I VAL 2.6 5.9 + - - -
191I SER* 1.3 75.5 - - - +
193I LYS* 1.3 68.5 + - - +
195I GLU* 3.2 15.1 + - - +
196I GLY 4.3 0.2 + - - -
861I NAG 2.8 67.4 + - + +
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Residues in contact with LYS 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I VAL* 4.5 20.5 - - + +
142I SER 5.5 1.1 - - - +
143I ALA* 4.5 17.3 - - + -
189I TRP* 3.1 20.3 + - + +
190I VAL* 2.8 8.3 + - - +
192I ASN* 1.3 83.2 - - - +
194I THR* 1.3 56.5 + - - +
195I GLU* 2.8 19.0 + - - +
220I LEU* 4.7 1.6 - - - +
861I NAG 5.8 0.2 - - - -
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Residues in contact with THR 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I VAL* 6.4 0.2 - - + -
143I ALA* 4.1 7.2 - - + -
190I VAL* 2.9 28.3 + - + +
191I SER* 3.8 1.7 - - - -
193I LYS* 1.3 74.1 - - - +
195I GLU* 1.3 56.6 + - - +
196I GLY 3.0 0.4 - - - -
197I ARG* 2.7 39.5 + - - +
198I ILE* 2.9 53.2 + - + -
218I THR* 3.9 12.3 - - + +
219I ILE 5.0 0.9 - - - +
220I LEU* 3.9 22.2 - - + -
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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