Contacts of the strand formed by residues 189 - 195 (chain H) in PDB entry 2HU4
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 TRP 189 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H SER* 3.5 41.3 - - - -
124H CYS* 3.9 8.3 - - - -
125H SER* 4.1 16.4 + - - -
128H GLU* 4.7 7.3 + - + +
130H ARG* 4.0 28.8 - - + +
132H PHE* 3.8 25.6 - + + -
172H ARG* 3.9 19.4 - - - +
174H GLU* 5.7 2.2 - - - +
182H ALA* 4.9 0.2 - - + -
183H CYS* 3.5 23.6 - - - -
184H HIS* 3.5 33.9 + + + -
188H SER* 1.3 74.7 - - - +
190H LEU* 1.3 63.3 + - - +
191H THR* 4.1 9.1 + - + +
206H LYS 3.4 3.3 - - - +
207H TYR* 3.4 3.0 - - - -
208H ASN* 2.8 34.8 + - - +
209H GLY 4.7 0.9 + - - -
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Residues in contact with LEU 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H ALA* 3.1 7.1 - - - +
183H CYS* 2.9 60.8 + - - +
185H ASP* 6.4 0.4 - - - -
188H SER 3.8 0.4 + - - -
189H TRP* 1.3 75.5 - - - +
191H THR* 1.3 76.6 + - - +
192H ILE* 4.1 12.6 - - + -
205H LEU* 4.6 4.5 - - + -
206H LYS 3.1 13.9 - - - +
207H TYR* 4.6 11.9 - - + -
230H CYS* 4.3 1.1 - - - -
237H CYS* 3.9 15.3 - - + -
257H MET* 3.9 34.3 - - + -
260H GLY* 4.2 20.4 - - - +
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Residues in contact with THR 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PHE* 4.3 4.9 - - + -
158H LEU* 4.2 11.9 - - + -
174H GLU* 3.3 38.4 + - + +
175H SER* 4.8 2.9 - - - -
181H SER 3.7 4.0 - - - -
182H ALA* 4.1 10.5 - - + -
189H TRP* 5.0 8.5 - - + +
190H LEU* 1.3 79.4 - - - +
192H ILE* 1.3 68.8 + - - +
193H GLY 4.2 0.7 - - - -
204H VAL 3.8 0.6 - - - +
205H LEU* 3.5 2.6 - - - -
206H LYS* 3.0 55.4 + - - +
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Residues in contact with ILE 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H LEU* 4.8 2.0 - - - -
179H SER 3.9 0.2 - - - +
180H ALA* 3.0 30.5 - - - +
181H SER* 2.8 30.9 + - - +
190H LEU* 4.1 13.7 - - + -
191H THR* 1.3 80.8 - - - +
193H GLY* 1.3 60.0 + - - +
194H ILE* 4.9 2.7 - - + -
203H ALA* 4.3 5.2 - - + -
204H VAL 3.8 2.5 - - - -
205H LEU* 3.7 20.6 - - + -
225H THR* 4.9 1.8 - - + -
230H CYS* 4.8 2.5 - - - -
239H THR* 3.9 17.7 - - + +
241H MET* 3.5 27.8 - - + -
257H MET* 3.7 33.7 - - + -
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Residues in contact with GLY 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H LEU* 5.2 0.9 - - - -
175H SER* 4.6 12.4 + - - -
176H VAL 4.2 5.8 - - - +
177H ALA* 3.5 20.0 - - - -
179H SER 3.8 0.4 - - - -
180H ALA* 4.4 1.1 - - - -
191H THR 4.2 0.4 - - - -
192H ILE* 1.3 74.8 - - - +
194H ILE* 1.3 63.6 + - - -
195H SER* 4.0 0.3 + - - -
202H VAL 3.6 1.7 - - - +
203H ALA* 3.2 0.9 - - - -
204H VAL* 2.8 42.9 + - - +
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Residues in contact with ILE 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H ALA* 3.2 1.5 - - - +
178H TRP* 2.9 41.6 + - + -
179H SER* 3.0 17.8 + - - +
192H ILE* 4.9 0.9 - - + -
193H GLY* 1.3 74.0 - - - -
195H SER* 1.3 64.3 + - - +
201H ALA* 3.7 12.6 - - + -
202H VAL 3.6 10.1 - - - +
203H ALA* 3.6 19.7 - - + +
223H LEU* 3.4 24.5 - - + +
224H ARG* 3.6 36.8 - - - +
225H THR* 3.7 19.1 - - + +
241H MET* 4.1 10.5 - - + -
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Residues in contact with SER 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F VAL* 4.8 11.0 - - - -
456F TRP* 4.0 5.2 - - - -
458F TRP* 3.4 22.2 + - - -
153H SER 5.0 1.6 + - - -
176H VAL* 3.6 29.6 - - - +
177H ALA* 4.2 0.9 - - - -
178H TRP* 3.4 14.5 - - - +
193H GLY 4.0 0.6 + - - -
194H ILE* 1.3 76.7 - - - +
196H GLY* 1.3 66.4 + - - +
201H ALA* 3.3 3.5 - - - -
202H VAL* 2.9 36.2 + - - +
204H VAL* 6.4 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