Contacts of the strand formed by residues 189 - 195 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G SER* 3.5 32.3 - - - -
124G CYS* 4.0 6.1 - - - -
125G SER* 4.2 14.1 - - - -
128G GLU* 4.7 6.0 + - + +
130G ARG* 3.9 28.8 - - + +
132G PHE* 3.5 31.6 - + - -
172G ARG* 4.1 19.3 - - - +
174G GLU* 5.8 2.7 - - - +
182G ALA* 4.8 0.9 - - + -
183G CYS* 3.5 29.6 - - - -
184G HIS* 3.4 38.3 + + + -
188G SER* 1.3 76.5 - - - +
190G LEU* 1.3 62.0 + - - +
191G THR* 4.2 7.6 - - + -
206G LYS 3.7 0.3 - - - +
207G TYR* 3.4 8.4 - - - -
208G ASN* 3.1 28.4 + - - +
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Residues in contact with LEU 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ALA* 2.9 28.1 - - - +
183G CYS* 2.8 39.2 + - - +
185G ASP 6.0 0.2 - - - +
188G SER 5.1 0.7 - - - +
189G TRP* 1.3 74.6 - - - +
191G THR* 1.3 69.0 + - - +
192G ILE* 4.6 6.3 - - + -
205G LEU* 4.7 5.6 - - + -
206G LYS 3.2 16.2 - - - +
207G TYR* 4.7 7.6 - - + -
230G CYS* 4.0 2.2 - - - -
237G CYS* 3.9 21.5 - - + -
257G MET* 4.0 25.6 - - + -
260G GLY* 3.6 29.4 - - - +
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Residues in contact with THR 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G PHE* 4.5 2.7 - - + -
158G LEU* 4.3 10.5 - - + -
174G GLU* 3.5 38.9 + - + +
175G SER* 4.9 4.4 - - - -
181G SER 3.6 2.7 - - - -
182G ALA* 4.2 12.1 - - + -
189G TRP* 5.3 6.5 - - + -
190G LEU* 1.3 78.9 - - - +
192G ILE* 1.3 69.9 + - - +
193G GLY 4.1 0.7 - - - -
204G VAL 4.2 0.7 - - - -
205G LEU* 3.4 3.3 - - - +
206G LYS* 2.9 59.1 + - - +
209G GLY 5.7 0.3 + - - -
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Residues in contact with ILE 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G LEU* 4.6 1.5 - - - +
179G SER 3.8 0.3 - - - +
180G ALA* 2.9 28.5 - - - +
181G SER* 2.7 41.3 + - - +
190G LEU* 4.6 12.8 - - + -
191G THR* 1.3 79.6 - - - +
193G GLY* 1.3 59.1 + - - +
194G ILE* 4.9 0.7 - - + -
203G ALA* 4.1 7.4 - - + -
204G VAL 3.5 3.4 - - - -
205G LEU* 3.4 26.0 - - + -
225G THR* 4.9 4.0 - - + -
230G CYS* 4.8 1.6 - - - -
239G THR* 4.2 11.2 - - + +
241G MET* 3.6 22.9 - - + -
257G MET* 3.5 31.4 - - + -
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Residues in contact with GLY 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G LEU* 5.1 0.4 - - - -
175G SER* 4.2 14.7 + - - -
176G VAL 4.0 5.8 - - - +
177G ALA* 3.3 20.6 - - - -
179G SER 3.8 0.2 - - - -
180G ALA* 4.5 1.8 - - - -
191G THR 4.1 0.4 - - - -
192G ILE* 1.3 75.1 - - - +
194G ILE* 1.3 60.3 + - - -
195G SER 4.1 0.3 + - - -
202G VAL 3.7 1.2 - - - +
203G ALA* 3.3 0.3 - - - -
204G VAL* 2.7 43.5 + - - +
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Residues in contact with ILE 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G ALA* 3.2 1.9 - - - +
178G TRP* 2.9 34.2 + - + -
179G SER* 2.9 20.1 + - - +
192G ILE* 4.9 1.6 - - + -
193G GLY* 1.3 73.4 - - - -
195G SER* 1.3 62.6 + - - +
201G ALA* 3.7 20.2 - - + -
202G VAL 3.6 9.4 - - - +
203G ALA* 3.5 22.0 - - + -
223G LEU* 3.3 42.6 - - + +
224G ARG* 3.8 17.0 - - - -
225G THR* 3.8 23.6 - - + +
241G MET* 4.4 3.1 - - + -
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Residues in contact with SER 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 4.8 7.0 - - - -
456E TRP* 3.4 8.1 - - - -
458E TRP* 3.3 25.5 + - - -
153G SER 4.8 2.1 + - - -
176G VAL* 3.8 28.2 - - - +
177G ALA* 4.2 2.2 - - - -
178G TRP* 3.4 14.6 - - - +
193G GLY 4.1 1.2 + - - -
194G ILE* 1.3 76.7 - - - +
196G GLY* 1.3 66.6 + - - +
201G ALA* 3.4 4.2 - - - -
202G VAL* 3.1 33.4 + - - +
204G VAL* 6.0 1.3 - - - +
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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