Contacts of the strand formed by residues 190 - 197 (chain G) in PDB entry 4D1Q
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 ASN 190 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181G LEU* 4.8 7.7 - - - +
182G TRP 3.7 6.4 + - - +
183G THR* 3.5 20.6 - - - +
188G LYS 3.9 2.1 + - - +
189G ARG* 1.3 72.4 - - - +
191G PHE* 1.3 66.4 + - - +
213G SER* 3.0 5.3 - - - -
214G LEU* 2.8 61.3 + - + +
216G PHE* 4.9 13.3 - - + +
218G ARG 4.9 2.5 + - - +
219G SER* 4.0 18.8 + - - -
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Residues in contact with PHE 191 (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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180G ASP 3.8 0.2 - - - +
181G LEU* 3.1 15.2 - - - +
182G TRP* 2.7 77.3 + + + +
184G ASP* 4.6 3.4 - - - -
189G ARG* 4.1 33.0 - - + -
190G ASN* 1.3 74.9 + - - +
192G LEU* 1.3 58.5 - - - +
193G GLY 4.1 0.4 - - - -
211G LEU* 3.7 32.5 - - + -
212G LYS* 3.5 4.7 - - - -
213G SER* 3.4 40.2 - - - -
214G LEU* 5.1 0.2 - - - -
582G ILE* 4.4 16.2 - - + -
591G GLN* 4.1 18.6 - - + -
594G VAL* 5.3 5.6 - - + -
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Residues in contact with LEU 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ILE* 4.2 19.1 - - + -
180G ASP 3.6 14.8 - - - +
181G LEU* 3.7 17.7 - - + -
191G PHE* 1.3 72.2 - - - +
193G GLY* 1.3 59.5 + - - +
194G VAL* 4.1 8.7 + - + -
210G GLY 3.7 1.6 - - - +
211G LEU* 3.3 5.8 - - - -
212G LYS* 2.9 35.0 + - + +
214G LEU* 4.8 6.7 - - + -
224G ILE* 3.5 39.5 - - + +
227G LYS* 3.7 13.0 - - + -
228G LEU* 3.6 23.3 - - + +
231G ILE* 4.1 11.6 - - + +
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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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179G ILE* 3.4 24.4 - - - +
180G ASP 2.9 15.4 + - - -
191G PHE 4.1 0.4 - - - -
192G LEU* 1.3 71.0 - - - +
194G VAL* 1.3 67.7 + - - +
210G GLY 3.6 5.8 - - - -
211G LEU* 3.7 14.3 - - - +
571G SER* 3.6 7.1 + - - -
574G THR* 5.2 4.7 - - - -
575G PHE* 4.0 10.2 - - - -
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Residues in contact with VAL 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* 4.9 2.5 - - + -
178G THR 3.5 4.7 - - - +
179G ILE* 3.8 15.9 - - + -
192G LEU* 4.2 4.9 - - + -
193G GLY* 1.3 77.4 - - - +
195G THR* 1.3 60.7 + - - +
208G ILE* 3.6 2.6 - - - +
209G LEU* 2.7 60.1 + - + +
210G GLY 3.0 10.8 + - - +
228G LEU* 3.8 12.3 - - + -
231G ILE* 3.3 33.2 - - + -
232G PHE* 4.3 15.9 - - + -
574G THR* 5.4 2.2 - - - +
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Residues in contact with THR 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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177G ALA* 3.2 10.4 - - - +
178G THR* 2.7 55.3 + - - -
194G VAL* 1.3 78.4 - - - +
196G LEU* 1.3 60.9 + - - +
197G HIS* 3.2 14.0 + - - -
206G ASP* 5.3 1.3 - - - +
207G LEU 3.3 16.6 - - - +
208G ILE* 4.6 4.5 - - + -
570G ALA* 3.4 23.6 - - + +
571G SER* 3.6 4.5 - - - +
574G THR* 3.3 26.7 - - - +
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Residues in contact with LEU 196 (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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166G ILE* 3.4 37.2 - - + -
170G VAL* 5.6 1.3 - - + -
175G ALA* 4.3 18.6 - - + -
176G SER 3.3 17.5 - - - +
177G ALA* 3.9 15.3 - - + -
194G VAL 4.1 0.6 + - - -
195G THR* 1.3 70.6 - - - +
197G HIS* 1.3 72.3 + - - +
198G TYR* 4.3 14.4 - - + -
205G ARG* 3.9 1.9 - - - +
206G ASP 3.9 0.2 - - - -
207G LEU* 3.0 38.9 + - + +
209G LEU* 3.5 36.3 - - + +
232G PHE* 4.5 9.2 - - + -
243G ILE* 5.0 1.6 - - + -
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Residues in contact with HIS 197 (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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174G GLY 3.7 0.3 - - - +
175G ALA* 3.3 3.6 - - - +
176G SER* 2.5 48.3 + - - +
177G ALA* 4.5 1.8 - - - -
178G THR 4.5 0.4 - - - -
195G THR* 3.2 27.3 + - - -
196G LEU* 1.3 84.2 - - - +
198G TYR* 1.3 68.2 + - - +
204G LEU* 5.5 1.1 - - + +
205G ARG* 3.2 19.5 + - - +
206G ASP* 3.4 25.3 - - - -
377G CYS* 3.5 25.5 + - - +
563G SER* 3.4 20.1 + - - +
565G PRO* 3.4 22.0 - - + +
570G ALA* 3.7 5.2 - - + +
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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