Contacts of the strand formed by residues 194 - 200 (chain q) in PDB entry 5GJQ
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 LYS 194 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216p ILE* 3.9 30.1 - - + -
217p THR 3.7 12.3 - - - +
218p PRO* 4.3 4.9 - - + -
219p LEU* 4.7 4.7 - - - +
160q PRO* 5.6 0.2 - - - +
191q GLU* 2.6 69.7 + - - +
192q LYS 3.7 0.4 - - - -
193q ASP* 1.3 85.7 - - + +
195q ILE* 1.3 66.0 + - - +
196q THR* 4.3 11.2 - - - +
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Residues in contact with ILE 195 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215p LYS 3.5 4.0 - - - +
216p ILE* 3.6 2.6 - - - +
217p THR* 3.0 40.7 + - - +
219p LEU* 3.7 29.2 - - + -
47q ASP* 5.3 2.2 - - - +
48q ARG* 4.2 9.4 - - - +
50q TYR* 3.7 33.4 - - + +
188q HIS* 5.3 0.4 - - - +
189q ILE 3.9 2.9 - - - -
190q ILE* 3.7 31.6 - - + -
191q GLU 5.0 0.4 - - - +
194q LYS* 1.3 83.4 - - - +
196q THR* 1.3 65.2 + - - +
197q THR* 4.2 13.9 - - - +
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Residues in contact with THR 196 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214p GLU* 5.8 1.1 - - + -
215p LYS 3.8 4.7 - - - +
216p ILE* 4.0 20.9 - - + +
188q HIS* 3.4 2.9 - - - +
189q ILE* 2.9 55.4 + - - +
191q GLU* 4.2 15.1 + - - -
194q LYS* 4.3 9.5 - - - +
195q ILE* 1.3 76.6 - - - +
197q THR* 1.3 63.1 + - - +
198q ARG* 3.5 43.5 + - + +
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Residues in contact with THR 197 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213p THR* 4.8 2.7 - - + +
214p GLU* 3.9 1.9 - - - -
215p LYS* 3.1 53.1 + - + +
50q TYR* 4.9 1.4 + - - -
186q ILE* 4.0 18.6 - - + -
187q VAL 3.4 2.9 - - - -
188q HIS* 2.7 38.2 + - + -
195q ILE* 4.0 9.6 + - - +
196q THR* 1.3 74.3 - - - +
198q ARG* 1.3 66.8 + - - +
199q THR* 5.2 2.9 - - + -
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Residues in contact with ARG 198 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211p VAL* 4.6 13.1 - - + +
213p THR 3.7 12.1 - - - +
214p GLU* 4.7 10.8 - - - +
216p ILE* 5.5 2.6 - - - +
160q PRO 5.3 1.4 + - - -
161q ASP* 4.5 14.5 + - - +
164q PHE* 3.3 61.8 - - + +
185q VAL 4.2 0.2 - - - +
186q ILE* 3.3 5.8 - - - +
187q VAL* 2.9 36.9 + - + +
189q ILE* 4.0 10.8 - - + +
196q THR* 3.5 30.1 + - + +
197q THR* 1.3 80.8 - - - +
199q THR* 1.3 66.8 + - - +
200q LEU* 4.2 2.2 + - + -
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Residues in contact with THR 199 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211p VAL* 3.8 2.4 - - - -
212p LEU* 2.8 50.1 + - - +
213p THR* 3.2 29.3 + - + -
26q ARG* 5.5 10.5 - - - +
185q VAL 3.4 8.7 - - - -
186q ILE* 4.2 20.2 - - + -
197q THR* 5.2 3.1 - - + -
198q ARG* 1.3 80.5 - - - +
200q LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 200 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209p THR* 3.9 4.7 - - + -
210p ALA 3.3 15.3 - - - +
211p VAL* 5.2 0.9 - - - -
212p LEU* 3.6 12.7 - - - +
164q PHE* 3.8 30.5 - - + -
168q SER* 3.7 28.0 - - - +
172q LEU* 3.8 24.2 - - + -
184q GLY* 5.0 1.9 - - - -
185q VAL* 2.9 48.4 + - + +
187q VAL* 4.0 9.2 - - + -
198q ARG* 4.9 0.4 - - + -
199q THR* 1.3 80.4 - - - +
201q LYS* 1.3 69.2 + - - +
202q ALA* 3.3 7.2 + - - +
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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