Contacts of the helix formed by residues 204 - 212 (chain O) in PDB entry 6RQT
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 THR 204 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202O ASN 4.0 0.4 + - - -
203O ASP* 1.3 99.4 - - - +
205O ARG* 1.3 72.3 + - - +
206O ARG* 3.6 6.4 + - + +
207O LYS* 3.9 22.5 + - + -
208O LEU* 3.6 8.8 - - - +
331O LYS* 5.6 0.4 - - - -
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Residues in contact with ARG 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204O THR* 1.3 82.8 + - - +
206O ARG* 1.3 93.5 + - + +
208O LEU* 3.3 14.3 + - - +
209O VAL* 3.5 21.1 + - + +
330O THR* 3.5 24.4 + - - +
331O LYS* 3.7 46.8 - - + +
334O SER* 5.7 3.6 - - - -
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Residues in contact with ARG 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O ILE 3.8 1.0 - - - +
165O PRO* 5.9 1.9 - - - +
204O THR* 3.5 4.6 + - + +
205O ARG* 1.3 104.0 - - + +
207O LYS* 1.3 64.0 + - + +
209O VAL* 4.6 4.7 - - - -
210O ASN* 3.4 24.3 + - - +
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Residues in contact with LYS 207 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O ILE* 2.9 62.6 - - + +
164O LEU* 5.4 9.3 - - + +
203O ASP* 3.3 30.3 - - - +
204O THR* 3.9 16.2 + - + -
205O ARG 3.3 0.6 - - - -
206O ARG* 1.3 78.5 - - + +
208O LEU* 1.3 67.6 + - + +
211O TYR* 3.7 2.3 + - - +
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Residues in contact with LEU 208 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O ILE* 5.8 1.6 - - + -
198O PHE* 6.2 2.0 - - + -
199O PRO* 3.7 47.8 - - + +
200O ASN 3.3 21.5 - - - +
201O LYS* 3.8 15.5 - - + -
203O ASP* 3.7 26.5 - - + +
204O THR 3.6 10.8 - - - +
205O ARG 3.3 6.5 + - - +
207O LYS* 1.3 78.8 - - + +
209O VAL* 1.3 60.3 + - + +
211O TYR* 3.1 27.5 + - - +
212O THR* 3.7 7.4 + - - +
331O LYS* 4.9 6.3 - - - +
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Residues in contact with VAL 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205O ARG* 3.5 22.7 + - + +
206O ARG* 5.2 3.1 - - - -
208O LEU* 1.3 76.6 - - + +
210O ASN* 1.3 64.7 + - + +
211O TYR 3.2 0.2 - - - -
212O THR* 2.3 38.7 + - + +
213O SER 4.0 1.0 + - - -
331O LYS* 4.4 8.5 - - + +
334O SER* 3.3 46.4 - - - +
335O ILE* 3.7 18.6 - - + -
338O LEU* 4.0 5.9 - - - +
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Residues in contact with ASN 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O PHE 4.1 2.2 - - - +
163O ILE 3.7 10.3 - - - +
164O LEU 4.5 10.7 - - - +
165O PRO* 4.9 8.7 - - + -
166O ILE* 4.5 6.2 - - + +
206O ARG 3.4 20.7 + - - +
208O LEU 3.2 0.6 - - - -
209O VAL* 1.3 82.5 - - - +
211O TYR* 1.3 61.2 + - - +
213O SER* 3.3 8.3 + - - +
214O ASN* 3.3 21.1 + - - +
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Residues in contact with TYR 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 3.4 41.6 - - + +
162O PHE* 3.3 30.9 + - + +
163O ILE* 3.7 22.6 + - + -
194O LEU* 3.8 13.7 + - - -
197O PHE* 3.8 21.2 + - + +
198O PHE* 5.3 7.9 - + - -
199O PRO* 6.0 1.3 - - + -
207O LYS 3.7 3.0 + - - +
208O LEU* 3.1 14.0 + - - +
210O ASN* 1.3 78.4 - - - +
212O THR* 1.3 63.5 + - + +
213O SER 3.3 0.5 + - - -
214O ASN 3.5 6.6 + - - -
215O LEU* 3.6 41.6 + - + +
232O LEU* 4.7 16.8 - - + +
233O LEU* 5.7 6.5 - - + +
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Residues in contact with THR 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198O PHE* 6.0 5.8 - - + -
208O LEU 3.8 11.0 - - - +
209O VAL* 2.3 42.4 + - + +
211O TYR* 1.3 82.5 - - + +
213O SER* 1.3 56.8 + - - +
215O LEU* 4.9 3.1 + - - +
216O LEU* 4.7 8.8 - - - +
233O LEU* 4.4 34.3 - - + +
335O ILE* 5.1 9.1 - - + +
338O LEU* 3.3 15.2 - - - +
339O VAL* 4.6 17.2 - - - +
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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