Contacts of the helix formed by residues 214 - 222 (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 ASN 214 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162O PHE* 3.3 30.5 - - + +
164O LEU 4.8 1.8 - - - +
166O ILE* 3.8 21.3 - - + -
169O THR* 5.4 2.0 - - + +
173O HIS* 2.8 41.0 + - + +
210O ASN 3.3 10.1 + - - +
211O TYR 3.5 4.3 + - - +
213O SER* 1.3 76.2 - - - +
215O LEU* 1.3 59.4 + - - +
216O LEU 3.5 0.8 + - - -
217O LYS* 4.2 9.1 - - - +
218O LEU 4.2 0.2 + - - -
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Residues in contact with LEU 215 (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* 5.7 4.3 - - + -
162O PHE* 3.9 12.1 - - + -
173O HIS* 4.3 2.2 - - + -
194O LEU* 5.6 9.4 - - + -
211O TYR* 3.6 55.1 + - + +
212O THR 4.9 2.9 + - - +
213O SER 3.2 1.4 - - - +
214O ASN* 1.3 82.9 - - - +
216O LEU* 1.3 62.5 + - - +
217O LYS 3.5 0.7 - - - -
218O LEU* 3.7 24.7 - - + +
219O ARG* 3.1 26.5 + - - +
229O ILE* 4.3 26.6 - - + +
233O LEU* 5.7 11.0 - - + -
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Residues in contact with LEU 216 (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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212O THR 4.7 11.9 - - - +
213O SER* 3.5 19.4 + - - +
215O LEU* 1.3 80.5 - - - +
217O LYS* 1.3 63.3 + - - +
219O ARG* 4.0 15.7 - - + +
220O GLY* 3.3 18.5 + - - -
230O TRP* 6.0 2.2 - - + -
338O LEU* 5.4 1.8 - - + +
339O VAL* 5.1 9.9 - - + +
342O HIS* 3.4 54.2 - - + +
343O VAL* 3.7 29.6 - - + -
346O GLN* 4.1 11.7 + - + +
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Residues in contact with LYS 217 (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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166O ILE* 5.2 15.6 - - + +
169O THR* 4.7 11.9 + - - -
170O VAL* 5.8 2.4 + - - +
173O HIS* 4.2 22.1 - - + +
174O ASP* 5.0 12.1 + - - +
213O SER 4.4 2.6 + - - +
214O ASN* 4.2 11.8 + - - +
216O LEU* 1.3 76.5 - - - +
218O LEU* 1.3 61.9 + - - +
220O GLY* 3.4 10.0 + - - -
221O TYR* 3.9 31.9 + - + +
342O HIS* 4.7 2.9 + - - -
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Residues in contact with LEU 218 (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* 5.7 5.8 - - + -
173O HIS* 3.5 38.4 - - + +
176O LEU* 3.7 39.7 - - + -
177O LYS* 4.7 9.3 - - + +
180O LEU* 5.4 9.4 - - + -
214O ASN 4.2 0.2 + - - -
215O LEU* 3.7 23.7 + - + +
216O LEU 3.3 0.2 - - - -
217O LYS* 1.3 81.5 - - - +
219O ARG* 1.3 61.6 + - - +
220O GLY 3.6 0.2 + - - -
221O TYR* 3.8 3.8 + - - +
222O CYS* 3.5 20.4 + - + +
229O ILE* 5.2 7.6 - - + -
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Residues in contact with ARG 219 (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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215O LEU 3.1 19.5 + - - +
216O LEU* 4.5 15.6 - - + +
217O LYS 3.4 0.2 - - - -
218O LEU* 1.3 75.4 - - - +
220O GLY* 1.3 65.5 + - - +
222O CYS 2.9 29.7 + - - +
223O SER* 3.8 10.5 + - - +
226O GLY* 3.6 20.4 + - - -
229O ILE* 3.7 36.1 - - + +
230O TRP* 3.1 46.2 - - - +
343O VAL* 6.2 0.4 - - - +
346O GLN* 4.8 21.2 + - - +
360O VAL* 5.1 21.0 - - - +
364O LEU* 6.1 0.4 - - - +
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Residues in contact with GLY 220 (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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216O LEU 3.3 18.9 + - - -
217O LYS 3.4 3.3 + - - -
218O LEU 3.3 1.2 - - - -
219O ARG* 1.3 76.8 - - - +
221O TYR* 1.3 67.5 + - - +
222O CYS 5.0 0.2 - - - -
223O SER* 4.7 8.2 - - - -
346O GLN* 4.3 18.3 - - - -
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Residues in contact with TYR 221 (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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174O ASP* 5.0 0.4 - - - -
177O LYS* 3.5 54.9 + - + +
180O LEU* 5.9 2.0 - - - +
181O ARG* 2.9 38.1 + - + +
217O LYS* 3.9 26.7 + - + +
218O LEU* 3.8 5.4 + - - +
219O ARG 3.2 0.4 - - - -
220O GLY* 1.3 83.0 - - - +
222O CYS* 1.3 58.8 + - + +
223O SER* 3.5 1.8 - - - -
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Residues in contact with CYS 222 (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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91D ARG* 5.9 2.7 - - - -
180O LEU* 3.7 42.0 - - + -
181O ARG* 4.9 0.7 - - - +
187O MET* 4.5 3.4 - - - -
218O LEU* 3.5 17.5 + - + +
219O ARG* 2.9 23.0 + - - +
221O TYR* 1.3 75.6 - - - +
223O SER* 1.3 59.9 + - - +
224O GLU* 5.1 0.7 - - - -
225O LEU* 3.9 26.9 + - - +
226O GLY 5.0 1.9 + - - -
229O ILE* 4.6 13.4 - - + +
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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