Contacts of the helix formed by residues 213 - 224 (chain O) in PDB entry 3MQT
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 ASP 213 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211O TRP* 4.3 1.8 - - - +
212O THR* 1.3 82.6 + - - +
214O TRP* 1.3 70.3 + - - +
215O GLN* 3.0 19.1 + - - +
216O LYS* 3.1 24.0 + - + +
217O ALA* 3.2 9.4 + - - +
236O LEU* 3.8 4.7 - - - +
230P TYR* 4.3 1.6 + - - -
254P ARG* 3.0 32.8 + - - -
277P SER* 5.9 0.7 - - - -
303P ASN* 4.1 9.4 + - - +
305P GLN* 3.3 27.6 - - + +
329P ILE 5.7 2.7 - - - +
331P GLU* 5.1 1.0 - - + +
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Residues in contact with TRP 214 (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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213O ASP* 1.3 74.8 + - - +
215O GLN* 1.3 82.1 + - + +
217O ALA* 3.3 3.7 + - - +
218O ARG* 2.7 67.5 + - + +
236O LEU* 3.7 17.4 - - + +
243O GLY* 3.6 18.2 - - - +
246O LYS* 3.3 54.3 - - + +
247O LEU* 3.5 19.8 - - + +
250O ALA* 3.8 15.5 - - + -
275P GLY 6.0 0.9 - - - -
277P SER* 4.1 8.4 + - - -
303P ASN* 2.9 46.7 + - + +
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Residues in contact with GLN 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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213O ASP* 3.0 12.5 + - - +
214O TRP* 1.3 110.5 - - + +
216O LYS* 1.3 55.7 + - - +
218O ARG* 3.1 33.2 + - - +
219O TRP* 3.2 25.3 + - - +
253P THR* 3.3 33.6 + - - -
254P ARG* 3.6 30.9 + - + +
255P LEU 4.8 0.4 - - - +
277P SER* 2.8 27.1 + - - +
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Residues in contact with LYS 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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183O ASP* 3.5 27.0 + - - +
211O TRP* 3.9 13.7 - - + +
213O ASP* 3.1 21.4 + - + +
215O GLN* 1.3 76.9 - - - +
217O ALA* 1.3 64.1 + - - +
219O TRP* 3.4 7.6 + - + +
220O THR* 3.2 24.1 + - - -
230P TYR* 5.5 2.0 - - + -
254P ARG* 3.4 17.0 - - - +
331P GLU* 2.9 38.3 + - + +
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Residues in contact with ALA 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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211O TRP* 3.7 23.0 - - + +
213O ASP 3.2 7.7 + - - +
214O TRP 3.5 8.1 - - - +
216O LYS* 1.3 75.2 - - - +
218O ARG* 1.3 65.8 + - - +
220O THR* 3.2 3.2 + - - -
221O PHE* 3.1 27.7 + - - -
235O CYS* 3.5 31.9 - - - -
236O LEU* 4.1 5.2 - - + -
247O LEU* 3.8 11.7 - - + -
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Residues in contact with ARG 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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214O TRP* 2.7 43.5 + - + +
215O GLN* 3.1 35.4 + - - +
216O LYS 3.3 0.2 - - - -
217O ALA* 1.3 72.3 - - - +
219O TRP* 1.3 63.7 + - - +
221O PHE* 3.9 0.5 - - - +
222O ARG* 2.9 37.8 + - + +
247O LEU* 3.7 16.5 - - + +
250O ALA* 3.7 30.3 + - + +
251O ILE* 5.2 4.1 - - + +
248P ALA 5.4 3.0 + - - -
249P ALA 5.3 3.4 + - - -
251P ILE 3.5 19.0 + - - -
252P ASN* 3.6 33.4 + - - +
253P THR 4.0 2.2 + - - +
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Residues in contact with TRP 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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183O ASP* 4.0 31.4 - - + -
184O LYS* 3.2 42.8 - - + -
187O VAL* 4.0 4.0 - - + -
215O GLN 3.2 11.0 + - - +
216O LYS* 3.7 11.9 - - + +
217O ALA 3.3 0.6 - - - -
218O ARG* 1.3 79.5 - - - +
220O THR* 1.3 73.8 + - - +
222O ARG* 3.7 18.3 + - - +
223O GLN* 2.8 59.9 + - + +
228P ASP* 2.7 41.7 + - - -
254P ARG* 6.0 0.4 - - - +
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Residues in contact with THR 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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183O ASP* 3.4 14.3 + - - +
186O ILE* 4.6 9.4 - - + -
187O VAL* 3.7 17.1 - - + +
211O TRP* 3.4 35.9 - - + -
216O LYS 3.2 12.0 + - - -
217O ALA 3.2 8.4 + - - -
219O TRP* 1.3 91.3 - - - +
221O PHE* 1.3 70.5 + - + +
223O GLN* 3.3 16.6 + - - +
224O LEU* 3.3 17.2 + - + +
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Residues in contact with PHE 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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175O ILE* 5.2 0.2 - - + -
190O LEU* 4.5 9.2 - - + -
205O VAL* 5.2 2.5 - - + -
207O CYS* 3.7 21.8 - - - -
211O TRP* 3.6 31.9 - + - -
217O ALA* 3.1 25.0 + - + +
218O ARG 4.5 0.2 - - - +
220O THR* 1.3 74.6 - - + +
222O ARG* 1.3 65.5 + - - +
224O LEU* 3.2 25.8 + - + +
225O GLU* 3.3 16.2 + - - +
229O LEU* 3.7 32.1 - - + -
232O ILE* 3.8 29.4 - - + -
235O CYS* 3.8 16.8 - - - -
247O LEU* 5.3 4.3 - - + -
251O ILE* 4.3 16.4 - - + -
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Residues in contact with ARG 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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218O ARG* 2.9 44.3 + - + +
219O TRP* 3.7 32.7 - - - +
221O PHE* 1.3 77.0 - - - +
223O GLN* 1.3 71.3 + - - +
224O LEU 3.2 0.5 + - - -
225O GLU* 3.3 38.8 + - - +
251O ILE* 5.6 1.2 - - - +
228P ASP* 4.5 5.9 + - - -
252P ASN* 3.1 59.5 + - - +
253P THR* 5.6 4.0 - - - +
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Residues in contact with GLN 223 (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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184O LYS* 4.3 7.9 + - - +
187O VAL* 3.6 29.2 - - + -
191O ARG* 2.9 31.1 + - - +
219O TRP* 2.8 61.6 + - + +
220O THR 3.3 8.4 + - - +
222O ARG* 1.3 93.4 - - - +
224O LEU* 1.3 59.9 + - - +
225O GLU 3.4 1.3 + - - -
226O ASP* 3.9 3.6 - - - +
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Residues in contact with LEU 224 (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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187O VAL* 3.7 36.1 - - + +
190O LEU* 3.5 34.8 - - + -
191O ARG* 3.7 17.5 - - + +
220O THR* 3.3 17.2 + - + +
221O PHE* 3.2 24.1 + - + +
222O ARG 3.1 1.4 - - - -
223O GLN* 1.3 77.6 - - - +
225O GLU* 1.3 63.6 + - - +
226O ASP* 3.2 3.8 - - - -
227O ILE* 3.1 43.1 - - + +
228O ASP 3.9 1.6 + - - -
229O LEU* 4.4 11.0 + - + +
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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