Contacts of the helix formed by residues 213 - 224 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230L TYR* 4.3 1.4 + - - -
254L ARG* 2.8 35.6 + - - -
277L SER* 5.7 2.1 - - - +
303L ASN* 4.1 9.1 + - - +
305L GLN* 3.3 28.5 - - + +
329L ILE 5.5 1.8 - - - +
331L GLU* 5.0 1.9 - - + +
211W TRP* 4.3 2.0 - - - +
212W THR* 1.3 80.0 + - - +
214W TRP* 1.3 68.1 + - - +
215W GLN* 3.0 21.7 + - - +
216W LYS* 3.1 25.1 + - + +
217W ALA* 3.3 8.7 + - - +
236W LEU* 4.0 4.0 - - - +
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Residues in contact with TRP 214 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L GLY 5.9 1.6 - - - -
277L SER* 4.1 8.1 + - - +
303L ASN* 2.9 46.8 + - + +
212W THR 3.6 0.8 + - - -
213W ASP* 1.3 73.1 + - - +
215W GLN* 1.3 84.0 + - + +
217W ALA* 3.4 4.0 + - - +
218W ARG* 2.8 60.0 + - + +
236W LEU* 3.7 18.1 - - + +
243W GLY* 3.5 18.8 - - - +
246W LYS* 3.4 54.9 - - + +
247W LEU* 3.7 19.1 - - + +
250W ALA* 3.7 16.4 - - + -
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Residues in contact with GLN 215 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L THR* 3.4 26.5 + - - +
254L ARG* 3.6 34.5 + - + +
255L LEU 4.9 0.2 - - - +
277L SER* 2.7 32.4 + - - +
213W ASP* 3.0 13.1 + - - +
214W TRP* 1.3 106.8 - - + +
216W LYS* 1.3 56.1 + - - +
218W ARG* 3.2 36.7 + - - +
219W TRP* 3.0 26.2 + - - +
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Residues in contact with LYS 216 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230L TYR* 5.8 0.9 - - + -
254L ARG* 3.4 13.5 - - - +
331L GLU* 3.0 42.7 + - + +
183W ASP* 3.1 35.4 - - - +
211W TRP* 3.8 13.2 - - + +
213W ASP* 3.1 20.2 + - + +
215W GLN* 1.3 75.4 - - - +
217W ALA* 1.3 65.5 + - - +
218W ARG 3.2 0.2 - - - -
219W TRP* 3.3 7.8 + - + +
220W THR* 3.1 26.3 + - - -
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Residues in contact with ALA 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211W TRP* 3.8 25.4 - - + -
213W ASP 3.3 4.8 + - - +
214W TRP 3.5 8.5 - - - +
216W LYS* 1.3 75.2 - - - +
218W ARG* 1.3 67.9 + - - +
220W THR* 3.1 2.2 + - - -
221W PHE* 3.0 29.5 + - - -
235W CYS* 3.7 31.0 - - - -
236W LEU* 4.3 2.9 - - + -
247W LEU* 4.0 13.7 - - + -
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Residues in contact with ARG 218 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249L ALA 5.7 1.2 + - - -
251L ILE 3.7 18.0 + - - -
252L ASN* 3.4 28.5 - - - +
253L THR 3.9 2.2 + - - +
214W TRP* 2.8 35.6 + - + +
215W GLN* 3.2 39.2 + - - +
217W ALA* 1.3 74.3 - - - +
219W TRP* 1.3 56.4 + - - +
221W PHE* 3.9 0.3 - - - +
222W ARG* 2.9 51.8 + - + +
247W LEU* 3.7 12.3 - - + +
250W ALA* 3.7 34.2 + - + +
251W ILE* 5.3 5.1 - - + +
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Residues in contact with TRP 219 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ASP* 2.9 40.2 + - - -
253L THR* 6.3 1.6 - - + -
254L ARG* 5.8 1.3 - - - +
183W ASP* 4.0 10.1 - - + -
184W LYS* 3.5 52.5 - - + -
187W VAL* 3.9 13.9 - - + -
215W GLN 3.0 14.6 + - - +
216W LYS* 3.5 12.8 - - + +
217W ALA 3.3 0.2 - - - -
218W ARG* 1.3 77.0 - - - +
220W THR* 1.3 88.9 + - - +
222W ARG* 3.3 19.0 + - - +
223W GLN* 3.1 59.8 + - + +
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Residues in contact with THR 220 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183W ASP* 3.3 25.7 + - - +
186W ILE* 4.6 8.5 - - + -
187W VAL* 4.0 15.2 - - + +
211W TRP* 3.4 29.4 - - + -
216W LYS 3.1 14.7 + - - -
217W ALA 3.1 7.2 + - - -
219W TRP* 1.3 85.2 - - - +
221W PHE* 1.3 63.2 + - + +
223W GLN* 3.2 18.5 + - - +
224W LEU* 3.3 24.7 + - + +
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Residues in contact with PHE 221 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190W LEU* 4.4 9.4 - - + -
205W VAL* 5.1 2.5 - - + -
207W CYS* 3.7 12.6 - - - -
211W TRP* 3.6 32.1 - + - -
217W ALA 3.0 28.0 + - - +
218W ARG 4.6 0.2 - - - +
220W THR* 1.3 76.5 - - + +
222W ARG* 1.3 64.3 + - - +
224W LEU* 3.3 21.6 + - + +
225W GLU* 3.2 24.1 + - - +
229W LEU* 3.7 32.3 - - + -
232W ILE* 3.6 37.0 - - + -
235W CYS* 3.7 17.3 - - - -
247W LEU* 5.5 3.6 - - + -
251W ILE* 4.5 16.6 - - + -
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Residues in contact with ARG 222 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ASP* 4.5 5.7 + - - -
252L ASN* 3.1 56.5 + - - +
253L THR* 5.3 4.9 - - - +
218W ARG* 2.9 46.3 + - + +
219W TRP* 3.3 34.0 + - - +
221W PHE* 1.3 74.7 - - - +
223W GLN* 1.3 74.0 + - - +
224W LEU 3.1 0.9 + - - -
225W GLU* 3.3 36.8 + - - +
251W ILE* 5.6 0.6 - - - +
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Residues in contact with GLN 223 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ASP* 5.2 1.0 + - - -
184W LYS* 4.5 6.2 + - - +
187W VAL* 3.8 18.8 - - + -
191W ARG* 2.7 31.9 + - - +
219W TRP* 3.1 74.0 + - + +
220W THR 3.2 7.1 + - - +
222W ARG* 1.3 89.6 - - - +
224W LEU* 1.3 58.9 + - - +
225W GLU 3.6 0.5 + - - -
226W ASP* 3.5 4.7 - - - +
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Residues in contact with LEU 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187W VAL* 3.5 39.9 - - + +
190W LEU* 3.5 33.9 - - + -
191W ARG* 3.8 15.3 - - + -
220W THR* 3.3 25.4 + - + +
221W PHE* 3.3 25.5 + - + +
222W ARG 3.1 1.0 - - - -
223W GLN* 1.3 78.2 - - - +
225W GLU* 1.3 65.0 + - - +
226W ASP* 3.1 5.4 - - - -
227W ILE* 2.9 37.4 + - + +
228W ASP 3.6 1.9 + - - -
229W LEU* 4.6 6.8 + - + +
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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