Contacts of the helix formed by residues 213 - 224 (chain B) in PDB entry 3NQ0
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 GLY 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B LYS* 3.2 30.5 - - - -
151B ARG* 3.9 4.3 - - - +
152B ASN* 4.2 4.9 - - - +
212B GLY* 1.3 72.1 - - - -
214B GLN* 1.3 54.9 + - - -
216B GLY* 2.7 27.4 + - - -
217B VAL* 4.0 4.0 + - - +
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Residues in contact with GLN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B THR* 3.7 16.7 + - - +
139B ILE 5.8 0.2 - - - +
146B SER* 4.8 4.6 + - - +
148B GLY 2.7 27.9 + - - -
149B LEU* 3.7 8.0 - - - +
150B LYS* 2.8 31.4 + - - +
213B GLY* 1.3 70.3 - - - -
215B MET* 1.3 57.8 + - - +
216B GLY 3.2 0.5 + - - -
217B VAL* 3.0 16.0 + - - +
220B THR* 3.0 46.3 + - - +
221B ALA* 3.2 7.5 + - - +
223B ASN* 4.1 17.5 - - + +
224B ASP* 5.1 6.3 - - + +
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Residues in contact with MET 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LYS 5.1 0.2 + - - -
207B VAL* 6.4 1.3 - - - -
208B HIS* 3.1 54.9 + - - +
211B VAL* 4.0 24.7 - - + -
212B GLY 3.2 12.1 + - - +
213B GLY 2.9 0.8 - - - -
214B GLN* 1.3 76.3 - - - +
216B GLY* 1.3 63.4 + - - +
217B VAL* 3.2 3.9 + - - -
221B ALA* 3.0 42.0 - - + +
224B ASP* 3.7 28.2 - - + +
226B VAL* 4.2 4.9 - - + -
227B PHE* 3.2 38.1 - - + -
230B HIS* 5.6 3.8 - - - -
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B HIS* 3.7 13.4 - - - +
209B ARG* 3.0 33.4 + - - -
212B GLY* 3.3 10.7 + - - -
213B GLY 2.7 20.5 + - - -
215B MET* 1.3 74.1 - - - +
217B VAL* 1.3 61.8 + - - +
218B VAL* 4.2 1.4 + - - +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ARG* 5.1 3.4 - - - +
213B GLY 4.0 2.2 + - - +
214B GLN* 3.0 5.5 - - - +
215B MET 4.3 2.7 - - - -
216B GLY* 1.3 83.1 - - - +
218B VAL* 1.3 67.3 + - - +
219B PRO* 3.3 11.2 - - + -
220B THR* 2.7 40.8 + - + +
221B ALA* 3.0 16.6 + - - +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B HIS* 3.3 33.1 + - + +
46B GLY* 6.2 2.0 - - - -
60B HIS* 3.5 27.8 - - + +
204B HIS* 6.2 3.1 - - + -
205B ASN* 6.2 1.6 - - - +
208B HIS* 5.9 9.8 - - + -
215B MET 4.8 1.2 + - - -
216B GLY 4.2 1.9 + - - +
217B VAL* 1.3 69.2 - - - +
219B PRO* 1.3 72.9 - - + +
221B ALA* 3.2 22.4 + - - +
502B CU 4.3 0.9 - - - -
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Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 4.4 10.0 - - - +
42B HIS* 4.9 1.1 - - - +
43B GLY* 4.3 25.1 + - - -
141B GLU* 3.5 38.0 - - + +
217B VAL* 3.3 14.8 - - + -
218B VAL* 1.3 96.7 - - + +
220B THR* 1.3 62.5 + - + +
222B PRO* 4.3 5.7 - - - +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 5.1 0.4 - - - -
139B ILE 4.5 2.5 - - - +
140B ASP* 4.4 6.3 - - - -
141B GLU* 4.1 28.5 - - + +
214B GLN* 3.0 25.1 + - - +
217B VAL* 2.7 32.9 + - + +
219B PRO* 1.3 82.2 - - + +
221B ALA* 1.3 65.4 + - - +
222B PRO* 3.4 4.5 - - - -
223B ASN* 2.8 34.3 + - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B HIS* 4.2 4.3 - - + +
214B GLN 3.3 10.7 - - - +
215B MET* 3.0 38.4 + - + +
217B VAL 3.0 9.2 + - - +
218B VAL* 3.2 20.2 - - - +
220B THR* 1.3 77.3 - - - +
222B PRO* 1.3 61.8 - - + +
223B ASN 3.1 5.7 + - - -
224B ASP* 3.3 12.3 + - - +
227B PHE* 3.3 16.4 - - + +
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Residues in contact with PRO 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 2.8 31.4 + - - -
39B ILE* 3.9 23.6 - - + -
42B HIS* 3.9 22.7 - - + +
72B TYR* 3.5 26.0 - - - +
218B VAL 3.8 6.7 - - - +
219B PRO 4.3 5.8 - - - +
220B THR 3.5 3.6 - - - -
221B ALA* 1.3 90.1 - - + +
223B ASN* 1.3 55.5 + - - +
224B ASP 3.0 7.8 + - - +
227B PHE* 3.9 20.9 - - + -
228B PHE* 4.6 4.3 - - + -
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Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 6.0 0.2 - - - +
35B TYR* 4.4 1.3 - - - -
39B ILE* 3.2 28.1 - - - +
136B TRP* 2.7 33.1 + - - +
137B THR 4.6 0.3 - - - +
138B THR* 3.3 28.2 - - + +
139B ILE 3.0 40.0 + - - +
149B LEU* 4.5 2.6 - - - +
214B GLN* 4.1 11.1 - - + +
220B THR* 2.8 35.3 + - - +
221B ALA 3.1 1.2 + - - -
222B PRO* 1.3 77.7 - - - +
224B ASP* 1.3 56.9 + - - +
225B PRO* 3.5 2.2 - - - +
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 4.1 0.3 + - - -
149B LEU* 3.6 16.7 - - + +
150B LYS 4.5 0.7 - - - +
151B ARG* 2.6 50.6 + - - +
211B VAL* 4.4 0.5 - - - +
214B GLN* 5.2 2.5 - - + -
215B MET* 3.7 27.3 + - + +
221B ALA 3.3 3.4 + - - +
222B PRO 3.0 3.8 - - - +
223B ASN* 1.3 79.6 - - - +
225B PRO* 1.3 69.3 - - - +
226B VAL* 3.0 19.7 + - - +
227B PHE* 2.8 24.8 + - - +
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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