Contacts of the helix formed by residues 210 - 223 (chain B) in PDB entry 2NPP
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 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B PHE* 3.7 12.1 + - - -
169B ARG* 4.0 3.1 - - - -
208B HIS* 2.8 22.7 + - - -
209B ASN* 1.3 74.4 - - - +
211B ILE* 1.3 63.2 + - - +
212B ALA 3.1 2.5 - - - -
213B GLU* 3.0 18.9 + - - +
214B LEU* 3.1 27.7 + - - +
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Residues in contact with ILE 211 (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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197B ILE* 5.7 0.4 - - + -
198B PHE* 3.6 32.0 - - + -
201B PHE* 3.8 28.3 - - + -
208B HIS* 3.0 50.2 + - + +
209B ASN 3.8 1.8 - - - -
210B GLY* 1.3 73.4 - - - +
212B ALA* 1.3 68.5 + - - +
214B LEU* 3.4 3.2 + - + +
215B LEU* 2.9 29.4 + - + +
244B LEU* 4.6 3.1 - - + -
253B TYR* 3.5 40.2 - - + -
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Residues in contact with ALA 212 (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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169B ARG* 5.9 0.2 - - - +
209B ASN 5.8 0.7 - - - +
210B GLY 4.9 0.2 - - - -
211B ILE* 1.3 78.0 - - - +
213B GLU* 1.3 68.1 + - - +
215B LEU* 2.8 25.7 + - - +
216B GLU* 3.0 19.1 + - - +
252B VAL* 4.1 16.5 - - + +
253B TYR* 3.7 23.9 - - + +
256B GLN* 4.1 15.1 - - + +
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Residues in contact with GLU 213 (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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161B PHE* 4.1 17.7 - - + -
166B PRO* 4.8 7.7 - - + +
169B ARG* 2.9 55.2 + - + +
170B ASP* 4.6 5.0 - - - +
173B LYS* 4.4 16.2 - - + +
209B ASN 3.6 0.5 - - - +
210B GLY* 3.0 29.9 - - - +
211B ILE 3.4 0.2 - - - -
212B ALA* 1.3 87.8 - - - +
214B LEU* 1.3 63.5 + - - +
216B GLU* 3.0 28.6 + - - +
217B ILE* 3.2 14.7 + - - +
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Residues in contact with LEU 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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158B LEU* 4.2 10.3 - - + -
161B PHE* 3.7 38.4 - - + -
176B LEU* 4.4 2.2 - - + -
194B ILE* 3.5 43.5 - - + -
197B ILE* 4.5 22.2 - - + -
198B PHE* 4.4 13.2 - - + -
208B HIS* 4.3 10.1 - - - +
210B GLY 3.1 17.6 + - - +
211B ILE* 3.8 4.9 - - - +
213B GLU* 1.3 78.9 - - - +
215B LEU* 1.3 61.6 + - - +
217B ILE* 3.6 8.2 + - + +
218B LEU* 3.1 27.9 + - - +
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Residues in contact with LEU 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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198B PHE* 3.7 24.9 - - + -
211B ILE* 2.9 20.6 + - + +
212B ALA 2.8 12.9 + - - +
214B LEU* 1.3 71.1 - - - +
216B GLU* 1.3 56.1 + - - +
218B LEU* 3.1 8.0 + - + +
219B GLY* 2.6 34.8 + - - -
241B LEU* 4.1 21.3 - - + -
244B LEU* 5.1 2.9 - - + -
253B TYR* 3.9 22.9 - - + +
256B GLN* 4.1 12.5 - - + +
257B LEU* 3.5 38.8 - - + +
260B CYS* 3.7 12.4 - - - -
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Residues in contact with GLU 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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170B ASP* 5.5 0.5 - - - +
173B LYS* 2.9 41.9 + - - +
212B ALA* 3.0 16.5 + - - +
213B GLU* 3.0 21.8 + - - +
215B LEU* 1.3 76.7 - - - +
217B ILE* 1.3 63.0 + - - +
219B GLY* 2.9 16.5 + - - -
220B SER* 3.4 8.7 + - - -
256B GLN* 4.4 24.3 - - + +
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Residues in contact with ILE 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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161B PHE* 3.7 18.2 - - + -
173B LYS* 3.2 36.6 - - + +
176B LEU* 3.7 33.7 - - + -
177B HIS* 4.6 24.1 + - + +
180B TYR* 5.7 2.2 - - + -
190B ILE* 6.1 0.4 - - + -
194B ILE* 5.3 3.8 - - + -
213B GLU 3.2 9.3 + - - +
214B LEU* 3.7 10.3 - - + +
215B LEU 3.2 0.2 - - - -
216B GLU* 1.3 80.8 - - - +
218B LEU* 1.3 63.9 + - + +
220B SER* 3.1 13.0 + - - -
221B ILE* 3.1 36.1 + - + +
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Residues in contact with LEU 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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191B ARG* 5.1 11.4 - - + -
194B ILE* 4.1 20.2 - - + -
195B ASN* 5.8 0.4 - - - +
198B PHE* 3.7 24.7 - - + -
214B LEU 3.1 15.0 + - - +
215B LEU* 3.1 13.5 + - + +
217B ILE* 1.3 76.9 - - - +
219B GLY* 1.3 69.1 + - - +
221B ILE* 3.0 26.3 + - + -
222B ILE* 2.7 38.5 + - + +
225B PHE* 6.1 1.1 - - + -
236B PHE* 3.7 37.5 - - + -
260B CYS* 4.7 2.2 - - - -
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Residues in contact with GLY 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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215B LEU 2.6 19.5 + - - -
216B GLU* 2.9 7.1 + - - -
218B LEU* 1.3 75.0 - - - +
220B SER* 1.3 59.7 + - - +
222B ILE* 3.4 5.4 + - - +
223B ASN* 3.1 22.0 + - - +
259B TYR* 4.2 25.0 - - - -
260B CYS* 3.9 15.2 - - - -
263B GLN* 4.8 0.7 - - - +
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Residues in contact with SER 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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177B HIS* 3.9 30.7 - - - -
216B GLU 3.4 7.1 + - - -
217B ILE* 3.1 8.7 + - - -
218B LEU 3.1 0.4 - - - -
219B GLY* 1.3 71.8 - - - +
221B ILE* 1.3 68.3 + - - +
223B ASN* 2.9 30.9 + - - +
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Residues in contact with ILE 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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177B HIS* 5.6 3.6 - - + -
180B TYR* 3.4 53.6 - - + +
190B ILE* 5.8 2.0 - - + -
191B ARG* 4.7 9.6 - - + -
194B ILE* 5.3 5.8 - - + -
217B ILE* 3.1 37.7 - - + +
218B LEU* 3.0 28.0 + - + +
220B SER* 1.3 75.5 - - - +
222B ILE* 1.3 64.6 + - - +
224B GLY* 3.9 7.3 - - - +
225B PHE* 2.9 32.5 - - + -
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Residues in contact with ILE 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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218B LEU* 2.7 31.1 + - + +
219B GLY* 3.5 4.5 - - - +
221B ILE* 1.3 72.4 - - - +
223B ASN* 1.3 54.1 + - - +
224B GLY 2.5 18.4 + - - -
225B PHE* 3.2 34.6 + - + +
236B PHE* 4.2 21.1 - - + -
260B CYS* 3.1 49.1 - - + +
263B GLN* 4.6 6.7 - - + +
264B PHE* 3.5 48.9 - - + +
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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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219B GLY 3.1 14.1 + - - +
220B SER* 2.9 16.6 + - - +
222B ILE* 1.3 74.8 - - - +
224B GLY* 1.3 56.9 + - - +
259B TYR* 3.4 12.8 + - - +
263B GLN* 3.1 43.3 - - + +
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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