Contacts of the helix formed by residues 202 - 212 (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 GLN 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B ASP* 4.5 18.3 + - + -
193B GLN* 5.0 4.0 - - - +
196B GLY* 3.0 21.0 + - - +
198B ILE 3.4 16.6 - - - +
199B ASN* 2.9 32.2 - - + +
200B GLY 4.7 0.2 - - - -
201B PRO* 1.3 78.4 - - - +
203B LEU* 1.3 80.6 + - + +
204B HIS 3.1 0.5 + - - -
205B ASN 2.9 6.8 + - - -
206B ARG* 2.7 46.5 + - - +
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Residues in contact with LEU 203 (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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94B TRP* 4.2 8.5 - - + -
163B PRO* 3.8 30.4 - - + +
167B ASP* 4.0 17.9 - - + +
168B VAL* 3.8 27.8 - - + +
171B ALA* 3.7 27.6 - - + -
193B GLN* 3.4 24.2 - - - +
194B LEU* 3.3 24.0 - - + +
202B GLN* 1.3 79.8 - - + +
204B HIS* 1.3 69.2 + - - +
206B ARG* 2.7 13.0 + - - +
207B VAL* 2.9 17.9 + - - +
237B ILE* 6.4 0.2 - - + -
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Residues in contact with HIS 204 (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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60B HIS* 5.0 9.6 - + - -
65B PHE* 3.7 25.2 - + + -
94B TRP* 5.0 1.6 - - - -
194B LEU* 3.0 18.0 + - + +
195B GLU* 3.2 14.8 + - + +
202B GLN 3.1 0.2 + - - -
203B LEU* 1.3 80.4 - - - +
205B ASN* 1.3 78.7 + - - +
206B ARG 3.1 0.2 + - - -
207B VAL* 3.1 10.6 + - - +
208B HIS* 2.9 44.0 + + - -
218B VAL* 6.2 3.1 - - + -
230B HIS* 3.2 38.6 - + + -
231B HIS* 3.4 22.0 + + - -
234B VAL* 4.4 9.6 - - + -
502B CU 4.4 1.6 - - - -
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Residues in contact with ASN 205 (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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195B GLU* 2.8 30.5 + - - +
196B GLY 3.4 17.9 - - - +
197B PHE* 3.3 38.1 - - - -
201B PRO* 4.3 8.9 - - + +
202B GLN 2.9 10.3 + - - +
204B HIS* 1.3 88.9 + - - +
206B ARG* 1.3 61.7 + - - +
208B HIS* 3.6 6.2 + - - +
209B ARG* 3.2 28.5 + - + +
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Residues in contact with ARG 206 (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 GLU 3.6 13.7 + - - -
159B ALA* 3.7 16.8 - - + +
160B PRO* 3.7 4.2 - - - +
161B THR* 2.7 62.6 + - - +
162B LEU 4.4 0.4 - - - -
163B PRO* 4.1 22.0 - - + -
167B ASP* 5.5 0.8 + - - -
201B PRO* 3.1 22.0 + - - +
202B GLN* 2.7 47.4 + - - +
203B LEU* 2.7 13.8 + - - +
205B ASN* 1.3 69.9 - - - +
207B VAL* 1.3 58.1 + - - +
209B ARG* 3.2 6.6 + - - +
210B TRP* 2.7 30.6 + - - +
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Residues in contact with VAL 207 (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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92B TRP* 3.7 28.3 - - + -
94B TRP* 3.7 24.2 - - + -
162B LEU* 4.3 5.4 - - + -
163B PRO* 3.9 13.2 - - + -
203B LEU 2.9 12.4 + - - +
204B HIS 3.1 0.4 + - - +
206B ARG* 1.3 74.5 - - - +
208B HIS* 1.3 64.8 + - - +
210B TRP* 3.0 15.9 + - - +
211B VAL* 3.0 20.1 + - + +
215B MET* 6.4 1.1 - - - -
230B HIS* 3.1 43.7 - - + +
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Residues in contact with HIS 208 (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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204B HIS* 2.9 58.1 + + - -
205B ASN* 3.8 7.4 - - - +
206B ARG 3.3 0.4 - - - -
207B VAL* 1.3 78.4 - - - +
209B ARG* 1.3 64.7 + - + +
211B VAL* 3.6 1.5 + - - +
212B GLY 3.2 18.7 + - - -
215B MET* 3.1 63.4 + - + +
216B GLY* 3.7 7.8 - - - +
218B VAL* 5.9 8.9 - - + +
221B ALA* 4.2 3.7 - - + +
227B PHE* 3.8 18.4 - + - -
230B HIS* 4.1 8.3 - + - -
231B HIS* 3.6 7.3 + + - -
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Residues in contact with ARG 209 (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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152B ASN 4.8 0.3 - - - +
155B ALA 5.3 0.3 + - - -
156B THR* 4.3 35.1 - - - +
158B GLU* 5.3 10.8 + - - -
159B ALA* 3.3 25.5 - - + +
201B PRO* 4.2 20.9 - - + -
205B ASN* 3.2 15.2 + - + +
206B ARG 3.2 5.0 + - - +
208B HIS* 1.3 81.1 - - + +
210B TRP* 1.3 63.9 + - - +
212B GLY* 3.7 8.6 + - - -
216B GLY* 3.0 37.3 + - - -
217B VAL* 5.1 4.2 - - - +
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Residues in contact with TRP 210 (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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92B TRP* 4.2 11.9 - + - -
103B PRO* 4.0 31.6 - - + +
104B SER* 4.6 2.7 - - - -
109B TRP* 4.3 7.6 - + - -
152B ASN 2.9 4.9 - - - +
153B PHE* 3.5 48.2 - + + -
154B GLY* 2.9 42.8 + - - +
155B ALA 4.4 0.2 + - - -
159B ALA* 4.0 7.6 - - + +
160B PRO 3.4 28.1 + - - -
161B THR* 3.8 16.2 - - - +
162B LEU* 3.7 33.1 - - + +
206B ARG 2.7 17.5 + - - +
207B VAL 3.0 9.5 + - - +
209B ARG* 1.3 72.8 - - - +
211B VAL* 1.3 86.2 + - + +
212B GLY 3.1 0.5 + - - -
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Residues in contact with VAL 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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92B TRP* 4.2 13.2 - - + -
109B TRP* 4.5 8.1 - - + -
151B ARG* 3.6 13.6 - - + -
152B ASN 2.8 27.7 + - - +
153B PHE* 3.6 21.1 - - + -
207B VAL* 3.0 29.9 + - + +
208B HIS* 5.0 0.4 - - - -
210B TRP* 1.3 91.8 - - + +
212B GLY* 1.3 64.9 + - - +
215B MET* 4.0 27.1 - - + -
224B ASP* 4.4 2.9 - - - +
226B VAL* 4.9 2.2 - - + -
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Residues in contact with GLY 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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150B LYS 4.1 2.3 - - - +
151B ARG* 4.2 0.7 - - - -
152B ASN* 3.8 10.8 - - - -
156B THR* 6.5 0.2 - - - -
208B HIS 3.2 11.9 + - - -
209B ARG* 4.1 7.2 - - - -
210B TRP 3.1 4.0 + - - -
211B VAL* 1.3 83.6 - - - +
213B GLY* 1.3 69.8 + - - -
214B GLN 3.6 0.2 + - - -
215B MET* 3.2 18.7 + - - +
216B GLY* 3.5 7.6 - - - -
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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