Contacts of the helix formed by residues 201 - 211 (chain B) in PDB entry 1NUS
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 SER 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LYS* 6.3 0.4 - - - -
169A SER* 3.6 27.1 - - - -
170A HIS 5.0 0.4 - - - -
171A ASP* 3.8 8.0 + - - +
175A TYR* 5.2 0.9 + - - -
167B ARG* 5.7 0.9 - - - +
199B GLU 3.8 2.4 + - - -
200B ILE* 1.3 75.2 - - - +
202B ALA* 1.3 57.0 + - - +
203B THR* 3.1 14.4 + - - -
204B TYR* 2.9 34.0 + - - +
205B ILE* 2.9 29.1 + - - +
502B APC 4.1 7.7 + - - -
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Residues in contact with ALA 202 (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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16B ASN 4.2 4.3 - - - +
17B PRO 4.2 18.8 - - - +
19B THR* 4.5 5.5 - - + +
22B HIS* 4.7 1.8 - - + -
200B ILE* 3.9 3.0 + - - +
201B SER* 1.3 72.1 + - - +
203B THR* 1.3 61.8 + - - +
205B ILE* 3.0 13.7 + - - +
206B ARG* 2.9 42.9 + - - +
502B APC 3.2 35.5 + - - +
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Residues in contact with THR 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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143A GLN* 5.7 0.2 + - - -
171A ASP* 3.7 7.0 - - - +
174A GLY* 3.6 30.5 - - - +
175A TYR* 3.6 31.6 - - + -
178A GLU* 4.4 5.0 + - - +
201B SER* 3.0 10.2 + - - -
202B ALA* 1.3 79.9 - - - +
204B TYR* 1.3 61.9 + - - +
206B ARG* 3.2 25.3 + - - +
207B ARG* 3.1 22.0 + - - +
502B APC 2.6 21.8 + - - -
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Residues in contact with TYR 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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171A ASP* 3.5 16.8 - - + +
200B ILE* 5.7 0.7 - - + -
201B SER* 2.9 29.0 + - - +
203B THR* 1.3 75.1 - - - +
205B ILE* 1.3 75.5 + - + +
207B ARG* 3.2 31.1 + - - +
208B ALA* 2.9 43.9 + - + +
213B GLN* 4.4 10.7 + - - +
214B SER 5.2 2.4 + - - -
215B VAL* 5.2 0.7 - - + -
218B LEU* 4.3 19.5 - - + -
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 3.9 24.7 - - + -
19B THR* 4.2 8.5 - - + -
200B ILE* 3.8 24.5 - - + -
201B SER 2.9 18.0 + - - +
202B ALA* 3.3 15.3 - - - +
204B TYR* 1.3 79.6 - - + +
206B ARG* 1.3 61.5 + - - +
208B ALA* 3.5 2.4 + - - +
209B LEU* 3.1 36.1 + - + +
215B VAL* 3.8 12.6 - - + +
218B LEU* 3.8 32.5 - - + -
219B ILE* 4.0 15.9 - - + -
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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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178A GLU* 2.6 45.0 + - - +
16B ASN* 2.6 54.0 + - - +
17B PRO* 4.0 5.4 - - + -
56B LYS* 3.3 8.3 - - - +
57B ASP* 4.2 4.8 + - - -
202B ALA* 2.9 23.9 + - - +
203B THR* 3.2 22.8 + - - +
205B ILE* 1.3 72.9 - - - +
207B ARG* 1.3 60.1 + - - +
209B LEU* 3.3 10.2 + - - +
210B GLY* 2.9 25.8 + - - -
233B TYR* 3.5 38.6 - - + +
502B APC 2.9 29.1 + - - -
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Residues in contact with ARG 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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171A ASP* 2.8 40.3 + - - +
173A LYS* 3.6 48.7 - - - +
174A GLY* 3.8 11.2 - - - +
177A ALA* 5.6 4.5 - - + -
178A GLU* 5.4 0.6 + - - -
203B THR 3.1 17.1 + - - +
204B TYR* 3.2 24.4 + - - +
206B ARG* 1.3 75.2 - - - +
208B ALA* 1.3 62.8 + - - +
210B GLY* 3.2 3.1 + - - -
211B GLN* 3.1 64.3 + - + +
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Residues in contact with ALA 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 TYR* 2.9 40.7 + - + +
205B ILE 3.7 4.3 - - - +
207B ARG* 1.3 76.5 - - - +
209B LEU* 1.3 61.0 + - - +
211B GLN* 3.0 8.7 + - - -
213B GLN* 2.9 48.6 + - + +
214B SER 4.6 1.3 - - - +
215B VAL* 3.7 17.5 - - + -
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Residues in contact with LEU 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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205B ILE* 3.1 34.1 + - + +
206B ARG 3.6 4.0 - - - +
207B ARG 3.3 0.2 - - - -
208B ALA* 1.3 76.7 - - - +
210B GLY* 1.3 57.9 + - - +
212B GLY* 2.9 20.4 + - - -
213B GLN 4.2 9.0 - - - +
215B VAL* 3.8 26.0 - - + -
224B ILE* 5.6 6.3 - - + -
227B ILE* 3.8 28.7 - - + -
232B LEU 5.3 1.6 - - - +
233B TYR* 3.8 37.6 - - + +
234B THR* 5.7 1.9 - - - +
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Residues in contact with GLY 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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206B ARG 2.9 13.8 + - - -
207B ARG* 3.2 4.4 + - - -
209B LEU* 1.3 76.4 - - - +
211B GLN* 1.3 59.3 + - - +
212B GLY 3.2 1.4 + - - -
233B TYR 3.3 17.6 + - - -
234B THR* 4.5 11.3 - - - -
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Residues in contact with GLN 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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173A LYS* 5.8 0.2 - - - +
204B TYR* 5.9 0.2 - - - -
207B ARG* 3.1 52.0 + - + +
208B ALA* 3.0 9.6 + - - +
210B GLY* 1.3 77.2 - - - +
212B GLY* 1.3 61.3 + - - +
213B GLN* 2.7 39.3 + - + +
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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