Contacts of the helix formed by residues 176 - 187 (chain B) in PDB entry 3NY5
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 THR 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A THR* 3.5 24.0 + - + +
174B GLY 4.3 0.2 + - - -
175B VAL* 1.3 76.4 - - - +
177B VAL* 1.3 54.1 + - - +
178B ARG* 3.5 5.9 - - - +
179B ASP* 2.9 36.6 + - - +
180B SER* 2.8 38.1 + - - -
210B TRP 3.7 11.4 - - - -
211B ASP* 3.5 27.1 + - + +
212B THR 3.3 5.8 - - - -
214B ILE* 4.3 0.2 - - - -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR* 1.3 72.1 - - - +
178B ARG* 1.3 63.2 + - - +
180B SER* 3.1 7.5 + - - -
181B LEU* 3.0 41.9 + - + +
197B VAL* 4.2 18.2 - - + -
208B ILE* 4.0 2.9 - - + -
209B GLY 4.4 2.9 - - - +
210B TRP* 3.5 24.0 + - + +
212B THR* 3.0 30.1 + - - +
214B ILE* 4.1 13.0 - - + -
217B LEU* 3.9 22.2 - - + -
222B LEU* 4.3 6.5 - - + -
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR* 3.5 7.4 - - - +
177B VAL* 1.3 76.0 - - - +
179B ASP* 1.3 68.0 + - - +
181B LEU* 3.6 0.9 - - - +
182B LYS* 2.7 32.6 + - + +
192B PRO* 3.8 24.9 - - + +
193B GLU* 3.0 34.2 + - - +
210B TRP* 3.1 47.3 + - + +
211B ASP* 3.0 38.0 + - - -
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Residues in contact with ASP 179 (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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175B VAL* 4.2 12.6 - - + -
176B THR* 2.9 28.4 + - - +
178B ARG* 1.3 86.6 - - - +
180B SER* 1.3 66.1 + - - +
181B LEU 3.1 0.5 + - - -
182B LYS* 3.6 25.2 + - - +
183B LYS 4.9 0.9 + - - -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.4 40.6 - - - +
170B PRO* 4.3 4.8 + - - +
175B VAL* 3.4 10.9 - - - +
176B THR 2.8 28.1 + - - -
177B VAL 3.1 5.1 + - - -
179B ASP* 1.3 74.9 - - - +
181B LEU* 1.3 60.1 + - - +
183B LYS* 5.1 2.8 + - - +
184B ALA* 5.4 1.2 + - - +
214B ILE* 3.4 29.3 - - - +
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Residues in contact with LEU 181 (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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159B VAL* 3.8 37.2 - - + -
161B LEU* 4.7 4.7 - - + -
167B THR* 4.0 16.6 - - + -
169B VAL* 4.0 9.4 - - + -
177B VAL* 3.0 33.3 + - + +
178B ARG 4.0 1.6 - - - +
180B SER* 1.3 81.8 - - - +
182B LYS* 1.3 64.0 + - - +
183B LYS 3.3 2.9 - - - -
184B ALA* 3.1 10.8 + - + +
185B LEU* 3.0 30.3 + - + +
197B VAL* 4.8 3.1 - - + -
210B TRP* 4.1 11.0 - - + -
214B ILE* 6.0 0.2 - - + -
222B LEU* 5.0 2.5 - - + -
224B VAL* 3.8 26.2 - - + -
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Residues in contact with LYS 182 (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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178B ARG* 2.7 22.2 + - + +
179B ASP* 3.6 23.2 + - - +
181B LEU* 1.3 70.4 - - - +
183B LYS* 1.3 59.7 + - - +
185B LEU* 3.3 5.6 + - - +
186B MSE 2.9 35.3 + - + +
190B LEU 5.1 0.2 - - - +
192B PRO* 4.9 15.8 - - + +
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Residues in contact with LYS 183 (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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179B ASP 4.9 1.2 + - - -
180B SER 5.1 1.9 + - - +
181B LEU 3.3 1.0 - - - -
182B LYS* 1.3 77.6 - - + +
184B ALA* 1.3 70.6 + - - +
186B MSE 3.2 7.1 + - + +
187B MSE 3.0 38.1 + - + +
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Residues in contact with ALA 184 (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 LEU* 4.3 5.4 - - + -
167B THR* 4.1 29.8 - - + +
169B VAL* 5.7 2.0 - - + -
180B SER 5.4 1.9 + - - +
181B LEU* 3.1 15.6 + - + +
183B LYS* 1.3 79.4 - - - +
185B LEU* 1.3 64.3 + - - +
187B MSE 3.5 13.5 + - + +
188B ARG* 3.0 39.8 + - - +
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Residues in contact with LEU 185 (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 LEU* 4.3 16.2 - - + -
181B LEU* 3.0 25.5 + - + +
182B LYS* 3.7 4.3 - - - +
184B ALA* 1.3 75.4 - - - +
186B MSE 1.3 55.1 + - - +
188B ARG* 2.8 23.8 + - - -
190B LEU* 2.9 58.6 + - + +
191B ILE* 4.2 2.9 - - - +
192B PRO* 3.8 37.9 - - + -
195B CYS* 4.6 1.3 - - - -
210B TRP* 3.8 20.6 - - + -
224B VAL* 4.0 19.3 - - + -
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Residues in contact with MSE 186 (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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182B LYS* 2.9 23.9 + - + +
183B LYS* 3.6 8.5 - - + +
185B LEU* 1.3 72.4 - - - +
187B MSE 1.3 61.8 + - - +
188B ARG 2.9 4.7 - - - -
189B GLY* 2.9 24.5 + - - -
190B LEU 3.6 16.3 + - - +
191B ILE* 5.2 10.5 - - + -
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Residues in contact with MSE 187 (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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183B LYS* 3.0 31.5 + - + +
184B ALA* 3.6 11.2 - - + +
185B LEU 3.2 0.2 - - - -
186B MSE 1.3 75.6 - - - +
188B ARG* 1.3 89.3 + - + +
189B GLY 3.4 0.2 - - - -
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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