Contacts of the helix formed by residues 178 - 189 (chain B) in PDB entry 3NTV
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 LEU 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN* 3.9 32.3 - - + +
28A TYR* 3.9 17.0 - - + -
29A LEU* 3.8 28.9 - - + -
177B VAL* 1.3 78.8 - - + +
179B TYR* 1.4 67.4 + - - +
180B HIS 3.3 1.1 - - - -
181B GLY* 2.9 18.1 + - - +
183B VAL* 3.4 23.7 + - + -
184B SER 5.2 0.4 - - - +
220B ASN* 3.8 31.6 - - + -
222B ASP 4.8 4.0 - - - +
223B ASP* 3.0 13.3 + - - +
224B GLY* 3.8 21.5 - - - +
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Residues in contact with TYR 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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151B ALA* 3.4 33.9 - - + -
176B ASN* 3.2 18.8 + - - -
177B VAL 3.5 1.0 - - - -
178B LEU* 1.4 75.5 - - - +
180B HIS* 1.3 77.6 + + - +
181B GLY 2.8 12.1 + - - -
182B PHE* 3.2 22.4 + + - -
183B VAL* 3.6 18.2 - - + -
194B VAL* 4.0 23.8 - - + +
197B MSE 3.6 34.2 - - + +
198B VAL* 3.9 13.2 - - + -
201B VAL* 4.0 11.9 - - + -
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MSE 5.9 0.3 - - - +
53B PRO* 6.3 2.9 - - + -
176B ASN* 3.3 32.9 + - - -
178B LEU* 3.3 1.7 + - - -
179B TYR* 1.3 99.3 + + - +
181B GLY* 1.3 54.6 + - - +
182B PHE* 3.8 14.1 - + + -
222B ASP 6.0 0.2 - - - -
223B ASP* 3.3 39.8 + - - +
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MSE 3.3 31.1 - - - +
25A ASN* 3.6 21.1 - - - +
178B LEU* 2.9 11.5 + - - +
179B TYR 2.8 0.4 + - - -
180B HIS* 1.3 78.6 - - - +
182B PHE* 1.4 60.0 + - - +
183B VAL 3.4 2.9 - - - -
184B SER* 3.3 12.8 + - - -
188B ILE* 4.9 1.3 - - - +
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Residues in contact with PHE 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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179B TYR* 3.2 28.1 + + - +
180B HIS* 4.7 13.9 - + + -
181B GLY* 1.4 75.5 - - - +
183B VAL* 1.3 59.8 + - - +
184B SER 3.4 0.7 - - - -
185B ASP 3.1 23.5 - - - +
186B ILE* 3.8 0.9 - - - -
188B ILE* 3.7 30.1 - - + -
189B VAL* 3.7 20.2 - - + -
194B VAL* 3.7 25.1 - - + -
198B VAL* 3.3 28.0 - - + +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.3 43.7 - - + +
177B VAL 3.8 7.2 - - - +
178B LEU* 3.4 30.6 + - + +
179B TYR* 3.6 16.8 - - + -
181B GLY 3.4 0.2 - - - -
182B PHE* 1.3 72.9 - - - +
184B SER* 1.4 61.9 + - - +
185B ASP 3.2 2.7 - - - -
198B VAL* 3.6 15.7 - - + +
201B VAL* 3.7 19.1 - - + -
202B GLN* 2.8 32.6 + - + -
205B ASN* 4.2 1.3 - - - +
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Residues in contact with SER 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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21A MSE 3.8 5.7 - - - -
24A LEU* 3.5 39.0 - - - +
25A ASN* 3.2 28.4 + - - -
27A LYS* 5.9 3.3 - - - -
28A TYR* 3.9 21.6 - - - +
178B LEU* 5.2 0.4 - - - +
181B GLY 3.3 10.1 + - - -
183B VAL* 1.4 77.1 - - - +
185B ASP* 1.3 62.6 + - - +
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Residues in contact with ASP 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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21A MSE 6.6 0.9 - - + -
24A LEU* 5.9 3.4 - - + -
182B PHE 3.1 11.3 + - - +
183B VAL 3.2 1.0 - - - -
184B SER* 1.3 85.2 + - - +
186B ILE* 1.3 63.2 + - - +
187B GLY* 2.9 27.2 + - - -
188B ILE* 3.3 36.7 + - + +
202B GLN* 5.2 0.2 - - - +
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Residues in contact with ILE 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 PHE 3.7 6.6 + - - -
185B ASP* 1.3 73.1 + - - +
187B GLY* 1.3 59.4 + - - +
188B ILE 3.2 0.4 - - - -
189B VAL* 3.1 28.7 + - + +
195B ARG* 3.3 48.2 + - + +
198B VAL* 3.6 26.9 - - + -
199B LYS* 3.8 14.4 - - + +
202B GLN* 4.1 18.9 - - - +
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Residues in contact with GLY 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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185B ASP* 2.9 15.4 + - - -
186B ILE* 1.3 81.3 - - - +
188B ILE* 1.3 59.6 + - - +
189B VAL 3.3 5.5 + - - +
190B ARG* 4.2 10.2 + - - -
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Residues in contact with ILE 188 (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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21A MSE 4.0 29.6 - - + -
181B GLY 4.9 1.1 - - - +
182B PHE* 3.7 37.1 - - + -
185B ASP* 3.3 36.8 - - + +
187B GLY* 1.3 74.4 - - - +
189B VAL* 1.4 64.1 + - + +
190B ARG* 3.4 19.3 + - - +
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Residues in contact with VAL 189 (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 PHE* 3.7 41.3 - - + +
186B ILE* 3.1 27.2 + - + +
187B GLY 4.0 6.1 - - - +
188B ILE* 1.4 78.9 - - + +
190B ARG* 1.3 65.8 + - - +
191B SER 3.3 23.3 - - - +
194B VAL* 3.7 12.1 - - + -
195B ARG* 3.4 35.1 + - + +
198B VAL* 4.0 11.0 - - + -
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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