Contacts of the helix formed by residues 196 - 214 (chain A) in PDB entry 1N0W
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 ASN 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA* 3.5 1.0 - - - +
195A PHE* 1.3 87.3 - - - +
197A THR* 1.3 59.6 + - - +
198A ASP* 2.9 18.4 + - - +
199A HIS* 2.8 32.6 + - - +
200A GLN* 2.9 27.2 + - - +
227A LEU* 3.7 15.5 - - - +
1522B LEU* 6.3 0.2 - - - +
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN* 1.3 73.2 - - - +
198A ASP* 1.3 69.8 + - - +
200A GLN* 3.4 8.5 + - - +
201A THR* 3.3 16.3 + - - -
227A LEU* 3.5 34.5 + - + +
228A TYR* 3.6 44.4 + - + -
244A HIS* 3.4 16.9 + - - -
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN* 2.9 10.7 + - - +
197A THR* 1.3 81.9 + - - +
199A HIS* 1.3 58.7 + - - +
201A THR* 3.2 4.9 + - - -
202A GLN* 2.9 27.6 + - - +
244A HIS* 3.6 21.3 + - - -
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ALA* 5.7 0.4 - - + -
193A ARG 3.3 20.6 - - - -
194A ALA* 3.4 4.2 - - - -
195A PHE* 3.0 23.8 + + + +
196A ASN* 2.8 27.8 + - - +
198A ASP* 1.3 74.9 - - - +
200A GLN* 1.3 65.2 + - - +
202A GLN* 3.1 14.3 + - + -
203A LEU* 2.9 38.0 + - + +
1521B LEU 4.2 0.4 - - - -
1522B LEU* 2.8 63.4 + - + +
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Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 4.8 9.8 - - + +
162A THR* 4.2 3.7 - - - +
194A ALA* 3.9 18.3 - - + +
196A ASN 2.9 12.7 + - - +
197A THR* 3.5 10.8 - - - +
198A ASP 3.2 0.2 - - - -
199A HIS* 1.3 78.6 - - - +
201A THR* 1.3 61.0 + - - +
203A LEU* 3.6 14.3 + - - +
204A LEU* 4.0 3.5 + - - +
221A VAL* 4.9 1.3 - - + -
223A SER 4.3 6.8 - - - +
224A ALA* 3.0 30.0 + - - +
227A LEU* 3.6 28.1 - - - +
228A TYR* 3.9 14.0 - - - -
248A PHE* 3.3 45.0 - - + -
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A THR 3.3 4.3 + - - -
198A ASP* 3.2 8.1 + - - +
199A HIS 3.2 0.2 - - - -
200A GLN* 1.3 77.1 - - - +
202A GLN* 1.3 68.4 + - - +
203A LEU 3.1 0.2 - - - -
204A LEU* 3.0 19.4 + - - +
205A TYR* 4.0 7.0 + - + -
228A TYR* 4.3 0.7 + - - -
244A HIS* 3.3 28.7 + - + +
247A ARG* 6.3 0.7 - - + -
248A PHE* 3.5 26.0 - - - +
251A MSE 3.8 28.7 - - + +
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Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP 2.9 17.6 + - - +
199A HIS* 3.6 18.8 - - + +
201A THR* 1.3 77.5 - - - +
203A LEU* 1.3 65.4 + - - +
205A TYR* 3.0 31.7 + - + +
206A GLN* 2.7 38.1 + - - +
1522B LEU* 4.5 1.0 + - - +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 4.0 35.4 - - + -
192A ALA* 3.9 18.2 - - + -
194A ALA* 4.1 12.8 - - + -
199A HIS* 2.9 36.6 + - + +
200A GLN* 3.7 7.6 - - - +
201A THR 3.1 0.4 - - - -
202A GLN* 1.3 79.6 - - - +
204A LEU* 1.3 57.5 + - - +
206A GLN* 3.2 12.8 + - - +
207A ALA* 2.8 28.3 + - - +
1522B LEU 3.5 24.2 - - - +
1524B PHE* 3.6 24.6 - - + -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 4.2 20.0 - - + -
200A GLN 4.1 0.9 - - - +
201A THR 3.0 11.8 + - - +
203A LEU* 1.3 75.2 - - - +
205A TYR* 1.3 60.1 + - - +
207A ALA* 3.5 5.1 - - + +
208A SER* 3.0 27.5 + - - -
219A LEU* 4.3 4.9 - - + -
248A PHE* 3.4 38.4 - - + -
251A MSE 3.6 39.3 - - + -
252A LEU* 3.8 26.9 - - + +
255A LEU* 3.9 12.6 - - + +
1546B PHE* 3.8 10.8 - - + -
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR* 4.2 12.8 - - + -
202A GLN* 3.0 26.9 + - + +
204A LEU* 1.3 76.2 - - - +
206A GLN* 1.3 63.7 + - - +
208A SER* 2.6 21.8 + - - -
209A ALA* 3.2 9.4 + - - +
247A ARG* 5.6 1.0 + - - -
251A MSE 3.8 16.5 - - + +
1539B LEU* 4.1 9.5 - - + +
1542B VAL* 4.2 13.2 - - + +
1543B LYS* 4.1 21.9 + - - -
1546B PHE* 3.5 35.4 - + + +
1547B ASP* 5.4 3.1 + - - -
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Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLN* 2.7 39.2 + - - +
203A LEU* 3.2 12.3 + - - +
205A TYR* 1.3 77.0 - - - +
207A ALA* 1.3 63.5 + - - +
209A ALA* 3.1 3.8 + - - +
210A MSE 2.9 28.4 + - - +
1522B LEU 3.2 15.6 - - - +
1523B GLY* 3.4 24.0 - - - -
1524B PHE* 3.9 16.5 - - + +
1534B ILE* 3.9 23.8 - - + +
1539B LEU* 4.3 9.9 - - + -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MSE 3.2 34.3 - - + +
160A ILE* 5.6 0.4 - - + -
203A LEU 2.8 17.6 + - - +
204A LEU* 3.5 15.0 - - + +
206A GLN* 1.3 77.5 - - - +
208A SER* 1.3 57.6 + - - +
210A MSE 3.2 5.6 + - - +
211A MSE 2.9 37.5 + - + +
219A LEU* 5.3 1.6 - - + -
255A LEU* 4.6 11.2 - - + -
1524B PHE* 4.4 2.0 - - + -
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU 3.0 12.6 + - - -
205A TYR* 2.6 25.6 + - - -
207A ALA* 1.3 75.8 - - - +
209A ALA* 1.3 61.7 + - - +
211A MSE 3.3 1.2 + - - -
212A VAL* 3.3 25.6 + - - +
255A LEU* 4.0 8.5 - - - +
259A PHE* 3.6 14.3 - - - -
1542B VAL* 3.1 19.4 - - - +
1545B LEU* 3.7 28.3 - - - -
1546B PHE* 4.1 4.7 - - - -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR 3.2 1.8 + - - +
206A GLN 3.1 5.5 + - - +
208A SER* 1.3 81.2 + - - +
210A MSE 1.3 63.2 + - - +
212A VAL* 3.2 13.4 + - - +
213A GLU* 3.4 16.3 + - - +
1534B ILE* 3.5 26.7 - - + -
1538B SER* 3.9 12.8 - - - +
1539B LEU* 3.5 35.4 - - + +
1542B VAL* 4.2 2.9 - - + -
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Residues in contact with MSE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MSE 4.1 11.0 - - + -
190A ALA* 3.5 21.8 - - + -
206A GLN 2.9 23.3 + - - +
207A ALA* 3.5 8.5 - - - +
209A ALA* 1.3 77.2 - - - +
211A MSE 1.3 57.5 + - - +
213A GLU* 3.1 10.3 + - - +
214A SER* 3.0 27.0 + - - +
216A TYR* 3.3 34.0 - - + +
1524B PHE* 3.5 33.9 - - + -
1532B VAL* 3.7 22.2 - - + -
1533B LYS 5.6 0.4 - - - +
1534B ILE* 3.7 24.7 - - + -
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Residues in contact with MSE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MSE 3.8 28.7 - - + -
207A ALA* 2.9 21.1 + - + +
208A SER 3.8 5.4 - - - +
209A ALA 3.3 0.4 - - - -
210A MSE 1.3 75.5 - - - +
212A VAL* 1.3 60.5 + - - +
214A SER 3.1 19.4 - - - +
216A TYR* 4.1 17.0 + - + -
218A LEU 4.9 0.4 - - - +
219A LEU* 4.0 33.0 - - + -
255A LEU* 4.5 9.2 - - + -
259A PHE* 3.5 52.1 - - + -
261A VAL* 4.2 21.5 - - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER 3.3 14.9 + - - +
209A ALA* 3.2 9.4 + - - +
210A MSE 3.1 0.6 - - - -
211A MSE 1.3 78.4 - - - +
213A GLU* 1.3 62.7 + - + +
259A PHE* 4.0 15.3 - - + -
1538B SER* 4.8 11.2 - - - +
1541B LYS* 4.6 24.7 - - + +
1542B VAL* 3.5 22.4 - - + -
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 3.4 6.2 + - - +
210A MSE 3.1 10.6 + - - +
212A VAL* 1.3 81.5 - - + +
214A SER* 1.3 64.4 + - - +
1533B LYS 3.9 13.9 - - - +
1534B ILE* 3.8 6.4 - - - +
1535B ALA* 2.9 28.1 + - - +
1538B SER* 2.6 33.6 + - - +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS* 3.4 37.7 + - - -
210A MSE 3.0 4.6 + - - -
211A MSE 3.1 19.1 - - - +
213A GLU* 1.3 84.3 + - - +
215A ARG* 1.3 64.0 + - - +
216A TYR* 3.4 18.1 + - - -
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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