Contacts of the helix formed by residues 201 - 218 (chain A) in PDB entry 3N2N
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 VAL 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 3.4 39.5 - - + +
65A PHE* 4.0 27.4 - - + -
148A LEU* 4.4 5.2 - - + -
178A VAL* 3.6 13.9 - - + -
179A GLY 2.9 21.8 + - - +
180A VAL* 3.7 25.8 - - + -
181A LYS 5.5 0.7 - - - +
199A PHE 3.9 0.2 + - - -
200A PRO* 1.3 71.6 - - - +
202A ASN* 1.3 72.3 + - - +
203A ASP 3.6 0.3 + - - -
204A GLY 3.7 5.6 + - - -
205A PHE* 4.4 2.6 + - - +
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 4.2 14.2 + - - +
200A PRO* 3.2 5.4 - - + +
201A VAL* 1.3 87.8 + - - +
203A ASP* 1.3 57.7 + - - +
205A PHE* 5.2 2.1 - - - +
206A GLN* 5.9 0.3 + - - +
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 4.3 16.2 - - - -
200A PRO* 3.1 26.8 + - + +
202A ASN* 1.3 76.3 - - + +
204A GLY* 1.3 64.4 + - - +
205A PHE 3.4 2.2 - - - -
206A GLN* 3.8 16.6 + - - +
207A ALA* 3.5 20.0 + - - +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.4 18.8 - - - -
178A VAL* 4.5 4.0 - - - -
199A PHE* 3.8 15.3 - - - -
200A PRO 2.7 16.5 + - - -
201A VAL 3.7 1.2 + - - -
202A ASN 3.6 0.8 - - - -
203A ASP* 1.3 76.2 - - - +
205A PHE* 1.3 60.1 + - - +
207A ALA* 3.5 1.4 + - - +
208A LEU* 2.9 34.8 + - - +
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Residues in contact with PHE 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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65A PHE* 3.2 21.6 - + + -
68A GLN* 3.6 61.2 - - + +
69A LEU* 3.8 30.5 - - + -
72A LYS* 3.7 28.3 - - + -
201A VAL 4.4 2.8 + - - +
202A ASN 5.2 1.5 - - - +
203A ASP 3.4 0.6 - - - -
204A GLY* 1.3 74.7 - - - +
206A GLN* 1.3 61.5 + - + +
208A LEU* 5.0 0.9 - - - -
209A GLN* 2.7 47.7 + - + +
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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 ASN 5.9 0.6 + - - +
203A ASP* 3.8 17.3 + - - +
204A GLY 3.5 0.4 - - - -
205A PHE* 1.3 87.8 - - + +
207A ALA* 1.3 63.2 + - - +
209A GLN* 3.8 11.4 + - - +
210A GLY* 3.2 19.4 + - - -
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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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199A PHE* 3.6 37.5 - - + -
203A ASP* 3.5 16.8 + - - +
204A GLY 3.5 2.6 + - - +
205A PHE 3.3 0.4 - - - -
206A GLN* 1.3 81.3 - - - +
208A LEU* 1.3 57.3 + - - +
210A GLY* 3.3 4.2 + - - -
211A ILE* 3.1 32.6 + - + +
186B THR* 5.1 0.2 + - - -
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Residues in contact with LEU 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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65A PHE* 3.8 9.2 - - + -
69A LEU* 4.6 8.7 - - + -
144A VAL* 5.5 1.6 - - + -
146A ILE* 3.9 30.3 - - + -
176A TYR* 3.8 37.2 - - + -
178A VAL* 3.6 31.6 - - + -
199A PHE* 4.5 10.5 - - + -
204A GLY 2.9 21.6 + - - +
205A PHE 4.3 0.7 - - - +
207A ALA* 1.3 72.3 - - - +
209A GLN* 1.3 61.2 + - - +
211A ILE* 3.7 14.2 - - + +
212A ILE* 2.8 41.0 + - + +
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Residues in contact with GLN 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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69A LEU* 4.1 8.6 - - + +
72A LYS* 3.2 48.0 - - + +
73A PHE* 3.3 24.3 - - + -
205A PHE* 2.7 34.2 + - + +
206A GLN* 3.8 14.9 + - - +
208A LEU* 1.3 73.1 - - - +
210A GLY* 1.3 65.4 + - - +
213A HIS* 2.9 38.5 + - - +
223A ACT 4.3 3.0 + - - -
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Residues in contact with GLY 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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206A GLN* 3.2 12.2 + - - -
207A ALA 3.7 3.8 - - - -
208A LEU 3.3 0.2 - - - -
209A GLN* 1.3 87.2 + - - +
211A ILE* 1.3 59.8 + - - +
213A HIS* 3.6 0.8 + - - -
214A SER* 3.1 12.1 + - - -
184B ASN* 2.9 33.5 + - - +
186B THR* 4.0 6.5 - - - -
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Residues in contact with ILE 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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144A VAL* 5.9 0.7 - - + -
176A TYR* 3.6 48.9 - - + +
199A PHE* 4.5 9.9 - - + -
207A ALA* 3.1 19.1 + - + +
208A LEU* 3.7 18.2 - - + +
209A GLN 3.3 0.2 - - - -
210A GLY* 1.3 73.4 - - - +
212A ILE* 1.3 62.2 + - + +
214A SER* 3.1 5.5 + - - -
215A ILE* 3.0 47.3 + - + +
186B THR* 3.6 24.5 - - + +
195B LYS* 3.9 14.1 - - - +
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Residues in contact with ILE 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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43A PHE* 3.7 33.1 - - + -
45A LEU* 4.0 25.4 - - + -
69A LEU* 3.9 31.9 - - + -
73A PHE* 3.6 35.4 - - + -
78A LEU* 4.5 6.7 - - + -
144A VAL* 6.4 0.7 - - + -
146A ILE* 4.7 6.5 - - + -
208A LEU* 2.8 27.1 + - + +
209A GLN 3.8 0.2 - - - +
211A ILE* 1.3 74.3 - - + +
213A HIS* 1.3 62.2 + - - +
215A ILE* 3.3 1.4 + - - -
216A LEU* 2.9 26.8 + - + +
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Residues in contact with HIS 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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73A PHE* 3.9 7.5 - - + -
209A GLN* 2.9 31.5 + - - +
210A GLY 3.7 4.5 - - - +
212A ILE* 1.3 75.0 - - - +
214A SER* 1.3 59.1 + - - +
216A LEU* 3.4 2.9 + - - +
217A LYS* 3.0 66.6 + - + +
223A ACT 2.7 32.0 + - - +
184B ASN* 3.5 23.8 - - + +
187B GLN* 4.6 5.8 + - - -
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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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210A GLY 3.1 14.6 + - - -
211A ILE 3.4 8.7 - - - -
213A HIS* 1.3 77.1 - - - +
215A ILE* 1.3 58.3 + - - +
217A LYS* 3.3 5.1 + - - +
218A LYS* 3.0 26.9 + - - +
184B ASN* 4.0 6.3 - - - -
186B THR* 3.6 24.3 - - - +
187B GLN* 3.9 12.1 + - - +
190B ARG* 2.7 39.3 + - - +
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Residues in contact with ILE 215 (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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40A TYR* 4.0 16.0 - - + +
43A PHE* 3.7 50.2 - - + +
142A ALA* 3.7 16.8 - - + -
144A VAL* 4.1 14.8 - - + -
174A ILE* 6.2 2.2 - - + -
176A TYR* 6.1 0.2 - - + -
211A ILE* 3.0 38.8 + - + +
212A ILE 3.3 4.2 + - - +
214A SER* 1.3 76.6 - - - +
216A LEU* 1.3 57.6 - - - +
218A LYS* 3.0 22.4 + - - +
219A SER* 3.3 10.9 + - - -
186B THR* 6.2 1.6 - - + -
190B ARG* 5.8 2.0 - - - +
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Residues in contact with LEU 216 (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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43A PHE* 4.0 21.5 - - + -
73A PHE* 3.6 37.0 - - + -
75A SER* 4.5 11.0 - - - +
77A GLN* 3.7 39.6 - - + +
78A LEU* 4.1 13.0 - - + +
212A ILE* 2.9 22.4 + - + +
213A HIS* 3.7 4.7 - - - +
214A SER 3.4 0.2 - - - -
215A ILE* 1.3 76.0 - - - +
217A LYS* 1.3 60.3 + - - +
219A SER* 2.7 29.6 + - - +
223A ACT 4.1 11.9 - - + +
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Residues in contact with LYS 217 (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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213A HIS* 3.0 45.2 + - - +
214A SER 3.6 8.5 - - - +
216A LEU* 1.3 77.3 - - - +
218A LYS* 1.3 56.9 + - - +
219A SER* 3.2 7.3 + - - +
223A ACT 4.8 5.7 + - - -
155B GLU* 4.6 19.0 - - + +
187B GLN* 3.6 26.2 - - - +
190B ARG* 5.5 0.4 - - - +
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Residues in contact with LYS 218 (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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36A SER 2.8 26.3 + - - -
37A MET* 3.9 12.1 - - - +
38A ALA 3.5 19.5 - - - -
39A CYS* 3.2 10.3 - - + -
40A TYR* 2.8 56.1 + - + -
140A ARG* 3.9 3.2 - - - +
214A SER 3.0 12.3 + - - +
215A ILE* 3.0 14.2 + - - +
217A LYS* 1.3 76.2 - - - +
219A SER* 1.3 57.2 + - - -
162B GLU* 5.9 1.1 + - - -
190B ARG* 4.0 36.0 - - - +
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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