Contacts of the helix formed by residues 201 - 216 (chain A) in PDB entry 3NC0
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 GLU 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TRP* 4.4 11.6 + - + -
143A PRO* 6.0 2.1 - - - +
147A PRO 4.8 7.0 - - - +
150A ILE* 3.0 38.8 - - + +
197A SER* 3.6 23.3 + - - +
198A MET* 3.7 3.4 - - - -
199A CYS 3.0 0.6 - - - -
200A ASN* 1.3 89.8 - - + +
202A PHE* 1.3 60.5 + - - +
203A SER 3.6 2.2 - - - +
204A GLN* 4.1 26.7 - - - +
205A ILE* 4.1 14.7 - - - +
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A MET* 3.3 16.1 + - + +
199A CYS* 3.2 11.5 + - - +
200A ASN 3.7 0.4 - - - -
201A GLU* 1.3 76.2 - - - +
203A SER* 1.3 68.3 + - - +
204A GLN 3.2 2.5 - - - -
205A ILE* 2.9 20.9 + - + +
206A PHE* 2.8 56.0 + + + -
232A PHE* 3.5 39.7 - + - -
235A TRP* 4.1 18.8 - + + -
236A ILE* 3.5 32.5 - - + -
237A PRO* 5.0 2.2 - - + -
240A TYR* 3.8 25.8 - + + +
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A CYS 4.9 0.4 + - - -
201A GLU 3.6 0.4 - - - -
202A PHE* 1.3 77.8 - - - +
204A GLN* 1.3 65.9 + - - +
206A PHE* 2.9 19.3 + - - +
207A GLN* 3.0 25.8 + - - +
240A TYR* 2.8 30.8 + - - -
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.7 18.0 + - + +
151A SER* 3.6 28.8 + - - +
154A VAL* 4.4 15.3 - - + +
158A ARG* 4.3 4.9 + - - -
200A ASN 5.4 0.2 - - - +
201A GLU* 4.1 27.3 - - - +
202A PHE 3.2 0.4 - - - -
203A SER* 1.3 77.7 - - - +
205A ILE* 1.3 61.9 + - + +
207A GLN* 3.5 29.3 - - - +
208A LEU* 3.5 7.3 + - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.4 41.1 - - + -
153A ILE* 5.2 0.9 - - + -
154A VAL* 4.6 12.1 - - + -
168A MET* 5.1 0.4 - - + -
171A LEU* 3.5 41.5 - - + -
198A MET* 6.0 6.3 - - + -
201A GLU 4.1 7.2 - - - +
202A PHE* 2.9 17.2 + - + +
204A GLN* 1.3 75.0 - - + +
206A PHE* 1.3 65.9 + - - +
208A LEU* 3.2 16.8 + - + +
209A CYS* 3.2 16.8 + - - -
232A PHE* 4.3 21.5 - - + -
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 2.8 44.5 + + + +
203A SER* 2.9 12.3 + - - +
205A ILE* 1.3 74.1 - - - +
207A GLN* 1.3 68.1 + - + +
209A CYS* 3.3 10.9 + - + +
210A GLN* 2.9 51.6 + - + +
213A MET* 6.0 2.5 - - + -
229A LEU* 5.4 6.1 - - + -
232A PHE* 5.9 0.7 - + - -
236A ILE* 4.3 10.1 - - + -
240A TYR* 3.6 49.1 - + + -
244A THR* 4.5 11.7 - - + -
246A LEU* 4.3 22.9 - - + -
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Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.9 19.5 + - - +
203A SER* 3.0 25.6 + - - +
204A GLN* 3.5 21.6 - - - +
206A PHE* 1.3 76.1 - - + +
208A LEU* 1.3 54.0 + - - +
210A GLN* 3.6 8.4 - - - +
211A PHE* 2.8 36.9 + - - +
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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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153A ILE 5.3 0.2 - - - -
154A VAL* 4.1 22.7 - - + -
157A SER* 3.7 32.5 - - - +
158A ARG* 4.1 36.0 - - + +
164A CYS* 4.9 3.8 - - - -
167A ASN* 6.2 0.2 - - + -
168A MET* 4.5 20.0 - - + -
171A LEU* 5.3 5.4 - - + -
204A GLN 3.5 6.5 + - - +
205A ILE* 3.2 15.2 + - - +
206A PHE 3.1 0.2 - - - -
207A GLN* 1.3 78.2 - - - +
209A CYS* 1.3 65.3 + - - +
211A PHE* 3.1 9.0 + - + +
212A VAL* 2.9 37.5 + - + +
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Residues in contact with CYS 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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168A MET* 4.0 25.4 - - - -
205A ILE* 3.2 15.4 + - - -
206A PHE* 3.7 12.3 - - + +
208A LEU* 1.3 78.1 - - - +
210A GLN* 1.3 63.8 + - - +
212A VAL* 3.2 6.2 + - - +
213A MET* 3.0 36.9 + - + +
225A THR* 3.8 20.1 - - + +
228A THR* 4.6 4.3 - - - -
229A LEU* 5.4 6.3 - - + -
232A PHE* 4.4 23.3 - - - -
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Residues in contact with GLN 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 PHE* 2.9 43.8 + - + +
207A GLN* 3.6 7.6 - - - +
209A CYS* 1.3 76.3 - - - +
211A PHE* 1.3 64.4 + - - +
213A MET* 3.1 24.2 + - + +
214A GLU* 3.1 17.1 + - + +
244A THR* 5.4 5.3 - - - +
245A LYS* 5.8 8.4 - - - +
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Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.9 33.2 - - + +
207A GLN 2.8 20.7 + - - +
208A LEU* 3.5 9.6 - - + +
210A GLN* 1.3 72.4 - - - +
212A VAL* 1.3 72.2 + - + +
214A GLU* 3.3 3.0 + - - -
215A ASN* 3.1 63.2 + - + +
216A SER* 6.1 0.7 - - - -
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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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164A CYS* 4.6 14.8 - - - -
168A MET* 5.1 1.6 - - - -
208A LEU* 2.9 36.3 + - + +
209A CYS* 3.4 8.7 - - - +
211A PHE* 1.3 84.2 - - + +
213A MET* 1.3 58.9 + - - +
216A SER* 2.8 53.3 + - - +
221A LEU* 4.1 14.1 - - + -
222A VAL* 4.2 10.1 - - + +
225A THR* 3.8 25.1 - - + +
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Residues in contact with MET 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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206A PHE* 6.0 2.5 - - + -
209A CYS* 3.0 37.7 + - + +
210A GLN* 3.1 15.0 + - + +
212A VAL* 1.3 78.1 - - + +
214A GLU* 1.3 58.5 + - + +
215A ASN 3.7 0.3 + - - -
216A SER 5.0 1.9 + - - +
222A VAL* 5.3 4.2 - - + +
225A THR* 4.7 10.5 - - + -
226A LEU* 4.2 12.1 - - + -
229A LEU* 3.9 30.7 - - + -
246A LEU* 4.1 15.0 - - + -
249A THR* 4.3 15.5 - - + -
250A LEU* 4.5 2.0 - - - -
253A LYS* 3.3 17.7 + - - +
254A PHE* 3.5 44.6 - - + -
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Residues in contact with GLU 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 GLN* 3.1 17.3 + - + +
211A PHE* 3.3 3.8 + - - +
212A VAL 3.2 0.2 - - - -
213A MET* 1.3 77.3 - - + +
215A ASN* 1.3 93.0 + - - +
249A THR* 6.0 2.9 - - + +
253A LYS* 3.3 21.2 + - + +
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Residues in contact with ASN 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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211A PHE* 3.1 56.4 + - + +
212A VAL 3.3 0.2 + - - -
213A MET 3.4 0.6 - - - -
214A GLU* 1.3 104.9 + - - +
216A SER* 1.3 67.5 + - - +
217A GLN* 3.3 6.1 + - - +
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Residues in contact with SER 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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161A GLU* 3.8 4.3 + - - -
211A PHE* 6.1 0.4 - - - -
212A VAL* 2.8 41.4 + - - +
213A MET 5.3 1.6 - - - +
215A ASN* 1.3 71.8 - - - +
217A GLN* 1.3 63.3 + - - +
218A ASN 3.5 12.6 + - - -
221A LEU* 3.3 24.6 - - - +
222A VAL* 3.6 15.2 - - - +
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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