Contacts of the helix formed by residues 219 - 239 (chain A) in PDB entry 1NOY
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 ASP 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A CYS* 4.3 4.0 - - - -
112A ASP* 3.3 17.0 + - - +
113A ILE* 3.0 36.1 + - + +
213A TRP 4.2 4.7 - - - +
214A ASN* 3.6 13.2 - - - +
215A ILE* 3.7 26.0 + - + +
218A PHE* 1.3 91.7 - - - +
220A VAL* 1.3 65.8 + - + +
222A TYR* 3.6 0.7 - - - +
223A ILE* 2.8 38.5 + - + +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TRP* 6.0 1.3 - - + -
210A PHE* 3.8 33.2 - - + -
215A ILE* 2.9 30.5 + - + +
216A GLU* 4.8 2.5 - - - +
219A ASP* 1.3 72.4 - - + +
221A PRO* 1.3 67.2 - - + +
223A ILE* 3.3 7.2 + - + +
224A MET* 2.8 36.3 + - + +
260A TYR* 3.9 25.1 - - + +
262A ILE* 4.1 13.2 - - + -
267A ILE* 4.2 16.2 - - + -
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Residues in contact with PRO 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 3.9 15.0 - - + -
124A MET* 6.3 0.2 - - + -
215A ILE 3.4 2.2 - - - +
216A GLU 2.9 29.2 - - - +
217A GLY 4.0 5.8 - - - +
218A PHE 3.5 10.8 - - - +
220A VAL* 1.3 93.6 - - + +
222A TYR* 1.3 56.1 + - - +
224A MET* 3.7 0.5 - - - +
225A ASN* 2.8 41.2 + - - +
258A GLU* 3.8 22.2 - - + +
259A ILE* 4.5 2.2 - - - -
260A TYR* 3.8 23.6 - - + +
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.0 15.3 - - + -
115A VAL* 3.3 24.8 - - + +
121A PRO* 3.6 29.8 - - + -
122A ASP 3.8 4.0 - - - -
123A PRO* 3.5 23.9 - - + +
126A ALA* 3.6 18.1 - - + +
127A GLU 3.5 3.0 + - - -
128A TYR* 2.5 47.9 + - - +
130A ILE* 4.6 5.4 - - + -
218A PHE* 2.9 31.7 + + + +
219A ASP 3.7 2.2 - - - +
221A PRO* 1.3 72.2 - - - +
223A ILE* 1.3 59.1 + - - +
225A ASN* 3.2 1.4 + - - +
226A ARG* 2.9 43.5 + - + +
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Residues in contact with ILE 223 (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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111A CYS* 4.0 18.2 - - - -
113A ILE* 3.4 36.1 - - + -
130A ILE* 6.0 4.9 - - + -
133A ILE* 5.2 3.6 - - + -
195A LEU* 5.5 7.4 - - + +
198A TYR* 4.2 23.6 - - + -
210A PHE* 5.8 2.0 - - + -
219A ASP* 2.8 28.4 + - + +
220A VAL* 3.7 7.9 - - + +
222A TYR* 1.3 72.2 - - - +
224A MET* 1.3 60.3 + - + +
226A ARG* 3.3 3.1 + - - +
227A VAL* 2.9 37.6 + - + +
239A PHE* 4.2 24.5 - - + -
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Residues in contact with MET 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 2.8 32.1 + - + +
221A PRO 3.8 3.1 - - - +
223A ILE* 1.3 75.4 - - + +
225A ASN* 1.3 63.7 + - - +
227A VAL* 3.5 3.2 + - - +
228A LYS* 3.0 25.5 + - - +
236A MET* 3.3 45.6 - - + +
239A PHE* 3.7 25.1 - - + -
245A VAL* 3.4 23.1 - - + -
260A TYR* 3.8 32.5 - - + -
262A ILE* 4.6 7.9 - - - -
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Residues in contact with ASN 225 (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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123A PRO 2.7 29.6 + - - +
124A MET* 3.3 13.2 + - - +
126A ALA* 3.5 12.4 - - + +
221A PRO* 2.8 24.9 + - - +
224A MET* 1.3 74.3 - - - +
226A ARG* 1.3 58.1 + - - +
228A LYS* 3.7 11.5 - - - +
229A MET* 3.1 26.9 + - - +
258A GLU* 3.1 25.1 + - - +
260A TYR* 2.6 27.5 + - - -
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Residues in contact with ARG 226 (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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126A ALA* 2.9 26.5 + - + +
127A GLU* 3.1 24.8 + - - +
128A TYR 3.4 21.4 + - - -
129A GLU* 3.7 12.7 - - - +
130A ILE* 4.3 6.7 - - + -
191A GLU* 2.5 51.1 + - - +
195A LEU* 4.3 7.9 - - + -
222A TYR* 2.9 25.1 + - + +
223A ILE* 4.1 2.5 - - - +
225A ASN* 1.3 74.3 - - - +
227A VAL* 1.3 68.4 + - - +
228A LYS 3.1 1.1 - - - -
229A MET* 3.0 17.2 + - - +
230A ILE* 2.8 44.8 + - + +
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Residues in contact with VAL 227 (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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195A LEU* 4.4 28.3 - - + -
198A TYR* 6.3 0.2 - - + -
199A ILE* 4.0 17.9 - - + -
223A ILE* 2.9 22.2 + - + +
224A MET 3.9 4.0 - - - +
226A ARG* 1.3 75.9 - - - +
228A LYS* 1.3 56.9 + - - +
231A LEU* 2.6 39.3 + - + -
232A GLY 3.0 4.3 + - - -
235A SER* 4.0 4.7 - - - -
236A MET* 3.6 33.9 - - + +
239A PHE* 4.0 21.5 - - + -
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Residues in contact with LYS 228 (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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224A MET 3.0 17.6 + - - +
225A ASN* 3.7 10.8 - - - +
227A VAL* 1.3 78.8 - - - +
229A MET* 1.3 56.7 + - - +
232A GLY* 2.8 35.5 + - - -
233A GLU* 2.9 55.7 + - + +
236A MET* 3.4 25.6 - - - +
260A TYR* 4.4 16.8 + - - +
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Residues in contact with MET 229 (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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125A LYS 4.5 7.2 - - - +
126A ALA 3.2 26.9 - - - +
127A GLU* 4.7 9.6 - - + -
225A ASN 3.1 15.1 + - - +
226A ARG* 3.0 22.4 + - - +
228A LYS* 1.3 79.9 - - + +
230A ILE* 1.3 64.8 + - + +
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Residues in contact with ILE 230 (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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191A GLU* 4.0 8.7 - - - +
192A ARG* 3.0 63.3 + - + +
195A LEU* 4.8 2.7 - - + -
226A ARG* 2.8 61.1 + - + +
229A MET* 1.3 84.7 - - + +
231A LEU* 1.3 79.2 + - + +
232A GLY 3.6 0.7 - - - -
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Residues in contact with LEU 231 (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 ARG* 3.9 30.7 - - + +
195A LEU* 3.8 33.7 - - + -
196A MET* 4.3 24.2 - - + +
199A ILE* 5.2 3.1 - - + -
227A VAL* 2.6 25.0 + - + +
230A ILE* 1.3 92.8 - - + +
232A GLY* 1.3 58.9 - - - +
234A ARG* 4.9 1.2 + - - +
235A SER* 2.8 40.7 + - - +
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Residues in contact with GLY 232 (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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227A VAL 3.0 3.4 + - - +
228A LYS* 2.8 25.0 + - - -
230A ILE 3.6 1.4 - - - -
231A LEU* 1.3 83.0 - - - +
233A GLU* 1.3 67.8 + - - -
234A ARG 3.2 2.7 - - - -
235A SER* 3.0 7.8 + - - -
236A MET 3.4 8.0 + - - -
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Residues in contact with GLU 233 (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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228A LYS* 2.9 58.3 + - - +
232A GLY* 1.3 72.4 - - - -
234A ARG* 1.3 64.8 + - - +
236A MET* 3.3 13.3 + - + +
237A LYS* 3.1 32.5 + - + +
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Residues in contact with ARG 234 (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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231A LEU 5.5 1.1 - - - +
232A GLY 3.2 1.2 + - - -
233A GLU* 1.3 79.4 - - - +
235A SER* 1.3 61.9 + - - +
237A LYS* 3.6 32.4 + - - +
238A ARG* 3.7 10.6 - - - +
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Residues in contact with SER 235 (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 ILE* 3.7 16.7 - - - +
227A VAL* 4.0 5.8 - - - -
231A LEU* 2.8 42.7 + - - +
232A GLY 3.0 2.9 + - - -
234A ARG* 1.3 76.5 - - - +
236A MET* 1.3 65.1 + - - +
237A LYS 3.1 1.8 - - - -
238A ARG* 3.0 30.6 + - - +
239A PHE* 4.4 0.5 + - - -
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Residues in contact with MET 236 (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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224A MET* 3.3 37.5 - - + +
227A VAL* 3.6 20.8 - - + +
228A LYS* 3.4 37.5 - - + +
232A GLY 3.4 5.6 + - - +
233A GLU* 3.3 16.7 + - + +
235A SER* 1.3 78.6 - - - +
237A LYS* 1.3 69.8 + - + +
239A PHE* 3.0 26.9 + - - -
245A VAL* 3.6 30.8 - - + +
260A TYR* 4.1 16.2 - - + -
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Residues in contact with LYS 237 (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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233A GLU* 3.1 24.7 + - + +
234A ARG* 3.7 25.6 - - - +
235A SER 3.1 0.4 - - - -
236A MET* 1.3 91.5 - - + +
238A ARG* 1.3 55.9 + - - +
239A PHE 3.1 5.9 + - - -
240A SER 3.1 11.6 + - - +
243A GLY* 3.4 41.4 - - - +
245A VAL* 3.7 17.7 - - + +
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Residues in contact with ARG 238 (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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196A MET* 4.2 4.0 + - - +
199A ILE* 3.2 33.5 - - + +
200A ASN* 3.5 25.7 + - - +
203A GLU* 3.0 39.4 + - - +
206A ARG* 2.3 29.5 + - - -
234A ARG 3.7 11.7 - - - +
235A SER* 3.0 21.1 + - - +
237A LYS* 1.3 75.1 - - - +
239A PHE* 1.3 51.8 + - - +
240A SER 3.2 4.9 - - - +
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Residues in contact with PHE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 4.1 19.7 - + - -
199A ILE* 3.8 31.0 - - + -
202A TRP* 3.5 53.3 - + + -
206A ARG* 2.5 29.5 + - - +
223A ILE* 4.2 19.1 - - + -
224A MET* 3.7 22.0 - - - -
227A VAL* 4.0 16.2 - - + -
235A SER 4.5 0.7 - - - -
236A MET* 3.0 30.5 + - - +
237A LYS 3.1 0.8 - - - -
238A ARG* 1.3 73.7 - - - +
240A SER* 1.3 55.0 + - - +
241A PRO* 3.7 1.7 - - - +
245A VAL* 4.5 1.1 - - + -
262A ILE* 3.8 22.2 - - + +
265A VAL* 4.8 0.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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