Contacts of the helix formed by residues 210 - 231 (chain A) in PDB entry 3NOR
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 ALA 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA* 4.3 23.8 - - + -
127A TYR* 4.3 6.9 + - + +
206A ALA 3.1 17.3 + - - +
207A ARG* 3.8 4.9 - - - +
208A GLN 3.3 0.2 - - - -
209A ARG* 1.3 76.5 - - - +
211A ALA* 1.3 59.2 + - - +
212A ASP 3.3 2.2 + - - -
213A SER* 3.3 9.2 + - - -
214A LEU* 2.8 31.7 + - + +
232A CIT 4.3 16.2 - - - +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG 3.2 12.0 + - - +
208A GLN* 3.5 16.8 - - - +
209A ARG 3.4 2.6 - - - -
210A ALA* 1.3 77.2 - - - +
212A ASP* 1.3 61.1 + - - +
214A LEU* 3.2 10.1 + - - +
215A HIS* 2.9 28.3 + - - +
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Residues in contact with ASP 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLN 4.9 0.6 + - - -
209A ARG 4.9 2.6 + - - +
210A ALA 3.3 0.4 - - - -
211A ALA* 1.3 79.8 - - - +
213A SER* 1.3 66.5 + - - +
215A HIS* 3.2 9.6 + - - +
216A LYS* 3.0 23.1 + - - +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 5.8 2.3 - - - +
127A TYR* 2.6 28.5 + - - -
209A ARG 5.3 2.2 + - - -
210A ALA* 3.3 10.7 + - - -
212A ASP* 1.3 80.5 - - - +
214A LEU* 1.3 56.0 + - - -
216A LYS* 3.7 5.8 - - - +
217A ARG* 2.8 43.3 + - - +
232A CIT 4.6 4.0 + - - -
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 3.9 22.2 - - - +
127A TYR* 3.8 22.4 - - + -
129A GLU* 3.7 32.5 - - + +
130A LEU* 4.3 11.9 - - + -
210A ALA* 2.8 23.2 + - + +
211A ALA* 3.6 8.1 - - - +
212A ASP 3.2 0.2 - - - -
213A SER* 1.3 73.2 - - - +
215A HIS* 1.3 58.6 + - - +
217A ARG 3.3 0.3 + - - -
218A ARG* 2.8 51.5 + - - +
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Residues in contact with HIS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA 2.9 13.6 + - - +
212A ASP* 3.3 14.1 + - - +
214A LEU* 1.3 78.9 - - - +
216A LYS* 1.3 62.4 + - - +
218A ARG* 3.5 24.5 + - - +
219A GLU* 3.3 49.6 + - + +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP 3.0 15.3 + - - +
213A SER* 3.7 7.2 - - - +
215A HIS* 1.3 80.1 + - - +
217A ARG* 1.3 62.5 + - - +
219A GLU* 3.3 19.0 + - - +
220A ILE* 3.1 46.0 + - + +
223A ARG* 4.6 9.7 - - - +
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 3.7 14.8 + - - -
75A THR* 3.7 19.1 + - - +
77A VAL* 4.8 7.0 - - - -
78A GLY* 4.7 8.5 - - - +
81A MET* 4.4 15.0 - - - -
105A SER* 3.4 17.5 - - - -
108A LEU* 3.9 14.4 - - - -
127A TYR* 3.5 29.9 - - + -
130A LEU* 3.7 11.7 - - + -
213A SER* 2.8 25.4 + - - +
214A LEU 3.9 1.8 - - - +
216A LYS* 1.3 78.2 - - - +
218A ARG* 1.3 50.9 + - - +
220A ILE* 3.4 14.3 + - + +
221A THR* 2.7 38.1 + - - -
232A CIT 2.8 40.9 + - - -
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Residues in contact with ARG 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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129A GLU* 3.0 28.7 + - - -
130A LEU* 3.7 22.6 - - + +
214A LEU* 2.8 45.5 + - + +
215A HIS* 3.7 37.8 + - - +
217A ARG* 1.3 70.1 - - - +
219A GLU* 1.3 61.4 + - - +
221A THR* 3.1 1.6 + - - -
222A LEU* 2.9 51.7 + - + +
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Residues in contact with GLU 219 (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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215A HIS* 3.3 38.9 + - + +
216A LYS* 3.5 21.6 + - - +
218A ARG* 1.3 79.3 - - + +
220A ILE* 1.3 61.3 + - + +
222A LEU* 3.5 7.6 + - - +
223A ARG* 3.2 43.9 + - - +
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Residues in contact with ILE 220 (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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78A GLY* 3.6 29.4 - - - +
81A MET* 3.8 28.3 - - + +
82A GLU* 3.8 25.3 - - + +
216A LYS* 3.1 35.0 + - + +
217A ARG* 3.6 12.1 - - + +
219A GLU* 1.3 73.2 - - - +
221A THR* 1.3 61.0 + - - +
223A ARG* 3.2 28.7 + - - +
224A ALA* 2.9 25.5 + - - +
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Residues in contact with THR 221 (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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81A MET* 3.5 20.8 - - - +
130A LEU* 3.6 41.7 - - + +
133A PRO* 3.9 15.5 - - + -
134A LEU* 3.8 17.9 - - + +
217A ARG 2.7 28.0 + - - -
218A ARG* 3.1 8.3 + - - -
220A ILE* 1.3 74.0 - - - +
222A LEU* 1.3 60.8 + - + +
224A ALA* 3.2 2.8 + - - +
225A ALA* 2.8 27.5 + - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 5.7 0.2 - - + -
133A PRO* 4.2 25.6 - - + -
218A ARG* 2.9 40.2 + - + +
219A GLU* 4.0 6.5 - - - +
220A ILE 3.2 0.2 - - - -
221A THR* 1.3 82.6 - - + +
223A ARG* 1.3 61.9 - - - +
225A ALA* 3.4 5.3 + - + +
226A ALA* 3.0 24.3 + - - +
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.8 44.2 + - - +
216A LYS* 4.6 9.9 - - - +
219A GLU* 3.2 33.7 + - - +
220A ILE* 3.2 24.4 + - - +
222A LEU* 1.3 78.1 - - + +
224A ALA* 1.3 61.2 + - - +
226A ALA* 3.3 6.2 + - - +
227A ARG* 3.1 42.8 + - - +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 4.2 12.6 - - + +
87A LEU* 6.1 0.2 - - + -
112A ALA* 3.9 33.1 - - + +
134A LEU* 4.4 4.5 - - + -
220A ILE* 2.9 17.4 + - + +
221A THR* 3.6 8.1 - - - +
223A ARG* 1.3 75.8 - - - +
225A ALA* 1.3 63.0 + - - +
227A ARG* 3.3 18.5 + - - +
228A LEU* 3.2 25.3 + - - +
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Residues in contact with ALA 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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133A PRO* 3.3 32.8 - - + +
134A LEU* 4.3 6.5 - - + +
221A THR 2.8 17.4 + - - +
222A LEU* 3.7 7.6 - - + +
224A ALA* 1.3 75.2 - - - +
226A ALA* 1.3 60.4 + - - +
228A LEU* 3.2 9.5 + - - +
229A ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 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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222A LEU 3.0 17.2 + - - +
223A ARG* 3.7 7.2 - - - +
225A ALA* 1.3 78.1 - - - +
227A ARG* 1.3 61.7 + - - +
229A ALA* 3.3 9.1 + - - +
230A ALA* 3.2 22.9 + - - +
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Residues in contact with ARG 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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81A MET 4.7 0.8 + - - -
82A GLU* 2.8 50.5 + - - +
87A LEU* 6.5 1.6 - - - -
223A ARG* 3.1 41.9 + - - +
224A ALA* 3.4 13.8 - - - +
225A ALA 3.2 0.2 - - - -
226A ALA* 1.3 78.1 - - + +
228A LEU* 1.3 63.3 + - + +
230A ALA* 3.2 14.6 + - - +
231A GLY 3.3 8.3 + - - -
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Residues in contact with LEU 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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91A ARG* 6.3 0.7 - - - -
111A GLY 3.4 25.4 - - - +
112A ALA* 3.7 18.8 - - - +
113A ALA 4.3 2.7 - - - +
114A GLY* 3.7 22.2 - - - +
117A GLN* 5.9 2.7 - - - +
133A PRO 6.0 0.2 - - - +
134A LEU* 4.7 13.2 - - + +
224A ALA 3.2 13.6 + - - +
225A ALA* 3.5 12.3 - - - +
227A ARG* 1.3 78.8 - - + +
229A ALA* 1.3 62.9 + - - +
231A GLY* 3.2 16.7 + - - -
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Residues in contact with ALA 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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225A ALA 2.9 13.6 + - - +
226A ALA* 3.6 12.1 - - - +
227A ARG 3.3 0.4 - - - -
228A LEU* 1.3 76.1 - - - +
230A ALA* 1.3 59.2 + - + +
231A GLY* 3.3 3.0 - - - -
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Residues in contact with ALA 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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226A ALA 3.2 15.0 + - - +
227A ARG* 3.2 6.3 + - - +
228A LEU 3.1 1.2 - - - -
229A ALA* 1.3 75.8 - - - +
231A GLY* 1.3 63.7 + - - +
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Residues in contact with GLY 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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227A ARG 3.3 8.1 + - - -
228A LEU 3.2 18.9 + - - -
229A ALA 4.0 3.8 - - - -
230A ALA* 1.3 79.6 - - - +
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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