Contacts of the helix formed by residues 217 - 236 (chain A) in PDB entry 3N1Y
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.4 17.4 - - + +
89A TRP* 2.8 37.9 + - + +
93A MET* 3.3 4.2 - - - +
212A ALA* 2.9 13.6 + - - +
215A ALA 3.3 0.8 - - - -
216A GLY* 1.3 77.3 - - - +
218A HIS* 1.3 56.8 + - - +
219A THR* 3.4 5.4 + - - -
220A PHE* 3.1 20.7 + - - -
221A ALA* 3.0 26.8 + - - +
500A GOL 2.8 36.0 + - - -
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Residues in contact with HIS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.1 2.0 - - + +
76A LEU* 3.6 24.0 - - + +
213A ALA* 4.2 29.3 - - + +
216A GLY* 3.4 19.0 + - - -
217A ASP* 1.3 71.3 - - - +
219A THR* 1.3 62.7 + - - +
221A ALA* 3.7 6.1 - - - +
222A SER* 2.7 35.6 + - - +
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Residues in contact with THR 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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72A ILE* 4.4 6.7 - - - -
73A LYS* 4.2 21.2 + - + -
76A LEU* 3.5 30.7 - - - +
144A PHE* 3.7 30.5 - - + -
217A ASP* 3.3 7.5 - - - -
218A HIS* 1.3 78.8 - - - +
220A PHE* 1.3 57.5 + - - +
222A SER* 3.4 2.6 + - - -
223A LEU* 3.0 26.9 + - - +
500A GOL 4.1 17.9 - - - -
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 3.4 20.2 - + + -
92A THR* 6.0 0.9 - - + -
93A MET* 3.7 24.5 - - + -
96A HIS* 3.8 27.4 - + + -
97A PHE* 3.6 35.0 - + - -
208A LEU* 3.7 24.7 - - + -
212A ALA* 3.7 6.3 - - + -
217A ASP* 3.1 25.1 + - - +
219A THR* 1.3 77.9 - - - +
221A ALA* 1.3 60.8 + - - +
223A LEU* 3.2 9.1 + - + +
224A ILE* 2.9 56.2 + - + +
500A GOL 3.9 8.5 - - - -
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Residues in contact with ALA 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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209A ALA* 3.6 19.2 - - - +
212A ALA* 3.5 18.3 - - + +
213A ALA* 3.8 13.2 - - + +
217A ASP 3.0 20.3 + - - +
218A HIS* 3.9 10.3 - - - +
219A THR 3.3 0.2 - - - -
220A PHE* 1.3 76.3 - - - +
222A SER* 1.3 61.9 + - - +
224A ILE 3.6 0.2 + - - -
225A SER* 3.0 28.0 + - - -
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 4.9 8.2 - - - +
72A ILE* 3.3 39.5 - - - +
218A HIS* 2.7 24.0 + - - +
219A THR 3.7 3.6 - - - -
221A ALA* 1.3 73.7 - - - +
223A LEU* 1.3 67.4 + - - +
225A SER* 3.5 6.1 + - - -
226A SER* 3.0 26.5 + - - -
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Residues in contact with LEU 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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69A ALA* 5.1 3.6 - - - +
97A PHE* 3.9 33.9 - - + -
140A ILE* 3.6 46.4 - - + +
141A GLN* 4.4 5.4 - - + -
144A PHE* 3.9 28.4 - - + -
219A THR 3.0 15.4 + - - +
220A PHE* 3.2 20.8 + - + +
222A SER* 1.3 78.4 - - - +
224A ILE* 1.3 69.9 + - + +
226A SER* 3.6 3.9 - - - -
227A ILE* 3.1 31.5 + - + +
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Residues in contact with ILE 224 (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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96A HIS* 3.7 32.3 - - + +
141A GLN* 4.0 8.7 - - - +
205A PHE* 3.1 49.6 - - + +
208A LEU* 4.1 5.2 - - + -
209A ALA* 3.8 13.9 - - + +
220A PHE* 2.9 50.8 + - + +
223A LEU* 1.3 78.7 - - + +
225A SER* 1.3 57.2 + - - +
227A ILE* 3.4 5.1 + - + +
228A GLN* 3.0 25.8 + - - +
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Residues in contact with SER 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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206A LEU* 5.9 2.0 - - - -
209A ALA* 3.9 15.2 - - - +
221A ALA 3.0 19.0 + - - -
222A SER* 3.5 7.6 + - - -
224A ILE* 1.3 74.3 - - - +
226A SER* 1.3 67.4 + - - +
228A GLN* 3.5 11.6 + - - +
229A THR* 3.2 27.6 + - - +
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Residues in contact with SER 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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65A LYS* 4.0 15.0 + - - +
69A ALA* 4.5 10.1 - - - -
136A ARG* 2.7 38.4 + - - -
140A ILE* 5.9 0.4 - - - -
222A SER 3.0 20.3 + - - -
223A LEU* 3.6 4.0 - - - -
225A SER* 1.3 78.0 + - - +
227A ILE* 1.3 62.2 + - - +
229A THR* 2.7 28.6 + - - -
230A ASP 3.7 0.7 + - - -
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Residues in contact with ILE 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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104A GLU* 4.5 3.1 - - - +
136A ARG* 3.7 19.1 - - - +
137A HIS* 3.5 46.0 + - + +
140A ILE* 3.6 25.4 - - + -
141A GLN* 4.8 7.6 - - - +
205A PHE* 3.5 26.5 - - + -
223A LEU* 3.1 25.1 + - + +
224A ILE* 3.6 8.1 - - + +
226A SER* 1.3 77.6 - - - +
228A GLN* 1.3 57.4 + - - +
230A ASP* 3.0 25.6 + - - +
231A GLU* 3.6 6.7 + - - +
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Residues in contact with GLN 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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202A ASN* 3.1 42.7 + - - +
205A PHE* 3.8 20.6 - - + -
206A LEU* 3.3 35.2 - - + +
224A ILE 3.0 17.1 + - - +
225A SER* 3.7 13.2 - - - +
226A SER 3.2 0.2 - - - -
227A ILE* 1.3 78.6 - - - +
229A THR* 1.3 70.2 + - + +
230A ASP 3.1 0.2 - - - -
231A GLU* 3.2 22.7 - - - +
232A SER* 4.4 1.9 + - - -
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Residues in contact with THR 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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65A LYS* 2.7 36.2 + - - +
225A SER 3.2 17.5 - - - +
226A SER* 2.7 19.8 + - - -
228A GLN* 1.3 87.3 - - + +
230A ASP* 1.3 60.2 + - - +
231A GLU 3.2 0.2 - - - -
232A SER* 4.5 9.9 + - - -
233A ARG* 4.9 4.2 + - - +
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Residues in contact with ASP 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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62A GLN* 3.0 16.2 + - - -
65A LYS* 2.7 30.2 + - - +
133A ASP* 3.4 20.8 - - - +
136A ARG* 2.5 34.3 + - - -
137A HIS* 3.0 25.3 + - + +
226A SER 4.0 0.4 - - - -
227A ILE 3.0 9.8 + - - +
229A THR* 1.3 77.5 + - - +
231A GLU* 1.3 65.4 + - - +
232A SER 3.6 0.4 - - - -
233A ARG* 3.1 27.6 + - - +
234A HIS* 3.4 4.1 + - - -
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Residues in contact with GLU 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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137A HIS* 4.1 7.1 - - - -
197A GLU* 3.2 23.3 - - - +
201A GLY* 5.2 3.6 - - - -
202A ASN* 3.2 29.2 - - - +
205A PHE* 5.3 4.9 - - - -
227A ILE* 3.6 9.1 + - - +
228A GLN* 3.2 20.9 + - - +
230A ASP* 1.3 76.4 - - - +
232A SER* 1.3 62.7 + - - +
234A HIS* 3.1 11.5 + - - -
235A ALA* 2.7 33.8 + - + +
501A P6G 4.1 5.5 - - - +
503A FE 4.0 8.5 - - - -
504A FE 2.4 30.8 - - - -
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Residues in contact with SER 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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51A TYR* 3.8 23.2 - - - +
202A ASN* 4.1 9.7 + - - +
228A GLN 4.4 2.8 + - - -
229A THR 4.5 6.9 + - - -
230A ASP 3.6 0.2 - - - -
231A GLU* 1.3 77.7 - - - +
233A ARG* 1.3 68.5 + - - +
234A HIS 3.1 0.7 + - - -
235A ALA* 4.3 7.4 - - - -
236A GLN* 3.4 23.6 + - - +
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Residues in contact with ARG 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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51A TYR* 5.0 6.5 - - - +
53A ILE* 3.9 43.6 - - + +
58A TYR* 3.4 17.4 - - - -
61A ILE* 5.4 3.2 - - - +
62A GLN* 3.0 29.1 + - - -
65A LYS* 4.5 5.7 - - - +
126A MET* 4.4 9.4 - - - +
129A PHE* 4.1 11.0 - - + -
133A ASP* 2.8 36.7 + - - +
229A THR 4.9 2.7 + - - +
230A ASP* 3.1 26.5 + - - +
231A GLU 3.1 1.0 - - - -
232A SER* 1.3 83.5 + - - +
234A HIS* 1.3 56.7 + - + +
236A GLN* 2.7 28.4 + - - +
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Residues in contact with HIS 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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111A GLU* 3.8 6.7 - - - +
126A MET 4.5 2.7 - - - +
130A GLY* 3.7 20.6 - - - +
133A ASP* 2.8 39.0 + - + +
134A GLU* 3.0 11.3 + - - -
137A HIS* 4.3 4.5 - + - -
193A THR* 3.4 7.6 - - - +
197A GLU* 3.3 15.0 - - - -
230A ASP 3.4 15.7 + - - -
231A GLU* 3.1 13.1 + - - -
233A ARG* 1.3 76.9 - - + +
235A ALA* 1.3 67.5 + - - +
236A GLN* 3.0 7.2 + - - -
237A GLN* 3.1 36.0 + - - +
504A FE 2.3 31.0 - - - -
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Residues in contact with ALA 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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193A THR* 2.9 23.0 + - - +
194A PHE* 4.0 1.0 + - - -
197A GLU* 3.8 25.4 - - + +
198A THR* 2.8 33.4 + - - +
202A ASN* 4.4 2.5 - - - +
231A GLU* 2.7 30.2 + - + +
232A SER* 4.3 4.0 - - - -
234A HIS* 1.3 73.1 - - - +
236A GLN* 1.3 60.4 + - - +
237A GLN 3.2 1.7 + - - -
238A GLY 4.0 0.7 + - - -
239A GLY 5.2 0.7 + - - -
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Residues in contact with GLN 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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49A GLU* 3.3 9.7 - - + +
50A PRO* 2.9 26.3 - - + +
51A TYR* 2.7 67.1 + - + +
126A MET* 3.8 10.9 - - - -
198A THR* 4.8 0.7 - - - -
232A SER* 3.4 11.1 + - - +
233A ARG* 2.7 29.2 + - - +
234A HIS 3.0 0.9 - - - -
235A ALA* 1.3 77.8 - - - +
237A GLN* 1.3 71.2 + - + +
238A GLY 3.2 1.1 + - - -
239A GLY* 3.5 4.4 + - - -
240A PRO* 3.2 21.0 - - - +
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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