Contacts of the helix formed by residues 214 - 229 (chain A) in PDB entry 6NFJ
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 ILE 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A TRP* 4.8 3.6 - - + -
198A LEU* 3.8 28.9 - - + -
202A LEU* 4.0 31.0 - - + +
206A TYR* 5.8 4.9 - - + -
208A GLY 3.4 31.2 - - - +
209A TRP* 3.6 31.2 - - + -
211A ASN 3.5 9.3 + - - +
213A THR* 1.3 78.6 + - - +
215A ILE* 1.3 63.6 + - + +
216A ASP 3.3 0.2 - - - -
217A ILE* 3.5 15.5 - - + -
218A PHE* 2.8 32.8 + - - +
272A ASN* 5.2 0.7 - - + -
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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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209A TRP* 5.3 0.2 - - + -
212A ASP* 3.4 25.6 - - + +
213A THR 3.2 0.8 - - - -
214A ILE* 1.3 80.3 - - + +
216A ASP* 1.3 60.8 + - - +
218A PHE* 3.6 3.1 + - - +
219A ASN* 3.2 24.8 + - - +
272A ASN* 3.8 36.8 - - + +
275A LYS* 3.7 48.5 - - + +
276A ALA* 3.9 15.0 - - + +
279A LYS* 4.1 15.6 - - + +
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Residues in contact with ASP 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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212A ASP 4.8 0.4 + - - -
213A THR* 3.7 8.0 + - - +
214A ILE 3.3 0.2 - - - -
215A ILE* 1.3 79.3 - - - +
217A ILE* 1.3 60.7 + - + +
219A ASN* 3.8 17.7 + - + +
220A ASP* 3.0 33.2 + - - +
279A LYS* 4.6 10.9 - - - +
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Residues in contact with ILE 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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155A TRP* 3.9 3.4 - - + -
162A GLY 3.8 23.0 - - - +
163A ILE* 4.8 10.3 - - + +
202A LEU* 3.8 39.3 - - + -
206A TYR* 4.2 24.7 - - + +
213A THR* 3.5 17.3 - - - +
214A ILE* 3.0 15.8 + - + +
216A ASP* 1.3 77.2 - - + +
218A PHE* 1.3 59.7 + - - +
220A ASP* 3.1 10.6 + - + +
221A TYR* 2.9 27.0 + - - +
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Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TRP* 3.7 30.8 - + + -
193A LEU* 4.0 26.5 - - + -
194A TYR* 4.1 14.1 - - + -
209A TRP* 4.2 15.5 - + + -
214A ILE 2.8 18.8 + - - +
215A ILE 4.0 2.7 - - - +
217A ILE* 1.3 73.5 - - - +
219A ASN* 1.3 56.8 + - - +
221A TYR* 3.4 7.5 + + - -
222A ALA* 2.8 28.2 + - - +
238A THR* 4.1 24.9 - - - -
239A ILE* 4.1 18.4 - - + -
276A ALA* 3.7 24.7 - - + -
280A VAL* 3.5 32.1 - - + -
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Residues in contact with ASN 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 ILE 3.2 17.9 + - - +
216A ASP* 3.9 17.1 + - - +
217A ILE 3.2 0.2 - - - -
218A PHE* 1.3 75.4 - - - +
220A ASP* 1.3 63.2 + - - +
222A ALA* 3.4 0.9 + - - +
223A THR* 2.9 26.5 + - - -
279A LYS* 4.0 23.2 + - + +
280A VAL* 4.0 15.3 - - + +
283A ASN* 2.5 37.7 + - - +
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Residues in contact with ASP 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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164A VAL* 3.3 26.7 + - + +
216A ASP* 3.0 21.2 + - - +
217A ILE* 3.1 13.4 + - + +
219A ASN* 1.3 78.6 + - - +
221A TYR* 1.3 65.1 + - - +
223A THR* 3.1 17.1 + - - -
224A TYR* 3.3 8.7 + - - +
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Residues in contact with TYR 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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153A ILE* 3.3 41.6 + - - +
155A TRP* 3.3 69.2 - + + +
158A LEU* 4.2 6.7 - - + -
159A PHE* 3.5 23.3 - + - -
162A GLY 4.7 0.2 - - - +
164A VAL* 3.5 10.7 - - + +
193A LEU* 3.4 34.3 + - + +
217A ILE 2.9 8.4 + - - +
218A PHE* 3.8 15.3 - + - +
220A ASP* 1.3 76.7 - - - +
222A ALA* 1.3 63.7 + - - +
224A TYR* 3.4 10.1 + - - +
225A CYS* 3.5 25.3 + - - -
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Residues in contact with ALA 222 (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 LEU* 3.6 27.6 - - + -
218A PHE* 2.8 18.7 + - + +
219A ASN* 3.6 5.4 - - - +
220A ASP 3.2 0.2 - - - -
221A TYR* 1.3 78.1 - - - +
223A THR* 1.3 57.6 + - - +
225A CYS* 3.3 3.2 + - - +
226A PHE* 2.9 40.1 + - + -
280A VAL* 3.7 28.0 - - + -
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Residues in contact with THR 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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219A ASN* 2.9 16.0 + - - -
220A ASP* 3.1 13.1 + - - -
222A ALA* 1.3 77.2 - - - +
224A TYR* 1.3 62.3 + - - +
226A PHE* 3.2 10.6 + - - +
227A GLN* 3.1 44.3 + - - +
283A ASN* 2.9 18.4 + - - +
288A PHE* 4.1 12.1 - - + -
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Residues in contact with TYR 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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158A LEU* 4.5 13.2 - - + -
159A PHE* 3.4 37.5 - + + -
164A VAL* 4.2 13.9 - - + +
165A THR 5.9 1.6 - - - -
166A VAL* 5.7 2.0 - - - -
167A ALA* 3.2 31.9 + - + +
172A LEU* 3.8 17.5 - - + +
220A ASP 3.3 8.3 + - - +
221A TYR 3.7 8.3 - - - +
222A ALA 3.2 0.6 - - - -
223A THR* 1.3 78.6 - - - +
225A CYS* 1.3 65.9 + - - +
227A GLN* 3.2 22.3 + - - +
228A MET* 3.0 60.5 + - + +
229A PHE* 5.0 2.7 - + - -
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Residues in contact with CYS 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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153A ILE* 4.2 4.9 - - - -
158A LEU* 4.4 5.6 - - - -
193A LEU* 3.5 34.5 - - + -
221A TYR* 3.5 31.6 + - - -
222A ALA 3.3 5.2 + - - +
224A TYR* 1.3 76.2 - - - +
226A PHE* 1.3 63.4 + - - +
227A GLN 3.2 0.2 - - - -
229A PHE* 3.1 47.3 + - + +
230A GLY 3.2 3.6 + - - -
236A TRP* 3.2 16.4 - - + -
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Residues in contact with PHE 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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193A LEU* 4.6 3.8 - - + -
222A ALA* 2.9 40.0 + - + +
223A THR* 3.2 7.4 + - - +
225A CYS* 1.3 77.2 - - - +
227A GLN* 1.3 58.2 + - - +
230A GLY* 3.3 6.2 - - - +
236A TRP* 3.9 28.7 - + - -
280A VAL* 3.5 20.4 - - + -
283A ASN* 4.3 7.0 - - - -
284A TYR* 3.5 32.5 - + + -
288A PHE* 3.5 38.0 - + + -
292A GLN* 2.6 31.4 + - - +
296A LEU* 3.5 28.5 - - + -
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Residues in contact with GLN 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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223A THR* 3.1 35.1 + - - +
224A TYR* 3.2 15.0 + - - +
226A PHE* 1.3 79.2 - - - +
228A MET* 1.3 74.7 + - + +
229A PHE 3.4 0.7 + - - -
230A GLY 3.7 3.1 + - - -
231A ASP* 4.4 8.5 + - - +
288A PHE* 3.6 20.5 - - + -
292A GLN* 4.5 2.3 + - - +
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Residues in contact with MET 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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172A LEU* 4.3 15.5 - - + -
224A TYR* 3.0 57.7 + - + +
227A GLN* 1.3 88.0 - - + +
229A PHE* 1.3 69.4 + - + +
231A ASP* 3.6 8.1 - - - +
232A ARG* 2.8 25.1 + - - +
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Residues in contact with PHE 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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153A ILE* 3.7 31.6 - - + -
158A LEU* 4.2 17.7 - - + -
172A LEU* 3.5 33.4 - - + -
175A TYR* 3.9 22.7 - + + -
176A SER* 4.6 7.4 - - - -
179A LEU* 3.7 23.8 - - + -
224A TYR* 5.0 4.9 - + - -
225A CYS* 3.1 29.7 + - + +
228A MET* 1.3 87.5 - - + +
230A GLY* 1.3 65.5 + - - +
231A ASP* 3.2 6.1 + - - -
232A ARG* 3.2 14.1 + - - +
233A VAL* 3.0 23.0 + - - +
236A TRP* 3.8 10.5 - - + -
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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
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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