Contacts of the helix formed by residues 201 - 217 (chain F) in PDB entry 3N3L
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 THR 201 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ARG* 5.4 1.1 - - - +
197F VAL* 3.0 15.4 + - - +
199F TYR 3.5 0.8 - - - -
200F LYS* 1.3 85.6 + - - +
202F ALA* 1.3 72.5 + - - +
203F PHE 3.3 1.9 + - - -
204F TYR* 3.6 8.0 + - - -
205F SER* 2.9 41.3 + - - +
206F PHE* 5.0 0.9 - - + -
236F GLY 4.8 7.0 - - - +
239F PHE* 4.4 18.8 - - + -
240F GLN* 3.7 24.8 + - + +
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Residues in contact with ALA 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F VAL 2.8 15.5 + - - +
198F LYS* 3.4 16.4 - - - +
201F THR* 1.3 77.6 - - - +
203F PHE* 1.3 64.4 + - - +
206F PHE* 3.0 25.5 + - - +
207F TYR 3.5 4.5 + - - -
233F LEU* 3.6 26.8 - - + +
236F GLY* 4.1 26.2 - - - -
237F GLU* 4.5 0.9 - - - +
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Residues in contact with PHE 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 4.8 1.3 - - + -
162F GLN* 3.5 30.5 - - + -
163F SER* 3.3 43.3 - - - -
166F GLN* 3.8 30.3 - - + +
167F THR* 5.5 0.2 - - - +
198F LYS* 3.1 17.9 + - + +
199F TYR 4.2 10.3 - - - +
201F THR 3.3 0.6 - - - -
202F ALA* 1.3 79.5 - - - +
204F TYR* 1.3 59.4 + - - +
207F TYR* 3.1 43.9 + + + +
208F LEU 3.0 23.7 + - - -
229F LYS* 4.3 16.8 - - + -
233F LEU* 3.8 15.9 - - + +
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Residues in contact with TYR 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ARG* 3.5 29.0 + - - -
92F VAL* 4.8 4.2 - - + +
95F LEU* 4.6 7.4 - - + -
96F GLN* 3.5 39.7 + - + +
99F PHE* 4.1 23.7 - + + +
100F LEU* 5.0 5.5 - - - +
163F SER* 4.3 8.7 - - - -
167F THR* 3.7 25.0 + - + +
199F TYR 5.3 0.4 + - - -
200F LYS 3.7 18.2 - - - -
201F THR* 3.6 9.9 + - - -
203F PHE* 1.3 80.5 - - - +
205F SER* 1.3 77.8 + - - +
208F LEU* 3.6 25.3 - - + +
209F PRO* 3.3 16.8 - - - +
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Residues in contact with SER 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MS0 3.1 24.0 - - - +
60F ARG* 3.0 42.3 + - - +
201F THR* 2.9 26.4 + - - +
204F TYR* 1.3 88.7 - - - +
206F PHE* 1.3 76.9 + - - +
209F PRO* 3.3 9.3 - - - +
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Residues in contact with PHE 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MS0 3.7 39.0 - + - +
201F THR* 5.0 1.1 - - + -
202F ALA* 3.0 11.8 + - - +
205F SER* 1.3 92.1 - - - +
207F TYR* 1.3 66.4 + - - +
209F PRO* 3.4 9.5 - - - +
210F ILE* 3.7 10.9 - - - +
232F LEU* 3.3 39.6 - - + +
235F MET* 4.1 22.9 - - + -
236F GLY* 3.3 29.6 - - - -
239F PHE* 3.6 40.8 - + + -
344F LEU* 4.5 5.4 - - + +
348F ILE* 4.1 13.0 - - + -
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Residues in contact with TYR 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 3.9 11.7 - - + +
162F GLN* 5.5 1.1 - - - -
202F ALA 3.5 1.6 + - - -
203F PHE* 3.1 52.2 + + + +
206F PHE* 1.3 76.8 - - - +
208F LEU* 1.3 59.1 + - - +
210F ILE* 3.2 3.1 + - - +
211F ALA* 2.7 60.1 + - + +
215F TYR* 4.5 3.5 + - - -
225F HIS* 2.8 38.2 + - - +
228F ALA* 4.9 4.0 - - + -
229F LYS* 3.6 48.0 + - + -
232F LEU* 3.6 15.3 - - + +
233F LEU* 4.5 11.9 - - + -
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Residues in contact with LEU 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F VAL* 4.3 14.8 - - + -
95F LEU* 3.5 33.0 - - + -
159F LEU* 3.4 30.3 - - + -
160F PHE* 4.2 26.7 - - + -
163F SER* 3.6 21.5 - - - +
203F PHE 3.0 6.0 + - - +
204F TYR* 3.6 21.1 - - + +
207F TYR* 1.3 79.0 - - - +
209F PRO* 1.3 69.7 - - + +
211F ALA* 4.3 4.9 - - - -
212F ALA* 3.0 21.9 + - + +
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Residues in contact with PRO 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MS0 4.7 0.9 - - - -
60F ARG* 3.8 22.4 - - + +
63F THR* 3.8 28.3 - - + -
64F VAL* 3.4 25.0 - - + +
92F VAL* 4.5 6.1 - - + -
204F TYR 3.3 18.4 - - - +
205F SER 3.3 17.9 - - - +
206F PHE 3.4 11.7 - - - +
207F TYR 3.4 4.3 - - - -
208F LEU* 1.3 92.1 - - + +
210F ILE* 1.3 59.8 + - - +
213F ALA* 3.4 17.3 + - - +
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Residues in contact with ILE 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F THR* 3.5 26.2 - - + -
67F ALA* 3.8 11.9 - - + -
71F LEU* 5.6 1.1 - - + -
206F PHE 3.7 11.7 - - - +
207F TYR 3.2 1.2 + - - -
209F PRO* 1.3 73.8 - - - +
211F ALA* 1.3 69.7 + - - +
213F ALA* 2.9 7.5 + - - +
214F MET* 2.8 44.2 + - + +
228F ALA* 4.8 2.9 - - + -
232F LEU* 3.6 33.9 - - + -
336F LEU* 5.0 3.8 - - + -
340F VAL* 3.7 30.7 - - + +
341F PHE* 5.1 3.4 - - + -
344F LEU* 4.3 7.2 - - + -
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Residues in contact with ALA 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 3.7 21.8 - - + -
207F TYR* 2.7 55.4 + - + +
208F LEU 3.9 0.9 - - - +
210F ILE* 1.3 72.4 - - - +
212F ALA* 1.3 63.7 + - - +
214F MET* 3.1 9.4 + - - +
215F TYR* 3.0 26.2 + - - -
225F HIS* 3.7 11.8 - - + -
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Residues in contact with ALA 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F VAL* 4.4 6.3 - - + -
88F VAL* 3.9 27.1 - - + -
92F VAL* 5.4 0.2 - - + -
156F LEU* 3.9 8.6 - - + +
159F LEU* 3.4 16.5 - - + +
160F PHE* 5.1 2.2 - - + -
208F LEU* 3.0 22.5 + - + +
209F PRO 3.6 5.2 - - - +
211F ALA* 1.3 74.6 - - - +
213F ALA* 1.3 64.5 + - - +
215F TYR* 3.1 6.1 + - - +
216F MET* 3.1 26.0 + - - +
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 3.9 16.9 - - - +
67F ALA* 3.6 32.5 - - + -
68F PHE* 4.0 11.0 - - - +
71F LEU* 4.0 6.1 - - + +
209F PRO 3.4 6.5 + - - +
210F ILE 2.9 7.5 + - - +
212F ALA* 1.3 78.6 - - - +
214F MET* 1.3 63.0 + - - +
216F MET* 3.2 13.4 + - - +
217F ALA* 3.1 22.0 + - - +
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Residues in contact with MET 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 3.8 21.3 - - + +
207F TYR* 5.5 0.4 - - - -
210F ILE* 2.8 36.4 + - + +
211F ALA* 3.3 15.0 - - - +
213F ALA* 1.3 75.8 - - - +
215F TYR* 1.3 57.3 + - - +
217F ALA* 2.8 18.8 + - - +
219F ILE* 3.0 43.4 + - + +
224F GLU* 4.0 5.8 - - + +
225F HIS* 3.9 34.3 - - + +
228F ALA* 3.9 23.1 - - + -
336F LEU* 3.9 20.4 - - + -
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Residues in contact with TYR 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F TYR* 3.5 23.5 - - + +
155F ASN* 3.5 49.6 + - + -
156F LEU* 4.0 13.9 - - + -
159F LEU* 4.1 28.7 - - + +
207F TYR* 4.5 2.9 + - - -
211F ALA 3.0 23.9 + - - -
212F ALA 3.1 5.4 + - - +
214F MET* 1.3 75.8 - - - +
216F MET* 1.3 64.2 + - - +
218F GLY* 3.0 13.5 + - - +
219F ILE 4.1 2.7 - - - +
220F ASP* 3.7 21.1 + - + -
225F HIS* 3.4 36.9 + + - -
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Residues in contact with MET 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F VAL* 4.8 4.7 - - - -
68F PHE* 4.7 17.0 - - + -
72F VAL* 4.7 6.2 - - - +
81F SER* 4.5 3.4 - - - +
84F ARG* 3.8 9.2 - - + +
85F ALA* 3.4 41.1 - - + +
88F VAL* 3.9 27.1 - - + -
152F TYR* 3.6 50.1 - - + +
156F LEU* 4.4 4.3 - - + -
212F ALA 3.1 17.4 + - - +
213F ALA* 3.2 11.2 + - - +
215F TYR* 1.3 75.9 - - - +
217F ALA* 1.3 58.1 + - - +
218F GLY 3.3 1.2 + - - -
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Residues in contact with ALA 217 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 3.8 30.5 - - + +
72F VAL* 3.9 17.9 - - + -
213F ALA 3.1 11.4 + - - +
214F MET 2.8 11.3 + - - +
216F MET* 1.3 79.7 - - - +
218F GLY* 1.3 57.1 + - - +
219F ILE* 3.2 14.7 + - + +
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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
------------------------------------------------------------
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