Contacts of the helix formed by residues 201 - 218 (chain F) in PDB entry 3N2N
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 VAL 201 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F GLU* 3.5 52.7 - - + +
65F PHE* 4.4 10.2 - - + -
148F LEU* 4.1 15.9 - - + -
178F VAL* 3.5 19.5 - - + -
179F GLY 2.9 24.1 + - - +
180F VAL* 4.4 10.1 - - + -
181F LYS 5.3 1.1 - - - +
199F PHE 3.8 0.4 + - - -
200F PRO* 1.3 72.3 - - - +
202F ASN* 1.3 72.6 + - + +
204F GLY* 3.3 9.9 + - - -
205F PHE* 4.3 4.0 + - - +
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Residues in contact with ASN 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLU* 6.1 0.2 - - - +
179F GLY 5.2 0.2 - - - +
200F PRO* 3.7 17.6 - - - +
201F VAL* 1.3 85.2 + - + +
203F ASP* 1.3 84.6 + - - +
205F PHE* 5.2 2.1 + - - +
206F GLN* 5.7 2.6 - - - +
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Residues in contact with ASP 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F PHE* 4.9 3.6 - - + -
200F PRO* 3.2 23.9 + - + +
202F ASN* 1.3 99.5 + - - +
204F GLY* 1.3 63.8 + - - +
205F PHE 3.5 2.0 + - - -
206F GLN* 3.7 11.7 + - + +
207F ALA* 3.4 21.3 + - - +
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Residues in contact with GLY 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F PHE* 3.3 17.3 - - - -
178F VAL* 4.6 2.5 - - - -
199F PHE* 4.2 13.0 - - - -
200F PRO 2.8 16.0 + - - -
201F VAL 3.3 4.8 + - - -
203F ASP* 1.3 75.7 - - - +
205F PHE* 1.3 66.2 + - - +
207F ALA* 3.3 1.6 + - - +
208F LEU* 2.9 30.6 + - - +
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Residues in contact with PHE 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F PHE* 3.3 19.5 - - + -
68F GLN* 3.6 68.0 - - + +
69F LEU* 3.7 24.7 - - + -
72F LYS* 4.7 14.4 - - + -
201F VAL 4.3 2.1 + - - +
202F ASN 5.2 1.7 + - - +
203F ASP 3.5 0.6 - - - -
204F GLY* 1.3 74.1 - - - +
206F GLN* 1.3 80.9 + - + +
208F LEU* 4.1 1.3 - - - +
209F GLN* 2.8 55.4 + - + +
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Residues in contact with GLN 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ASN 5.7 2.5 - - - +
203F ASP* 3.7 12.4 + - + +
204F GLY 3.4 0.2 - - - -
205F PHE* 1.3 96.2 - - + +
207F ALA* 1.3 61.5 + - - +
209F GLN* 3.0 37.6 + - - +
210F GLY* 3.4 4.2 + - - -
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Residues in contact with ALA 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F PHE* 3.7 38.1 - - + -
203F ASP 3.4 13.4 + - - +
204F GLY 3.3 3.9 + - - +
205F PHE 3.2 0.6 - - - -
206F GLN* 1.3 79.2 - - - +
208F LEU* 1.3 61.8 + - - +
210F GLY* 3.4 3.6 + - - -
211F ILE* 3.2 27.7 + - + +
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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
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65F PHE* 4.2 11.4 - - + -
69F LEU* 4.4 9.4 - - + -
144F VAL* 5.6 1.3 - - + -
146F ILE* 3.9 27.4 - - + -
176F TYR* 4.1 22.9 - - + -
178F VAL* 4.0 18.2 - - + -
199F PHE* 3.6 29.2 - - + -
204F GLY 2.9 25.1 + - - +
205F PHE 4.1 0.9 - - - +
207F ALA* 1.3 74.6 - - - +
209F GLN* 1.3 61.1 + - - +
211F ILE* 3.1 20.9 + - + +
212F ILE* 2.8 39.0 + - + +
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Residues in contact with GLN 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LEU* 4.0 9.3 - - + +
72F LYS* 4.9 12.2 - - + +
73F PHE* 3.2 33.2 - - + -
205F PHE* 2.8 50.0 + - + +
206F GLN* 3.0 33.0 + - - +
208F LEU* 1.3 72.2 - - - +
210F GLY* 1.3 69.7 + - - +
213F HIS* 2.9 31.7 + - - +
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Residues in contact with GLY 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ASN* 2.9 29.6 - - - +
186E THR* 4.2 4.9 - - - -
206F GLN 3.4 2.2 + - - -
207F ALA 3.4 7.0 + - - -
208F LEU 3.2 0.8 - - - -
209F GLN* 1.3 92.0 + - - +
211F ILE* 1.3 58.0 + - - +
213F HIS* 3.4 2.2 + - - +
214F SER* 3.0 21.0 + - - -
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Residues in contact with ILE 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E THR* 3.5 26.9 - - + +
195E LYS* 3.9 14.1 - - - +
144F VAL* 5.8 1.3 - - + -
176F TYR* 3.6 47.3 - - + +
199F PHE* 4.2 12.3 - - + -
207F ALA* 3.2 19.8 + - + +
208F LEU* 3.1 20.1 + - + +
210F GLY* 1.3 75.9 - - - +
212F ILE* 1.3 58.6 + - + +
214F SER* 3.2 3.8 + - - -
215F ILE* 3.0 47.3 + - + +
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Residues in contact with ILE 212 (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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43F PHE* 3.6 31.0 - - + -
45F LEU* 4.0 25.1 - - + -
69F LEU* 3.8 31.6 - - + -
73F PHE* 3.7 35.7 - - + -
78F LEU* 4.3 7.0 - - + -
144F VAL* 6.3 1.1 - - + -
146F ILE* 4.6 4.0 - - + -
208F LEU* 2.8 30.0 + - + +
211F ILE* 1.3 73.4 - - + +
213F HIS* 1.3 60.3 + - - +
215F ILE* 3.4 1.1 + - + -
216F LEU* 2.9 32.6 + - + +
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Residues in contact with HIS 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ASN* 3.7 21.1 - - + +
187E GLN* 4.7 5.2 + - - -
73F PHE* 3.9 11.2 - - + -
209F GLN* 2.9 23.1 + - - +
210F GLY* 3.6 4.9 - - - +
212F ILE* 1.3 76.6 - - - +
214F SER* 1.3 57.3 + - - +
216F LEU* 3.4 5.4 + - - +
217F LYS* 3.0 63.3 + - + +
223F ACT 3.0 29.4 + - - +
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Residues in contact with SER 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ASN* 3.9 7.0 - - - -
186E THR* 3.6 21.9 - - - +
187E GLN* 3.5 27.9 + - - +
190E ARG* 2.9 23.9 + - - -
210F GLY 3.0 14.1 + - - -
211F ILE 3.2 8.7 + - - -
213F HIS* 1.3 75.3 - - - +
215F ILE* 1.3 62.8 + - - +
217F LYS* 3.3 5.0 + - - +
218F LYS* 3.1 21.7 + - - +
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Residues in contact with ILE 215 (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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186E THR* 6.1 0.9 - - + -
190E ARG* 4.6 10.3 - - - +
40F TYR* 3.9 14.6 - - + +
43F PHE* 3.6 39.2 - - + -
142F ALA* 3.6 27.1 - - + -
144F VAL* 4.0 19.3 - - + -
174F ILE* 6.0 3.4 - - + -
176F TYR* 5.9 0.4 - - + -
211F ILE* 3.0 39.9 + - + +
212F ILE* 4.6 0.4 - - + -
214F SER* 1.3 74.6 - - - +
216F LEU* 1.3 58.8 + - - +
218F LYS* 3.0 21.9 + - - +
219F SER* 3.2 10.2 + - - -
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Residues in contact with LEU 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F PHE* 3.8 20.6 - - + -
73F PHE* 3.6 37.7 - - + -
75F SER* 4.7 10.3 - - - +
77F GLN* 3.9 37.6 - - + +
78F LEU* 4.2 12.6 - - + +
212F ILE* 2.9 21.8 + - + +
213F HIS* 3.7 5.2 - - - +
215F ILE* 1.3 75.4 - - - +
217F LYS* 1.3 59.6 + - + +
219F SER* 2.8 29.5 + - - -
223F ACT 4.3 9.9 - - - +
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Residues in contact with LYS 217 (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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155E GLU* 4.5 17.7 - - - +
187E GLN* 3.6 26.0 - - - +
213F HIS* 3.0 46.1 + - - +
214F SER 3.3 8.9 + - - +
216F LEU* 1.3 77.4 - - + +
218F LYS* 1.3 55.9 + - - +
219F SER* 3.2 8.2 + - - +
223F ACT 5.6 1.8 - - - -
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Residues in contact with LYS 218 (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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162E GLU* 5.5 4.3 - - - -
190E ARG* 3.3 39.3 - - - +
36F SER 3.3 22.3 + - - -
37F MET* 4.1 11.4 - - - +
38F ALA 2.6 31.1 + - - -
39F CYS* 3.2 9.5 - - - -
40F TYR* 2.9 45.6 + - + -
140F ARG* 3.5 7.7 - - - +
214F SER 3.1 11.7 + - - +
215F ILE* 3.0 13.5 + - - +
217F LYS* 1.3 76.0 - - - +
219F SER* 1.3 60.0 + - - +
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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
------------------------------------------------------------
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