Contacts of the helix formed by residues 199 - 217 (chain F) in PDB entry 2CNW
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 LYS 199 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ASP* 3.0 42.9 + - - -
272C VAL 5.4 0.4 + - - -
273C SER* 5.3 5.5 - - - +
1001C GDP 4.5 2.0 + - - -
196F LEU* 3.1 21.6 + - + +
197F HIS 3.2 0.6 - - - -
198F THR* 1.3 90.4 - - - +
200F HIS* 1.3 57.6 + - - +
201F ASN* 3.2 15.9 - - - +
202F LEU* 2.8 40.3 + - + +
203F MET* 3.0 14.9 + - - +
3001F 5GP 4.4 14.8 + - - -
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Residues in contact with HIS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F HIS 5.5 0.7 - - - -
198F THR 3.8 4.6 + - - -
199F LYS* 1.3 71.9 - - - +
201F ASN* 1.3 58.9 + - - +
203F MET* 3.3 11.5 + - + +
204F GLU* 2.9 64.9 + - + +
207F LYS* 4.9 3.8 - - - -
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Residues in contact with ASN 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F LYS* 3.8 19.2 - - - +
200F HIS* 1.3 81.7 + - - +
202F LEU* 1.3 77.2 + - - +
204F GLU* 3.5 9.1 + - - +
205F GLU* 3.0 26.0 + - - +
3001F 5GP 4.7 19.8 + - - -
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F ARG* 2.8 51.7 + - + +
196F LEU 4.8 2.0 - - - +
199F LYS* 2.8 32.2 + - + +
201F ASN* 1.3 95.3 + - - +
203F MET* 1.3 61.3 + - - +
205F GLU* 3.3 8.5 + - - +
206F LEU 3.1 13.3 + - - -
3001F 5GP 3.3 71.8 - - + +
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Residues in contact with MET 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F ARG* 4.1 9.4 - - - -
196F LEU 4.5 0.2 - - - +
197F HIS* 3.7 36.1 - - + +
199F LYS 3.0 15.9 + - - +
200F HIS* 3.3 13.2 + - - +
202F LEU* 1.3 77.5 - - - +
204F GLU* 1.3 56.3 + - + +
206F LEU* 3.4 9.7 + - + +
207F LYS* 3.1 31.6 + - - +
242F LYS* 3.6 25.4 - - + +
243F PHE* 3.6 43.3 - - + -
246F ALA* 3.7 21.9 - - + +
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Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F HIS* 2.9 51.7 + - + +
201F ASN* 3.6 8.3 - - - +
203F MET* 1.3 73.8 - - - +
205F GLU* 1.3 60.6 + - - +
207F LYS* 2.8 43.2 + - - +
208F LYS* 2.9 28.9 + - - +
211F ARG* 4.6 9.5 + - - -
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Residues in contact with GLU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F ASP* 5.5 2.7 - - - +
169F PRO* 3.8 29.2 - - + +
170F ALA* 6.5 0.2 - - + -
193F ALA* 5.6 0.9 - - - +
195F ARG* 2.8 30.5 + - - +
201F ASN 3.0 15.4 + - - +
202F LEU* 3.3 12.9 + - + +
204F GLU* 1.3 75.0 - - - +
206F LEU* 1.3 56.1 + - - +
208F LYS* 3.3 14.3 + - + +
209F VAL* 3.0 32.8 + - + +
3001F 5GP 2.3 48.7 + - - +
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Residues in contact with LEU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 4.7 7.6 - - + +
108F VAL* 3.8 20.2 - - + -
192F THR* 3.7 33.7 - - + +
195F ARG* 3.8 18.7 - - - +
202F LEU 3.1 12.2 + - - +
203F MET* 3.4 14.4 - - + +
205F GLU* 1.3 75.3 - - - +
207F LYS* 1.3 62.4 + - - +
209F VAL* 3.0 19.8 + - + +
210F LYS* 3.1 14.0 + - - +
243F PHE* 3.6 37.0 - - + -
247F VAL* 3.9 18.2 - - + -
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Residues in contact with LYS 207 (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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200F HIS* 4.9 4.8 - - - -
203F MET* 3.1 13.9 + - - +
204F GLU* 2.8 43.6 + - - +
206F LEU* 1.3 77.3 - - - +
208F LYS* 1.3 62.0 + - - +
210F LYS* 3.4 5.9 + - - +
211F ARG* 3.1 44.8 + - - +
245F GLU* 4.5 12.5 + - - -
246F ALA* 3.4 39.3 - - - +
247F VAL* 4.0 6.9 - - - +
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Residues in contact with LYS 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F ASP* 3.7 18.4 + - - +
170F ALA* 3.6 23.6 - - + -
204F GLU 2.9 13.5 + - - +
205F GLU* 3.4 15.9 - - + +
206F LEU 3.2 0.2 - - - -
207F LYS* 1.3 73.3 - - - +
209F VAL* 1.3 59.5 + - - +
211F ARG* 3.5 21.1 + - - +
212F ALA* 3.0 25.8 + - - +
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 4.0 23.3 - - + -
169F PRO* 3.8 19.5 - - + +
170F ALA* 3.6 27.8 - - + +
173F ALA* 3.8 21.8 - - + -
190F VAL* 4.6 3.6 - - + -
192F THR* 4.9 6.3 - - + -
195F ARG* 6.0 2.0 - - - +
205F GLU* 3.0 21.2 + - + +
206F LEU* 3.0 14.5 + - + +
208F LYS* 1.3 72.3 - - - +
210F LYS* 1.3 66.6 + - - +
212F ALA* 3.2 5.7 + - - +
213F ILE* 3.1 22.0 + - + +
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Residues in contact with LYS 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 3.9 16.5 - - + +
206F LEU 3.1 11.0 + - - +
207F LYS* 3.6 10.3 - - - +
208F LYS 3.4 0.2 - - - -
209F VAL* 1.3 78.2 - - - +
211F ARG* 1.3 61.2 + - + +
213F ILE* 3.2 11.3 + - - +
214F ALA* 3.1 20.6 + - + +
221F PRO* 3.7 27.5 + - + +
224F VAL* 3.9 18.6 - - - +
246F ALA 5.6 0.2 - - - +
247F VAL* 2.8 41.1 + - + +
248F GLY* 4.6 3.0 + - - -
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Residues in contact with ARG 211 (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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204F GLU* 4.6 9.1 + - - -
207F LYS* 3.1 47.2 + - - +
208F LYS* 3.7 27.4 - - - +
210F LYS* 1.3 74.0 - - + +
212F ALA* 1.3 54.8 + - - +
214F ALA* 3.1 8.8 + - - +
215F LYS* 2.8 35.8 + - - +
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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
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170F ALA* 3.2 35.2 - - + +
174F TYR* 3.5 22.0 - - + +
208F LYS 3.0 15.1 + - - +
209F VAL 3.2 11.2 + - - +
211F ARG* 1.3 74.1 - - - +
213F ILE* 1.3 62.0 + - - +
215F LYS* 3.2 19.7 + - - +
216F ALA* 3.3 9.4 + - - +
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Residues in contact with ILE 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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104F VAL* 4.1 18.8 - - + -
106F LEU* 4.1 25.8 - - + -
173F ALA* 4.3 10.8 - - + -
174F TYR* 5.2 0.2 - - - +
177F VAL* 4.0 27.8 - - + +
190F VAL* 4.2 7.9 - - + -
209F VAL* 3.1 17.2 + - + +
210F LYS* 3.2 8.9 + - - +
212F ALA* 1.3 74.7 - - - +
214F ALA* 1.3 48.9 + - - +
216F ALA* 3.0 5.9 + - - +
217F ASP* 2.8 31.5 + - - +
220F GLU* 3.6 13.2 - - + -
221F PRO* 3.5 38.4 - - + -
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Residues in contact with ALA 214 (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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210F LYS* 3.1 9.8 + - + +
211F ARG* 3.1 11.9 + - - +
213F ILE* 1.3 72.9 - - - +
215F LYS* 1.3 64.3 + - - +
217F ASP 3.2 11.7 - - - +
218F PRO* 3.3 30.5 - - + +
220F GLU 3.2 15.5 - - - +
221F PRO* 5.1 0.7 - - + -
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Residues in contact with LYS 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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174F TYR* 3.4 38.4 + - + -
211F ARG 2.8 13.0 + - - +
212F ALA* 3.4 13.7 - - - +
213F ILE 3.2 0.4 - - - -
214F ALA* 1.3 80.1 - - - +
216F ALA* 1.3 58.7 + - - +
218F PRO* 5.2 2.6 - - - +
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Residues in contact with ALA 216 (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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174F TYR* 3.5 26.2 - - + +
177F VAL* 3.8 23.8 - - + -
178F GLN* 3.5 18.4 - - - +
181F LYS* 2.6 28.5 + - - -
212F ALA 3.3 1.9 + - - +
213F ILE 3.0 7.8 + - - +
215F LYS* 1.3 79.7 - - - +
217F ASP* 1.3 58.0 + - - +
218F PRO* 4.3 3.4 - - - +
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Residues in contact with ASP 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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103F ARG* 4.3 14.9 + - - -
177F VAL* 4.0 14.7 - - + +
180F MET* 5.1 1.4 - - - +
181F LYS* 4.2 13.9 - - + +
213F ILE 2.8 6.2 + - - +
214F ALA* 3.2 14.5 - - - -
215F LYS 3.5 0.2 - - - -
216F ALA* 1.3 81.0 - - - +
218F PRO* 1.4 60.1 - - - +
219F GLU* 3.2 25.2 + - - +
220F GLU* 2.8 53.1 + - + +
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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