Contacts of the helix formed by residues 197 - 214 (chain B) in PDB entry 4FG9
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B HIS* 3.3 61.6 + - + +
138B VAL* 4.2 16.7 - - + +
196B SER* 1.3 80.9 - - - +
198B ALA* 1.3 64.2 + - + +
199B VAL 3.1 3.1 - - - -
200B ASP* 3.1 13.6 + - - +
201B CYS* 4.0 1.7 + - - -
266B THR* 3.9 28.5 - - - +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU* 4.6 0.7 - - - +
196B SER* 3.2 13.4 + - - +
197B LYS* 1.3 81.8 - - + +
199B VAL* 1.3 60.3 + - - +
201B CYS* 3.2 20.0 + - - +
202B TRP 3.3 5.4 + - - -
261B PRO* 3.9 29.8 - - + +
264B ARG* 3.0 31.7 + - + +
265B PHE 5.7 1.3 - - - +
266B THR* 6.4 2.5 - - + -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.0 7.4 - - + -
140B ARG* 3.6 31.5 - - + +
184B TYR 4.5 0.5 - - - +
186B ALA* 3.8 13.1 + - + +
188B GLU* 3.6 12.6 - - - +
189B VAL* 3.6 16.2 - - + -
195B TYR* 3.6 28.7 - - + -
196B SER 3.2 21.1 - - - +
197B LYS 3.1 1.2 - - - -
198B ALA* 1.3 75.2 - - - +
200B ASP* 1.3 63.8 + - - +
202B TRP* 3.5 5.2 - - - +
203B SER* 3.1 23.6 + - - -
264B ARG* 3.9 6.5 - - - +
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 4.1 14.2 - - + +
133B HIS* 3.3 23.6 + - - +
138B VAL* 3.4 11.8 - - - +
139B HIS* 3.1 27.8 + - - +
140B ARG* 2.7 33.4 + - - -
142B LEU* 4.4 7.0 - - + +
197B LYS 3.1 9.2 + - - +
199B VAL* 1.3 77.0 - - - +
201B CYS* 1.3 59.2 + - - +
202B TRP 3.2 0.2 - - - -
203B SER* 3.2 9.0 + - - -
204B ILE* 3.0 33.8 + - - +
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Residues in contact with CYS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B HIS* 4.5 3.4 - - - -
197B LYS 4.3 9.6 - - - -
198B ALA* 3.2 14.7 + - - +
200B ASP* 1.3 73.2 - - - +
202B TRP* 1.3 65.2 + - - +
204B ILE* 3.5 9.3 + - - +
205B GLY 3.1 16.8 + - - -
256B LEU* 3.4 24.5 - - + +
264B ARG* 4.3 2.7 - - - -
265B PHE 3.3 28.7 - - - +
266B THR* 3.8 4.3 - - - -
267B CYS* 3.6 37.0 - - - -
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Residues in contact with TRP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLY 2.7 20.7 + - - -
184B TYR 3.4 16.4 - - - -
185B VAL 3.3 4.9 + - - -
186B ALA* 3.5 13.0 - - + -
187B PRO* 3.6 27.8 - - + -
198B ALA 3.3 4.0 + - - -
199B VAL 3.5 9.9 - - - +
200B ASP 3.2 0.2 - - - -
201B CYS* 1.3 75.8 - - - +
203B SER* 1.3 68.2 + - - +
205B GLY* 3.0 12.1 + - - -
206B VAL* 3.0 18.8 + - + +
218B PHE* 3.8 29.8 - + - -
230B ILE* 4.2 7.0 - - + -
233B ALA* 3.7 21.3 - - + -
256B LEU 3.7 9.0 - - - -
257B MET* 3.6 16.5 - - + +
258B GLU 3.4 48.5 - - - -
259B LYS 4.0 1.1 - - - -
264B ARG* 3.7 16.5 - - - +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG 4.9 4.3 + - - -
142B LEU* 3.8 37.2 + - - +
184B TYR* 2.7 29.9 + - - +
199B VAL 3.1 12.2 + - - -
200B ASP* 3.2 12.1 + - - -
202B TRP* 1.3 79.6 - - - +
204B ILE* 1.3 57.2 + - - +
206B VAL* 3.2 5.1 + - - +
207B ILE* 3.0 33.4 + - - +
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.9 30.0 - - + +
125B VAL* 3.9 23.6 - - + -
126B LEU* 4.0 25.8 - - + -
129B VAL* 4.1 28.9 - - + -
142B LEU* 3.9 9.0 - - + -
200B ASP 3.0 21.4 + - - +
201B CYS* 3.8 9.9 - - - +
202B TRP 3.2 0.2 - - - -
203B SER* 1.3 73.8 - - - +
205B GLY* 1.3 57.6 + - - +
207B ILE* 3.4 9.1 + - + +
208B ALA* 2.9 28.1 + - - +
256B LEU* 4.2 6.5 - - + -
267B CYS* 4.3 2.5 - - - -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B CYS 3.1 6.7 + - - -
202B TRP 3.0 8.5 + - - -
204B ILE* 1.3 77.6 - - - +
206B VAL* 1.3 60.0 + - - +
208B ALA* 3.4 6.6 + - - +
209B TYR* 3.1 17.3 + - - +
253B ILE* 3.9 6.1 - - - +
256B LEU* 3.7 27.3 - - - +
257B MET* 3.6 19.2 - - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO 5.1 1.3 - - - +
183B GLY* 3.3 29.8 - - - +
184B TYR* 3.8 27.4 - - + -
202B TRP* 3.0 27.9 + - + +
203B SER 3.5 6.3 - - - +
205B GLY* 1.3 73.7 - - - +
207B ILE* 1.3 64.6 + - - +
209B TYR* 3.2 5.8 + - - +
210B ILE* 3.2 22.6 + - + +
216B PRO* 6.1 0.2 - - + -
217B PRO* 3.8 25.8 - - + -
218B PHE* 4.7 0.4 - - + -
257B MET* 3.9 17.7 - - + -
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.9 26.2 - - + -
104B PHE* 5.1 2.9 - - + -
122B ILE* 4.3 5.6 - - + -
125B VAL* 5.5 2.7 - - + -
142B LEU* 4.4 24.0 - - + +
143B LYS* 4.5 7.6 - - - -
144B PRO* 4.5 4.7 - - + -
147B LEU* 4.0 22.9 - - + -
184B TYR* 4.1 17.5 - - + -
203B SER 3.0 23.9 + - - +
204B ILE* 3.6 12.8 - - + +
206B VAL* 1.3 74.4 - - - +
208B ALA* 1.3 57.9 + - - +
210B ILE* 3.3 9.8 + - - +
211B LEU* 2.9 38.9 + - + +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.8 21.3 - - + +
204B ILE 2.9 17.8 + - - +
205B GLY* 3.5 7.2 - - - +
206B VAL 3.3 0.2 - - - -
207B ILE* 1.3 75.3 - - - +
209B TYR* 1.3 63.2 + - - +
211B LEU* 3.3 4.9 + - - +
212B LEU* 3.3 28.8 + - + +
252B PHE* 4.1 16.4 - - + -
253B ILE* 3.9 18.6 - - + -
275B TRP* 5.2 4.3 - - + -
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLY 3.1 12.3 + - - +
206B VAL* 3.3 11.4 - - - +
208B ALA* 1.3 75.7 - - - +
210B ILE* 1.3 62.5 + - - +
212B LEU 3.1 9.5 + - - -
213B CYS* 3.3 34.7 + - - -
215B TYR* 3.4 28.4 - + - -
217B PRO* 3.4 42.1 + - + +
235B TYR* 4.1 8.3 - + - -
236B GLU 2.9 26.2 + - - -
237B PHE* 3.8 20.0 - + - -
238B ASP* 3.7 2.4 + - - -
242B TRP* 3.6 30.2 + + - -
253B ILE* 3.7 16.9 - - + +
257B MET* 4.2 9.0 - - - -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 3.5 30.6 - - + -
184B TYR* 3.4 37.5 - - + +
206B VAL* 3.2 20.5 + - + +
207B ILE* 3.8 5.8 - - - +
209B TYR* 1.3 69.7 - - - +
211B LEU* 1.3 58.6 + - - +
212B LEU 3.0 6.9 + - - -
214B GLY* 2.7 48.2 + - - +
215B TYR 3.7 20.4 - - - +
216B PRO* 3.9 20.0 - - + -
217B PRO* 4.2 1.6 - - + -
290B VAL* 4.3 2.4 - - - +
294B ILE* 5.0 1.6 - - + +
298B PHE* 4.4 7.2 - - + -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.9 12.6 - - + -
104B PHE* 3.7 16.4 - - + -
107B ILE* 3.3 33.4 - - + -
113B TYR* 2.6 40.9 + - - +
118B ALA* 4.3 13.5 - - + +
121B LEU* 4.2 13.9 - - + -
122B ILE* 3.6 35.7 - - + -
207B ILE* 2.9 26.7 + - + +
208B ALA* 3.3 6.5 + - - +
210B ILE* 1.3 75.7 - - - +
212B LEU* 1.3 59.8 + - - +
213B CYS 3.7 0.2 - - - -
290B VAL* 4.1 4.5 - - - +
294B ILE* 6.0 0.7 - - - -
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 4.0 18.8 - - + -
118B ALA* 3.8 25.6 - - + -
208B ALA 3.3 11.4 + - - +
209B TYR 3.1 5.1 + - - +
210B ILE 3.0 1.2 - - - -
211B LEU* 1.3 80.7 - - - +
213B CYS* 1.3 59.8 + - - +
241B TYR 4.8 2.8 - - - +
242B TRP* 3.7 14.7 - - + -
245B ILE* 3.5 25.5 - - + +
249B ALA* 3.9 24.2 - - + -
253B ILE* 3.7 25.8 - - + -
275B TRP* 3.9 21.5 - - + -
286B ILE* 4.5 8.5 - - + -
290B VAL* 3.9 11.9 - - - +
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Residues in contact with CYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TYR* 3.3 35.6 + - - -
210B ILE 3.3 0.2 + - - -
211B LEU 3.7 0.2 - - - -
212B LEU* 1.3 79.0 - - - +
214B GLY* 1.3 59.8 + - - +
215B TYR* 3.3 45.2 - - + -
241B TYR* 4.5 9.9 - - + +
242B TRP* 3.5 22.2 - - + +
289B SER* 4.0 1.6 + - - +
290B VAL* 3.8 14.7 + - - +
293B GLN* 3.3 23.0 - - - +
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Residues in contact with GLY 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 2.7 25.2 + - - +
213B CYS* 1.3 77.8 - - - +
215B TYR* 1.3 58.2 + - - +
290B VAL* 3.7 13.8 - - - +
293B GLN* 3.2 31.7 - - - +
294B ILE* 3.2 15.6 + - - +
297B ASN* 3.9 0.9 + - - -
298B PHE* 4.3 4.0 - - - -
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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
------------------------------------------------------------
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