Contacts of the helix formed by residues 196 - 213 (chain B) in PDB entry 1YRP
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 LEU 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B HIS* 3.2 64.4 - - + +
134B ARG* 4.2 13.9 - - + +
135B ILE 4.1 15.5 - - - +
136B ALA* 4.0 14.6 - - + -
168B ILE* 3.7 28.5 - - + +
195B GLY* 1.3 70.4 - - - -
197B GLU* 1.3 69.8 + - + +
198B ALA 3.2 1.5 + - - -
199B ASP* 3.3 9.8 + - - +
200B MET* 3.9 2.4 + - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 4.5 1.7 - - - +
193B PRO 5.4 1.4 - - - +
194B LEU* 4.7 0.9 - - - -
195B GLY* 3.1 18.6 + - - -
196B LEU* 1.3 84.1 + - + +
198B ALA* 1.3 64.8 + - - +
200B MET* 3.0 22.2 + - - +
201B TRP 3.2 8.8 + - - -
260B PRO* 3.4 27.8 - - + +
261B LYS* 3.4 30.2 + - + +
263B ARG* 3.4 27.4 + - + +
264B MET 5.7 1.3 - - - +
265B TPO 6.2 4.0 - - + -
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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
----------------------------------------------------------
138B PHE* 3.8 30.3 - - + -
185B ALA* 4.1 8.1 + - + +
187B GLU* 3.5 21.2 + - + +
188B ILE* 3.9 21.1 - - + -
194B LEU* 5.4 1.1 - - + -
195B GLY 3.8 2.8 + - - +
196B LEU 3.2 0.8 - - - -
197B GLU* 1.3 79.8 - - - +
199B ASP* 1.3 61.7 + - - +
201B TRP* 3.2 6.6 + - - +
202B SER* 3.1 22.3 + - - -
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Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.5 2.7 - - + +
130B LEU* 5.9 0.2 - - - +
131B HIS* 3.3 24.7 + - + +
136B ALA* 3.4 7.7 - - - +
137B HIS* 2.8 24.2 + - - +
138B PHE* 2.8 31.3 + - - -
140B LEU* 3.4 27.3 - - + +
195B GLY 5.1 0.2 + - - -
196B LEU 3.3 10.4 + - - +
197B GLU 3.2 0.6 - - - -
198B ALA* 1.3 78.7 - - - +
200B MET* 1.3 59.3 + - - +
202B SER* 3.2 7.7 + - - -
203B ILE* 3.0 31.2 + - - +
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.7 0.9 - - + -
131B HIS* 4.0 11.7 - - + -
196B LEU 4.1 9.2 - - - +
197B GLU* 3.0 14.7 + - - +
199B ASP* 1.3 73.3 - - - +
201B TRP* 1.3 64.6 + - - +
203B ILE* 3.6 15.3 + - + -
204B GLY 3.2 15.6 + - - -
255B LEU* 3.4 38.0 - - + +
263B ARG* 4.0 5.2 - - - -
264B MET 3.3 22.4 - - - +
265B TPO 3.9 4.7 - - - +
266B ILE* 3.7 56.5 - - + +
269B SER* 3.9 9.9 - - - +
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Residues in contact with TRP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU 5.1 0.6 + - - -
183B PHE 3.3 20.9 + - - -
184B VAL 3.2 12.1 + - - -
185B ALA* 3.5 22.9 - - + -
186B PRO* 3.6 29.8 - - + -
197B GLU 3.2 4.8 + - - -
198B ALA 3.2 9.5 + - - +
200B MET* 1.3 76.7 - - - +
202B SER* 1.3 62.6 + - - +
204B GLY* 3.2 4.5 + - - -
205B VAL* 3.1 28.9 + - + +
217B PHE* 3.4 37.8 - + - -
229B ILE* 3.8 24.5 - - + -
232B VAL* 4.2 7.9 - - + -
255B LEU 3.7 10.3 - - - -
256B LEU* 3.7 41.3 - - + +
257B VAL 3.9 5.4 - - - -
263B ARG* 3.6 20.3 - - - +
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE 5.1 4.9 + - - -
140B LEU* 3.6 36.8 + - - +
183B PHE* 3.1 25.7 + - - +
184B VAL* 5.1 0.5 - - - -
185B ALA 5.5 0.2 + - - -
198B ALA 3.1 12.5 + - - -
199B ASP* 3.2 12.7 + - - -
201B TRP* 1.3 76.5 - - - +
203B ILE* 1.3 51.7 + - - +
205B VAL* 3.0 8.9 + - - +
206B ILE* 2.7 38.6 + - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.7 27.4 - - + -
123B ILE* 4.1 13.7 - - + -
124B LEU* 4.0 24.2 - - + -
127B VAL* 4.1 25.4 - - + -
140B LEU* 4.2 7.6 - - + -
199B ASP 3.0 19.7 + - - +
200B MET* 3.9 23.1 - - + +
201B TRP 3.3 0.2 - - - -
202B SER* 1.3 74.8 - - - +
204B GLY* 1.3 50.9 + - - +
206B ILE* 3.2 11.8 + - + +
207B THR* 2.7 43.9 + - - +
251B PHE* 4.7 1.3 - - + -
255B LEU* 4.0 13.0 - - + -
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B MET 3.2 5.5 + - - -
201B TRP 3.2 8.1 + - - -
203B ILE* 1.3 78.4 - - - +
205B VAL* 1.3 55.7 + - - +
207B THR* 3.6 4.8 + - - -
208B TYR* 3.1 26.5 + - - +
252B ILE* 3.8 12.2 - - - +
255B LEU* 3.6 27.9 - - - +
256B LEU* 4.2 11.2 - - - +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU 4.0 13.2 - - - +
183B PHE* 3.6 26.0 - - + +
201B TRP* 3.1 35.6 + - + +
202B SER* 3.0 9.9 + - - +
204B GLY* 1.3 74.1 - - - +
206B ILE* 1.3 64.6 + - - +
208B TYR* 3.3 3.8 + - - +
209B ILE* 3.0 27.9 + - + +
215B SER* 4.3 2.2 - - - +
216B PRO* 3.9 22.7 - - + -
217B PHE* 4.0 11.7 - - + -
256B LEU* 3.8 10.8 - - + -
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 5.2 2.2 - - + -
120B LEU* 5.5 5.6 - - + -
123B ILE* 5.5 9.2 - - + -
140B LEU* 3.7 35.2 - - + +
141B LYS* 3.9 13.9 - - - +
142B PRO* 4.2 10.8 - - + -
145B ILE* 3.9 23.1 - - + -
183B PHE* 4.5 3.1 - - + -
202B SER 2.7 23.7 + - - +
203B ILE* 3.6 14.1 - - + +
205B VAL* 1.3 72.4 - - - +
207B THR* 1.3 53.1 + - - +
209B ILE* 3.0 12.3 + - - +
210B LEU* 2.7 60.2 + - + +
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Residues in contact with THR 207 (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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120B LEU* 3.4 20.7 - - + +
203B ILE 2.7 29.3 + - - -
204B GLY* 3.7 5.6 - - - -
206B ILE* 1.3 72.1 - - - +
208B TYR* 1.3 63.2 + - - +
210B LEU* 3.2 9.4 + - + +
211B LEU* 3.1 26.0 + - + +
251B PHE* 3.8 12.3 - - + -
252B ILE* 3.6 24.2 - - + -
274B TRP* 3.7 34.8 - - + -
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Residues in contact with TYR 208 (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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204B GLY 3.1 14.7 + - - +
205B VAL 3.4 9.4 - - - +
206B ILE 3.3 0.2 - - - -
207B THR* 1.3 75.2 - - - +
209B ILE* 1.3 53.3 + - - +
211B LEU* 4.0 0.6 - - - +
212B SER* 2.7 57.2 + - - -
214B ALA* 3.3 17.3 - - + -
215B SER 4.5 0.4 - - - -
216B PRO* 3.4 36.9 + - + +
234B TYR* 3.7 27.9 - + - +
235B ASP 2.9 23.9 + - - -
236B PHE* 4.5 3.6 - + - -
237B ASP* 4.3 5.7 + - - +
240B TYR* 5.5 2.3 - + - -
241B PHE* 3.4 30.0 - + - -
252B ILE* 4.1 23.0 - - + +
256B LEU* 4.9 0.7 - - + -
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 5.4 1.6 - - - +
102B PHE* 6.6 0.2 - - + -
105B LEU* 4.1 24.9 - - + +
142B PRO* 4.7 9.9 - - + -
182B GLU* 5.2 0.4 - - - +
183B PHE* 3.4 37.7 - - + -
205B VAL* 3.0 23.1 + - + +
206B ILE* 3.0 9.3 + - - +
208B TYR* 1.3 74.6 - - - +
210B LEU* 1.3 62.7 + - + +
213B GLY* 2.8 36.4 + - - +
214B ALA 3.2 20.9 - - - +
215B SER* 3.8 17.5 - - - +
216B PRO* 4.2 0.2 - - + -
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Residues in contact with LEU 210 (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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101B LEU* 4.2 15.3 - - + -
105B LEU* 4.1 31.1 - - + +
110B SER* 4.6 1.7 - - - -
111B LEU* 3.7 35.7 + - + +
116B ALA* 3.8 21.8 - - + +
119B PHE* 4.3 14.1 - - + -
120B LEU* 3.7 29.4 - - + +
123B ILE* 6.5 0.7 - - + -
142B PRO* 5.9 0.9 - - + -
206B ILE* 2.7 40.4 + - + +
207B THR* 3.2 6.9 + - - +
209B ILE* 1.3 76.2 - - + +
211B LEU* 1.3 64.3 + - + +
213B GLY* 4.6 0.7 + - - -
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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
----------------------------------------------------------
110B SER* 3.6 14.4 + - - -
111B LEU 4.5 10.1 - - - +
113B GLU* 4.3 13.9 - - + +
116B ALA* 3.4 32.3 - - + -
207B THR* 3.1 13.9 + - + +
208B TYR 4.1 1.3 - - - +
210B LEU* 1.3 80.6 - - + +
212B SER* 1.3 60.5 + - - +
240B TYR* 5.4 2.9 - - - +
241B PHE* 4.5 10.1 - - + -
244B THR* 4.0 28.0 - - + +
248B ALA* 4.1 12.6 - - + -
252B ILE* 3.8 24.9 - - + -
274B TRP* 4.1 16.2 - - + -
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Residues in contact with SER 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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109B GLU* 6.0 0.3 - - - +
110B SER* 3.5 10.2 + - - -
208B TYR* 2.7 32.4 + - - -
211B LEU* 1.3 75.5 - - - +
213B GLY* 1.3 58.4 + - - +
214B ALA* 3.0 20.8 + - - -
240B TYR* 3.5 53.6 - - - -
241B PHE* 3.6 18.6 - - - -
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Residues in contact with GLY 213 (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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51A SER* 3.5 11.8 + - - -
105B LEU* 5.9 1.3 - - - -
109B GLU* 4.6 9.9 - - - -
110B SER* 4.2 7.3 + - - -
209B ILE* 2.8 35.8 + - - +
210B LEU 5.3 0.2 - - - -
211B LEU 3.6 0.8 - - - -
212B SER* 1.3 71.4 + - - +
214B ALA* 1.3 60.2 + - - +
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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