Contacts of the helix formed by residues 199 - 216 (chain B) in PDB entry 5Y3R
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 GLU 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B LYS* 2.7 40.5 + - - -
197B ILE* 2.6 25.9 - - - +
198B THR* 1.3 69.6 - - - +
200B GLN* 1.3 54.0 + - - +
201B GLN 3.1 0.2 - - - -
202B LYS* 2.7 44.4 + - + +
203B GLU* 2.6 32.9 + - - +
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Residues in contact with GLN 200 (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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138B LEU 3.7 8.1 - - - +
139B SER* 4.4 13.7 - - - +
140B SER 3.0 9.2 + - - +
141B ARG* 3.5 26.1 + - - +
142B PHE* 3.0 32.3 - - - -
198B THR* 3.2 6.5 - - - +
199B GLU* 1.3 76.2 - - - +
201B GLN* 1.3 59.2 + - + +
203B GLU* 2.9 23.2 + - - +
204B GLY 3.0 22.2 + - - -
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Residues in contact with GLN 201 (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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19B THR* 3.4 9.9 - - - +
22B ASN* 4.4 5.7 + - - +
137B ASP* 2.9 48.1 + - - +
138B LEU* 3.1 12.8 - - - +
139B SER* 2.6 29.0 + - - +
166B PRO* 4.1 9.3 - - - +
167B PHE* 4.0 24.7 - - + -
197B ILE* 4.2 2.6 - - + -
198B THR* 2.8 37.2 + - - +
200B GLN* 1.3 71.0 - - + +
202B LYS* 1.3 57.6 + - - +
204B GLY 3.8 0.5 - - - -
205B LEU* 2.9 23.7 + - - +
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Residues in contact with LYS 202 (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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167B PHE* 5.6 0.4 - - - -
169B LEU* 4.3 13.5 + - - +
195B LYS* 3.7 14.1 - - - +
197B ILE* 3.6 21.6 - - + +
198B THR 3.3 1.8 + - - -
199B GLU* 2.7 50.0 + - + +
201B GLN* 1.3 71.7 - - - +
203B GLU* 1.3 58.3 + - - -
205B LEU* 2.9 32.5 - - + +
206B GLU* 2.9 33.3 + - + +
209B LYS* 5.6 0.4 - - - +
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Residues in contact with GLU 203 (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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142B PHE* 4.4 4.5 - - + -
199B GLU* 2.6 42.2 + - - +
200B GLN* 2.9 27.7 + - - +
202B LYS* 1.3 73.3 - - - +
204B GLY* 1.3 67.8 + - - +
206B GLU* 3.0 13.6 + - + +
207B ILE* 2.9 26.2 + - + +
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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
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138B LEU* 3.2 18.5 - - - +
142B PHE* 3.2 35.8 - - - -
200B GLN 3.0 10.9 + - - -
203B GLU* 1.3 75.7 - - - +
205B LEU* 1.3 62.4 + - - +
207B ILE* 2.9 15.6 + - - +
208B VAL 2.9 12.3 + - - -
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Residues in contact with LEU 205 (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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138B LEU* 3.4 8.3 - - + +
165B LEU* 5.3 2.2 - - + -
167B PHE* 4.6 16.2 - - + -
169B LEU* 3.6 25.4 - - + +
197B ILE* 4.5 4.5 - - + -
201B GLN 2.9 19.4 + - - +
202B LYS* 2.9 48.7 - - + +
203B GLU 3.1 0.2 - - - -
204B GLY* 1.3 74.7 - - - +
206B GLU* 1.3 55.9 + - - +
208B VAL* 3.4 3.0 + - + +
209B LYS* 2.8 55.8 + - - +
224B ILE* 3.8 22.4 - - + -
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Residues in contact with GLU 206 (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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202B LYS* 2.9 24.6 + - + +
203B GLU* 3.0 12.3 + - + +
205B LEU* 1.3 76.6 - - - +
207B ILE* 1.3 65.5 + - + +
209B LYS* 2.3 47.3 + - - +
210B MET* 2.9 37.8 + - + +
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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
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107B PHE* 5.4 7.6 - - + -
108B LEU* 6.1 1.8 - - + -
138B LEU* 5.4 0.9 - - + -
142B PHE* 3.5 41.7 - - + -
143B SER 4.5 11.7 - - - +
144B LYS* 3.6 37.0 - - + +
147B LEU* 5.8 2.6 - - + +
203B GLU* 2.9 16.9 + - + +
204B GLY* 2.9 10.3 + - - +
206B GLU* 1.3 77.7 - - + +
208B VAL* 1.3 62.4 + - + +
210B MET* 2.9 26.5 + - + +
211B VAL* 3.0 23.0 + - + +
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Residues in contact with VAL 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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107B PHE* 5.7 1.3 - - + -
136B THR* 5.4 0.4 - - + -
138B LEU* 3.5 39.3 - - + -
163B PHE* 3.4 55.2 - - + -
204B GLY 2.9 8.0 + - - +
205B LEU* 3.9 3.8 - - + +
207B ILE* 1.3 73.5 - - + +
209B LYS* 1.3 67.2 + - - +
211B VAL* 3.0 8.5 + - + -
212B MET* 2.8 34.7 + - - +
224B ILE* 4.7 7.6 - - + -
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Residues in contact with LYS 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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169B LEU* 3.6 23.7 - - - +
202B LYS* 5.6 0.2 - - - +
205B LEU* 2.8 43.2 + - - +
206B GLU* 2.3 53.4 + - - +
208B VAL* 1.3 75.4 - - - +
210B MET* 1.3 68.6 + - + +
213B ILE* 2.9 34.7 + - - +
221B LEU* 3.6 34.5 - - + +
224B ILE* 4.2 4.5 - - + -
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Residues in contact with MET 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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144B LYS* 6.0 4.5 - - + -
147B LEU* 4.7 20.0 - - + -
151B ILE* 4.7 0.9 - - - -
206B GLU* 2.9 33.7 + - + +
207B ILE* 2.9 12.1 + - + +
209B LYS* 1.3 90.1 - - + +
211B VAL* 1.3 58.1 + - - +
213B ILE* 3.1 16.2 - - + +
214B SER* 2.3 38.3 + - - +
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Residues in contact with VAL 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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108B LEU* 5.2 1.8 - - + -
111B LEU* 4.5 25.1 - - + -
147B LEU* 4.7 11.9 - - + -
150B ILE* 6.5 0.2 - - + -
151B ILE* 3.5 30.3 - - + +
161B LEU* 4.2 18.8 - - + -
163B PHE* 4.4 9.0 - - + -
207B ILE* 3.0 25.9 + - + +
208B VAL* 3.0 11.2 + - + +
210B MET* 1.3 76.2 - - + +
212B MET* 1.3 57.2 + - - +
214B SER* 3.1 4.9 + - - -
215B LEU* 3.0 25.8 + - + +
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Residues in contact with MET 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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161B LEU* 4.2 15.7 - - + +
163B PHE* 3.3 44.0 - - + -
208B VAL* 2.8 31.5 + - - +
209B LYS 4.1 1.1 - - - +
211B VAL* 1.3 68.8 - - - +
213B ILE* 1.3 63.2 + - - +
214B SER 2.9 5.7 + - - -
215B LEU 3.1 9.9 + - - +
216B GLU* 3.3 7.9 + - + +
217B GLY 2.9 17.2 + - - +
220B GLY* 3.0 39.5 - - - +
221B LEU* 4.6 2.9 - - + -
223B GLU* 3.5 31.4 - - + +
224B ILE* 3.5 13.7 - - - -
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Residues in contact with ILE 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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209B LYS 2.9 25.3 + - - +
210B MET* 3.1 29.8 - - + +
212B MET* 1.3 76.8 - - - +
214B SER* 1.3 62.6 + - - +
217B GLY* 3.2 22.3 + - - -
218B GLU* 3.4 38.3 - - + +
221B LEU* 5.0 6.0 - - + +
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Residues in contact with SER 214 (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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147B LEU* 4.3 7.6 - - - +
148B ASP* 4.4 8.3 - - - +
151B ILE* 3.4 25.1 - - - +
155B LYS* 2.9 14.4 + - - -
210B MET* 2.3 26.7 + - - +
211B VAL 3.2 5.8 - - - -
212B MET 2.9 1.0 - - - -
213B ILE* 1.3 82.1 - - - +
215B LEU* 1.3 65.5 + - - +
217B GLY 4.6 0.3 + - - -
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Residues in contact with LEU 215 (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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151B ILE* 3.1 38.6 - - + +
154B LEU* 4.0 17.9 - - + -
155B LYS* 3.1 42.7 - - + +
159B ILE* 3.4 20.9 - - + +
161B LEU* 4.7 11.0 - - + -
211B VAL* 3.0 12.5 + - + +
212B MET 3.1 0.2 + - - -
214B SER* 1.3 76.9 - - - +
216B GLU* 1.3 100.0 + - + +
217B GLY 3.6 0.2 + - - -
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Residues in contact with GLU 216 (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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159B ILE 2.7 25.6 - - - +
160B SER* 3.2 6.8 - - - -
161B LEU* 3.2 37.8 + - - +
212B MET* 3.3 9.1 + - - +
215B LEU* 1.3 93.8 - - + +
217B GLY* 1.3 58.5 + - - +
219B ASP* 3.2 22.0 - - - +
220B GLY* 5.7 3.9 - - - +
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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
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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