Contacts of the helix formed by residues 175 - 193 (chain B) in PDB entry 5CYP
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 THR 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASP* 5.1 6.3 - - + -
229A HIS* 5.8 3.4 + - + -
241A ARG* 4.6 11.4 - - - +
242A LYS* 4.0 34.5 - - + +
173B THR 5.4 0.7 - - - +
174B LEU* 1.3 77.5 - - - +
176B LEU* 1.3 59.4 + - - +
177B GLU* 3.5 8.7 + - - +
178B GLU* 3.2 36.7 + - - +
179B ARG* 2.8 30.6 + - - +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 1.3 74.1 - - - +
177B GLU* 1.3 63.7 + - - +
179B ARG* 3.4 23.7 + - - +
180B VAL* 3.2 41.8 + - + +
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Residues in contact with GLU 177 (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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229A HIS* 5.8 5.8 - - + +
175B THR* 3.3 7.0 + - - +
176B LEU* 1.3 81.7 - - - +
178B GLU* 1.3 62.9 + - + +
180B VAL* 3.4 7.0 + - - +
181B HIS* 3.2 22.9 + - - +
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASP* 5.1 2.8 - - - +
241A ARG* 3.1 23.4 + - - -
301A GSP 2.3 39.8 + - - +
144B GLY* 5.9 1.4 - - - -
174B LEU* 3.4 22.0 - - + +
175B THR* 3.2 34.7 + - - +
177B GLU* 1.3 77.0 - - + +
179B ARG* 1.3 57.7 + - - +
181B HIS* 3.5 6.7 + - - +
182B PHE* 2.9 31.5 + - - +
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 4.7 4.0 - - + +
171B ALA* 2.7 34.9 + - + +
172B ASP* 4.6 2.4 - - - +
174B LEU* 3.5 24.0 + - + +
175B THR 2.8 18.9 + - - +
176B LEU* 3.7 36.3 - - - +
177B GLU 3.3 0.2 - - - -
178B GLU* 1.3 77.6 - - - +
180B VAL* 1.3 60.9 + - + +
182B PHE* 3.8 1.6 - - - +
183B LYS* 3.0 47.2 + - + +
223B ALA* 3.9 24.6 - - + +
257B GLU* 5.1 5.4 - - - -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.2 31.5 + - + +
177B GLU* 3.8 6.3 - - - +
179B ARG* 1.3 79.8 - - + +
181B HIS* 1.3 61.5 + - - +
183B LYS* 3.5 6.5 + - - +
184B GLN* 3.1 24.3 + - + +
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Residues in contact with HIS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.6 44.5 + - + +
144B GLY* 4.1 16.2 + - - -
177B GLU 3.2 14.2 + - - +
178B GLU* 3.9 6.6 + - - +
180B VAL* 1.3 77.2 - - - +
182B PHE* 1.3 64.2 + - - +
184B GLN* 3.4 7.6 + - + +
185B ARG* 3.0 42.4 + - + +
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Residues in contact with PHE 182 (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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140B ILE* 3.9 9.2 - - + -
141B PRO 3.5 21.5 - - - -
142B ALA* 4.0 13.7 - - - -
143B THR* 4.1 4.3 - - - -
144B GLY* 3.7 26.0 - - - -
145B HIS 3.4 25.1 - - - -
168B ILE* 3.7 35.0 - - + -
174B LEU* 3.9 18.4 - - + -
178B GLU 2.9 18.2 + - - +
179B ARG 3.8 3.8 - - - +
181B HIS* 1.3 78.7 - - - +
183B LYS* 1.3 59.9 + - - +
185B ARG* 3.1 4.8 + - + -
186B ILE* 2.8 57.1 + - + +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 3.7 13.4 - - + +
179B ARG* 3.0 30.1 + - + +
180B VAL* 3.8 7.0 - - - +
182B PHE* 1.3 76.8 - - - +
184B GLN* 1.3 52.9 + - - +
186B ILE* 3.9 0.7 - - - +
187B THR* 2.6 39.5 + - - +
218B GLU 5.0 5.8 - - - +
219B MET* 3.3 21.5 - - - +
220B ILE 4.9 1.8 - - - +
221B PRO* 3.1 36.9 + - + +
223B ALA* 3.2 29.1 - - - +
257B GLU* 3.4 16.5 + - - -
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 3.1 17.6 + - + +
181B HIS* 3.6 9.4 - - + +
183B LYS* 1.3 79.4 - - - +
185B ARG* 1.3 59.7 + - - +
187B THR* 3.8 5.3 - - - -
188B ALA* 3.3 21.5 + - - +
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 5.3 6.7 - - - +
63A LYS* 5.0 4.2 - - - +
145B HIS* 4.3 8.1 - - - +
146B SER* 3.3 45.1 - - - +
181B HIS* 3.0 33.9 + - + +
182B PHE* 3.7 7.0 - - + +
184B GLN* 1.3 76.7 - - - +
186B ILE* 1.3 64.9 + - - +
188B ALA* 3.3 11.5 + - - +
189B ASP* 2.3 62.0 + - - +
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Residues in contact with ILE 186 (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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140B ILE* 3.7 20.0 - - + -
145B HIS 4.5 5.6 - - - +
147B LEU* 3.6 32.3 - - + +
182B PHE* 2.8 56.5 + - + +
183B LYS 3.9 0.4 - - - +
185B ARG* 1.3 73.6 - - - +
187B THR* 1.3 59.7 + - - +
189B ASP* 3.1 6.0 + - - +
190B LEU* 2.9 44.3 + - + +
221B PRO* 3.7 31.2 - - + -
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Residues in contact with THR 187 (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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183B LYS 2.6 23.7 + - - -
184B GLN* 3.8 6.9 - - - -
185B ARG 3.3 0.2 - - - -
186B ILE* 1.3 78.9 - - - +
188B ALA* 1.3 61.7 + - - +
190B LEU* 3.4 9.7 + - - +
191B LEU* 3.1 44.6 + - + +
217B ARG 5.9 2.7 - - - +
220B ILE* 3.5 18.6 + - - +
221B PRO* 5.4 0.2 - - - -
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Residues in contact with ALA 188 (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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184B GLN 3.3 15.6 + - - +
185B ARG* 3.7 16.2 - - - +
186B ILE 3.3 0.4 - - - -
187B THR* 1.3 79.3 - - - +
189B ASP* 1.3 59.0 + - - +
191B LEU* 3.4 10.0 + - - +
192B SER* 2.9 31.2 + - - -
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B SER* 3.4 6.7 - - - -
147B LEU* 2.9 47.2 + - + +
152B ILE* 5.8 0.9 - - - -
185B ARG* 2.3 51.8 + - - +
186B ILE* 3.1 7.7 + - - +
188B ALA* 1.3 74.1 - - - +
190B LEU* 1.3 60.8 + - - +
192B SER* 2.9 8.2 + - - -
193B ASN* 2.8 45.0 + - - +
195B ILE* 5.3 0.2 - - - -
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Residues in contact with LEU 190 (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* 4.0 14.4 - - + -
155B MET* 3.6 26.2 - - + -
166B PRO* 3.8 24.0 - - + -
186B ILE* 2.9 32.9 + - + +
187B THR* 3.7 8.1 - - - +
189B ASP* 1.3 77.2 - - - +
191B LEU* 1.3 64.0 + - + +
193B ASN 3.5 0.2 + - - -
194B GLY 3.2 2.4 + - - -
195B ILE* 2.9 60.6 + - + +
197B VAL* 4.3 10.5 - - + -
220B ILE* 4.3 11.7 - - + -
221B PRO* 5.7 0.2 - - + -
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Residues in contact with LEU 191 (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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187B THR* 3.1 36.2 + - + +
188B ALA* 3.7 7.9 - - - +
190B LEU* 1.3 79.7 - - + +
192B SER* 1.3 60.9 + - - +
194B GLY* 3.2 13.0 + - - -
201B LYS* 4.2 21.3 - - - +
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Residues in contact with SER 192 (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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188B ALA 2.9 18.7 + - - -
189B ASP* 2.9 20.4 + - - -
191B LEU* 1.3 77.6 - - - +
193B ASN* 1.3 64.5 + - - +
194B GLY 3.3 1.4 + - - -
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Residues in contact with ASN 193 (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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152B ILE* 3.3 42.9 - - + +
156B LYS* 5.6 3.9 - - + +
189B ASP* 2.8 33.2 + - - +
192B SER* 1.3 83.0 + - - +
194B GLY* 1.3 63.5 + - - +
195B ILE* 3.2 22.6 + - + +
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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