Contacts of the helix formed by residues 172 - 191 (chain B) in PDB entry 3RC0
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 GLY 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLY 3.6 0.2 + - - -
171B THR* 1.3 77.7 + - - +
173B VAL* 1.3 63.0 + - - +
174B PRO* 4.1 0.6 - - - +
175B GLU* 3.4 18.8 + - - +
176B ALA* 3.2 21.3 + - - +
291B TRP* 4.1 13.1 - - - -
475B EDO 3.2 21.3 + - - -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 3.8 14.4 - - + -
164B ARG* 5.3 0.4 - - - -
168B LEU* 3.7 25.4 - - + -
171B THR* 3.3 13.9 - - - +
172B GLY* 1.3 75.4 - - - +
174B PRO* 1.4 72.9 - - + +
176B ALA* 3.0 6.3 + - - +
177B VAL* 2.8 39.5 + - + +
291B TRP* 3.7 35.4 - - + +
294B ILE* 3.9 12.6 - - + -
295B HIS* 4.4 8.3 - - + -
457B VAL* 4.9 0.2 - - + -
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Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 3.8 31.1 + - + +
165B ARG* 4.5 18.8 - - + +
168B LEU* 3.2 35.0 - - + +
169B GLN* 4.1 6.1 - - - +
172B GLY 3.6 3.8 - - - +
173B VAL* 1.4 94.4 - - + +
175B GLU* 1.3 68.3 + - - +
177B VAL* 3.4 2.1 + - - +
178B GLU* 3.1 31.3 + - - +
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLN* 6.1 0.2 - - - -
170B GLY 5.2 1.0 + - - -
172B GLY* 3.4 17.4 - - - +
174B PRO* 1.3 87.2 - - - +
176B ALA* 1.3 63.6 + - - +
178B GLU* 3.5 10.0 + - - +
179B LYS* 3.2 22.7 + - - +
475B EDO 3.1 40.0 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY 3.2 11.4 + - - +
173B VAL* 3.0 8.1 + - - +
175B GLU* 1.3 79.1 - - - +
177B VAL* 1.3 58.0 + - - +
179B LYS* 3.4 8.5 + - - +
180B ASP* 3.0 33.4 + - - +
291B TRP* 4.4 11.7 - - + -
295B HIS* 3.8 28.7 - - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 4.4 2.0 - - + -
157B MET* 3.6 37.9 - - + +
164B ARG* 3.4 37.5 - - - +
173B VAL* 2.8 37.4 + - + +
174B PRO 3.9 0.9 - - - +
176B ALA* 1.3 76.0 - - - +
178B GLU* 1.3 57.9 + - - +
180B ASP* 3.1 8.0 + - - +
181B LEU* 2.9 34.6 + - + +
295B HIS* 4.1 14.4 - - + -
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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
----------------------------------------------------------
161B GLU* 5.0 9.7 - - - +
164B ARG* 5.3 2.0 - - - +
165B ARG* 5.9 2.6 - - - -
174B PRO 3.1 18.6 + - - +
175B GLU* 3.7 9.2 - - - +
176B ALA 3.3 0.2 - - - -
177B VAL* 1.3 78.5 - - - +
179B LYS* 1.3 60.9 + - - +
181B LEU* 3.6 9.4 + - - +
182B ALA* 3.3 21.8 + - - +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 3.9 25.0 - - - +
175B GLU 3.2 11.5 + - - +
176B ALA* 3.7 10.5 - - - +
177B VAL 3.3 0.2 - - - -
178B GLU* 1.3 77.8 - - - +
180B ASP* 1.3 68.2 + - - +
182B ALA* 3.5 5.1 + - - +
183B ASN* 3.0 40.1 + - - +
351B GLU* 5.7 2.6 + - - -
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B MET* 5.5 6.8 - - + +
176B ALA 3.0 17.4 + - - +
177B VAL* 3.1 10.0 + - + +
179B LYS* 1.3 79.8 - - - +
181B LEU* 1.3 60.6 + - + +
183B ASN* 3.2 8.3 + - - +
184B ILE* 2.9 45.6 + - + +
217B VAL* 6.5 0.2 - - - -
221B MET* 4.3 14.3 - - + +
295B HIS* 2.5 36.1 + - - -
478B EDO 5.4 6.9 - - - -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B MET* 4.0 27.1 - - + +
164B ARG* 3.7 26.5 - - - +
177B VAL* 2.9 27.2 + - + +
178B GLU* 3.9 8.1 - - - +
179B LYS 3.3 0.2 - - - -
180B ASP* 1.3 77.9 - - + +
182B ALA* 1.3 59.3 + - - +
184B ILE* 3.9 4.5 - - - +
185B ARG* 3.3 24.6 + - - +
214B HIS* 3.8 31.0 + - + +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU 3.3 14.5 + - - +
179B LYS* 3.9 6.3 - - - +
180B ASP 3.2 0.8 - - - -
181B LEU* 1.3 78.0 - - - +
183B ASN* 1.3 65.4 + - - +
185B ARG* 4.0 4.0 - - - +
186B SER* 3.1 24.9 + - - -
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Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 3.7 28.9 - - + +
179B LYS* 3.0 41.1 + - - +
180B ASP* 3.2 7.1 + - - +
182B ALA* 1.3 77.5 - - - +
184B ILE* 1.3 65.8 + - - +
186B SER* 3.8 5.6 - - - -
187B GLU* 3.0 30.6 + - + +
478B EDO 3.5 27.0 + - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B MET* 3.5 32.1 - - + -
180B ASP* 2.9 31.2 + - + +
181B LEU* 3.9 4.5 - - - +
183B ASN* 1.3 78.7 - - - +
185B ARG* 1.3 63.7 + - - +
187B GLU* 4.4 2.9 - - - -
188B TYR* 3.1 19.9 + - - +
210B LEU* 5.0 0.2 - - + -
213B TYR* 3.5 32.2 - - + -
214B HIS* 3.6 32.5 - - + +
217B VAL* 3.9 19.5 - - + -
478B EDO 3.8 19.1 - - - -
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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
----------------------------------------------------------
181B LEU 3.3 15.3 + - - +
182B ALA* 4.2 4.3 - - - +
184B ILE* 1.3 80.5 - - - +
186B SER* 1.3 57.0 + - - +
189B GLN* 2.8 57.6 + - + +
210B LEU* 4.6 20.4 - - + -
214B HIS* 5.2 4.5 - - + +
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Residues in contact with SER 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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182B ALA 3.1 20.6 + - - -
183B ASN* 3.8 7.2 - - - -
185B ARG* 1.3 75.1 - - - +
187B GLU* 1.3 64.4 + - - +
189B GLN* 4.2 2.6 - - - +
190B SER* 2.8 36.8 + - - -
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 2.8 38.0 + - - -
119B GLN 4.5 0.5 + - - -
120B SER* 3.2 4.2 + - - -
123B VAL* 3.9 12.3 - - + +
126B LEU* 4.7 0.2 - - - +
183B ASN* 3.0 18.1 + - + +
184B ILE 3.8 1.8 - - - +
186B SER* 1.3 77.4 - - - +
188B TYR* 1.3 51.5 + - - +
191B ILE* 2.7 37.0 + - + +
192B VAL* 2.7 16.6 + - - -
213B TYR* 2.7 28.0 + - - +
478B EDO 2.7 43.4 + - - -
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Residues in contact with TYR 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 ILE 3.1 17.4 + - - +
185B ARG 4.1 1.3 - - - +
187B GLU* 1.3 78.4 - - - +
189B GLN* 1.3 75.5 + - - +
192B VAL* 3.8 15.3 - - + -
193B LEU* 2.9 64.2 + - + +
194B PRO* 3.5 0.2 - - - +
196B MET* 3.9 21.1 - - + -
207B VAL 5.5 0.2 - - - -
208B ARG 3.3 8.0 + - - -
209B SER 3.1 33.7 + - - -
210B LEU* 3.5 40.0 + - + -
213B TYR* 3.7 27.6 - + + -
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Residues in contact with GLN 189 (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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185B ARG* 2.8 42.1 + - + +
186B SER* 4.2 3.1 - - - +
188B TYR* 1.3 93.0 - - + +
190B SER* 1.3 59.5 + - - +
193B LEU* 4.8 9.1 - - - +
194B PRO* 3.5 17.7 - - - +
210B LEU* 4.9 9.7 - - - +
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B SER* 2.8 26.0 + - - -
189B GLN* 1.3 80.3 - - - +
191B ILE* 1.3 72.9 + - - +
194B PRO* 4.0 10.9 - - - +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA 3.6 22.7 - - - +
116B LEU* 4.2 20.2 - - + +
117B GLN 3.3 27.4 - - - +
118B SER* 4.4 11.2 - - - -
123B VAL* 4.3 10.8 - - + -
187B GLU* 2.7 24.9 + - + +
189B GLN 3.7 0.4 - - - -
190B SER* 1.3 91.7 - - - +
192B VAL* 1.3 64.3 + - + +
193B LEU 3.6 1.1 - - - -
194B PRO* 3.7 4.6 - - - +
195B PHE* 3.1 26.0 + - - +
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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