Contacts of the helix formed by residues 171 - 187 (chain C) in PDB entry 5MR4
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 ASN 171 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ALA 3.4 10.7 + - - +
168C CYS 2.9 9.4 + - - +
169C ASN 4.7 0.4 - - - -
170C LEU* 1.3 78.8 - - - +
172C ASP* 1.3 68.4 + - - +
173C ASN* 3.3 14.8 - - - +
174C CYS* 3.1 30.0 + - + +
175C LYS* 2.8 25.3 + - - +
211C VAL* 5.6 0.2 - - - +
212C PRO* 5.8 1.0 - - - +
215C TYR* 3.1 35.4 + - + +
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Residues in contact with ASP 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 5.5 0.7 - - - +
128A ARG* 3.5 36.7 + - - -
170C LEU 4.1 1.6 + - - -
171C ASN* 1.3 73.8 - - - +
173C ASN* 1.3 63.4 + - - +
175C LYS* 3.8 20.0 + - - +
176C LYS* 3.1 46.5 + - - +
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Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASN* 3.3 9.4 - - - +
172C ASP* 1.3 79.9 - - - +
174C CYS* 1.3 61.9 + - - +
176C LYS* 4.7 6.4 - - - +
177C LEU* 3.1 42.5 + - - +
210C ARG* 3.0 33.3 + - - +
211C VAL* 3.8 12.5 - - - +
212C PRO* 4.4 8.5 - - - +
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Residues in contact with CYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C CYS* 2.1 58.5 - - - +
171C ASN* 3.1 18.2 - - + +
173C ASN* 1.3 74.7 - - - +
175C LYS* 1.3 54.5 + - - +
177C LEU 3.8 0.2 - - - -
178C ARG* 2.8 37.9 + - - +
207C PHE* 3.8 11.1 - - - -
211C VAL* 3.7 31.4 - - + -
215C TYR* 3.8 12.3 - - + -
219C MET* 4.6 0.7 - - - -
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 6.5 0.4 - - + -
128A ARG* 5.3 4.0 - - - +
171A GLU* 2.8 35.4 + - - +
173A GLU 3.7 14.4 - - - +
174A VAL* 4.0 18.4 - - + -
175A SER 5.7 0.2 - - - +
168C CYS 3.2 5.3 + - - +
169C ASN* 3.7 39.1 - - - +
171C ASN 2.8 18.6 + - - +
172C ASP* 3.8 21.2 + - - +
174C CYS* 1.3 76.9 - - - +
176C LYS* 1.3 85.6 + - - +
178C ARG* 3.9 1.8 - - - +
179C SER* 3.0 29.8 + - - -
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Residues in contact with LYS 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 6.1 2.0 - - + -
173A GLU* 5.0 3.9 - - - +
172C ASP* 3.1 48.3 + - - +
173C ASN* 3.7 7.2 - - - +
175C LYS* 1.3 96.2 - - - +
177C LEU* 1.3 67.8 + - + +
179C SER* 3.8 3.9 - - - -
180C SER* 2.9 29.6 + - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASN* 3.1 31.5 + - - +
176C LYS* 1.3 87.9 - - + +
178C ARG* 1.3 63.8 + - - +
180C SER* 3.5 8.2 + - - -
181C TYR* 3.3 24.9 + - - +
203C ALA 4.8 1.4 - - - +
206C GLN* 3.9 12.1 - - + +
207C PHE* 3.8 11.7 - - + +
210C ARG* 3.5 54.7 - - + +
211C VAL* 3.6 24.2 - - + -
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Residues in contact with ARG 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU* 2.8 42.6 + - - -
175A SER 3.4 10.0 + - - +
176A PHE* 4.4 0.6 - - - +
183A TYR* 4.1 19.4 + - - -
165C ALA* 4.0 17.5 + - - +
168C CYS* 3.9 16.8 - - - -
169C ASN* 3.2 26.5 + - - +
174C CYS 2.8 23.9 + - - +
175C LYS 3.9 2.5 - - - +
177C LEU* 1.3 70.1 - - - +
179C SER* 1.3 66.2 + - - +
180C SER 3.3 0.3 + - - -
181C TYR* 3.3 25.3 + - + +
182C ILE* 2.9 46.9 + - + +
207C PHE* 3.7 7.0 - - + -
219C MET* 3.8 15.6 - - + +
232C ARG* 4.2 4.0 - - - +
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 2.8 43.6 + - - +
174A VAL* 3.5 5.2 - - - -
175A SER* 2.7 42.7 + - - -
185A THR* 3.8 0.2 - - - +
175C LYS 3.0 20.1 + - - -
176C LYS 3.8 2.9 - - - -
178C ARG* 1.3 78.5 - - - +
180C SER* 1.3 57.6 - - - +
183C SER* 2.9 25.5 + - - -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 3.5 9.8 + - - -
176C LYS 2.9 19.0 + - - -
177C LEU* 3.7 10.3 - - - -
178C ARG 3.2 0.2 - - - -
179C SER* 1.3 76.9 - - - +
181C TYR* 1.3 61.7 + - - +
183C SER* 3.2 3.5 + - - -
184C ILE* 3.1 38.8 + - - +
203C ALA* 4.6 4.7 - - - +
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 4.7 2.4 + - - -
177C LEU 3.3 13.1 + - - +
178C ARG* 3.3 30.5 + - + +
180C SER* 1.3 75.3 + - - +
182C ILE* 1.3 78.4 + - + +
184C ILE* 4.6 0.4 - - - +
185C CYS* 2.9 42.5 + - + -
203C ALA* 3.7 35.4 - - + +
204C LEU* 3.6 24.9 - - + +
207C PHE* 3.6 39.0 - + + -
208C PHE* 6.1 0.2 - + - -
219C MET* 4.5 4.3 - - - +
236C THR* 2.6 42.5 + - - +
237C ILE* 4.6 4.7 - - - -
238C LEU* 4.9 2.5 - - + -
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 3.7 28.3 - - - +
183A TYR* 3.6 51.6 - - + -
184A HIS 4.6 1.1 - - - +
185A THR* 4.1 4.7 - - - +
178C ARG* 2.9 52.9 + - + +
179C SER 3.9 3.4 - - - +
181C TYR* 1.3 95.2 - - + +
183C SER* 1.3 57.1 + - - +
185C CYS 3.8 0.2 - - - -
186C ASN* 2.9 36.8 + - + +
238C LEU* 3.8 6.0 - - + +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 3.1 19.4 + - - -
185A THR* 3.5 25.1 - - - -
187A HIS* 5.8 2.2 - - - -
179C SER 2.9 18.4 + - - -
180C SER* 3.2 6.4 + - - -
182C ILE* 1.3 77.1 - - - +
184C ILE* 1.3 64.6 + - - +
186C ASN* 4.2 3.0 - - - +
187C ARG* 3.4 42.5 + - - +
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C SER* 3.1 28.1 + - - +
181C TYR* 4.1 3.1 - - - +
183C SER* 1.3 80.8 + - - +
185C CYS* 1.3 61.1 + - - +
186C ASN 3.4 0.5 + - - -
187C ARG* 3.5 28.6 + - - +
195C CYS* 4.5 4.5 - - - +
196C ASN* 4.6 6.0 + - + +
199C LYS* 3.7 43.3 - - + +
200C CYS* 3.7 28.4 - - - +
203C ALA* 3.9 18.4 - - + -
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Residues in contact with CYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C TYR* 2.9 38.5 + - - +
184C ILE* 1.3 78.4 - - - +
186C ASN* 1.3 57.6 + - - +
187C ARG 3.4 0.2 - - - -
194C ARG* 3.8 3.8 + - - -
195C CYS* 3.5 9.5 - - - +
200C CYS* 2.1 61.7 - - - -
204C LEU* 4.4 3.6 - - - -
237C ILE 4.7 1.8 - - - -
238C LEU* 4.0 22.5 - - + +
241C CYS* 3.3 21.5 - - - +
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Residues in contact with ASN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.6 16.8 + - - +
183A TYR* 3.0 42.8 + - - +
184A HIS* 4.7 2.8 - - - +
185A THR* 5.6 1.6 + - - +
182C ILE* 2.9 21.0 + - + +
183C SER* 4.2 4.7 - - - +
185C CYS* 1.3 76.4 - - - +
187C ARG* 1.3 60.2 + - - +
188C GLU* 3.4 3.3 + - - +
194C ARG* 2.9 42.4 + - - +
238C LEU* 3.9 10.7 - - + +
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Residues in contact with ARG 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A HIS* 5.8 5.3 + - - -
183C SER* 3.4 40.2 + - - +
184C ILE* 3.9 21.4 - - - +
185C CYS 3.4 2.2 - - - -
186C ASN* 1.3 75.3 - - - +
188C GLU* 1.3 71.4 + - - +
189C ILE* 4.2 12.5 - - + +
194C ARG 3.7 1.8 - - - -
195C CYS* 3.4 20.6 - - - +
196C ASN 4.3 0.3 + - - -
199C LYS* 5.7 2.4 - - - +
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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
------------------------------------------------------------
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