Contacts of the helix formed by residues 171 - 187 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ALA 3.3 13.7 + - - +
168D CYS 3.0 6.2 + - - +
169D ASN 4.7 0.4 - - - -
170D LEU* 1.3 78.1 - - - +
172D ASP* 1.3 68.4 + - - +
173D ASN* 3.4 15.4 - - - +
174D CYS* 3.1 30.6 - - + +
175D LYS* 2.9 24.7 + - - +
211D VAL* 5.7 0.2 - - - +
212D PRO* 5.8 1.2 - - - +
215D TYR* 3.1 37.8 + - + +
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Residues in contact with ASP 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.9 2.9 - - - +
128B ARG* 3.0 37.5 + - - -
169D ASN 5.7 0.3 - - - +
170D LEU 4.1 3.1 + - - +
171D ASN* 1.3 74.0 + - - +
173D ASN* 1.3 61.9 + - - +
175D LYS* 3.8 14.9 + - - +
176D LYS* 3.1 47.5 + - - +
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Residues in contact with ASN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ASN* 3.3 10.9 - - - +
172D ASP* 1.3 74.9 - - - +
174D CYS* 1.3 64.3 + - - +
176D LYS* 3.5 6.9 + - - +
177D LEU* 3.1 41.7 + - - +
210D ARG* 3.0 31.2 + - - +
211D VAL* 4.0 11.1 - - - +
212D PRO* 4.3 8.5 - - - +
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Residues in contact with CYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D CYS* 2.0 56.9 - - - +
171D ASN* 3.1 17.9 - - + +
173D ASN* 1.3 73.2 - - - +
175D LYS* 1.3 56.5 + - - +
177D LEU 3.3 0.3 + - - -
178D ARG* 2.7 39.2 + - - +
207D PHE* 3.8 11.4 - - - -
211D VAL* 3.7 32.8 - - + -
215D TYR* 3.9 12.3 - - + -
219D MET* 4.5 0.4 - - - -
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Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 6.1 2.5 - - + +
128B ARG* 5.1 5.9 - - - +
171B GLU* 2.8 35.6 + - - +
173B GLU 3.8 14.8 - - - -
174B VAL* 3.9 24.0 - - + -
175B SER 5.4 0.2 + - - -
168D CYS 3.1 9.7 + - - +
169D ASN* 3.8 29.8 - - - +
171D ASN 2.9 18.0 + - - +
172D ASP* 3.8 14.3 + - - +
174D CYS* 1.3 77.7 - - - +
176D LYS* 1.3 89.9 + - - +
178D ARG* 3.8 2.2 - - - +
179D SER* 3.0 28.8 + - - -
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Residues in contact with LYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 6.1 0.2 - - - +
173B GLU* 5.4 3.6 - - - +
172D ASP* 3.1 40.5 + - - +
173D ASN* 3.8 7.4 - - - +
174D CYS 3.2 0.2 - - - -
175D LYS* 1.3 100.3 - - - +
177D LEU* 1.3 69.1 + - + +
179D SER* 3.8 3.9 - - - -
180D SER* 2.9 29.7 + - - -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ASN* 3.1 31.5 + - - +
176D LYS* 1.3 88.2 - - + +
178D ARG* 1.3 64.0 + - - +
180D SER* 3.6 8.8 - - - -
181D TYR* 3.3 24.3 + - - +
203D ALA 4.8 2.3 - - - +
206D GLN* 3.9 17.0 - - + +
207D PHE* 3.8 11.0 - - + +
210D ARG* 3.5 39.7 - - + +
211D VAL* 3.9 23.3 - - + -
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Residues in contact with ARG 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU* 2.8 42.0 + - - -
175B SER 3.4 10.6 + - - +
176B PHE* 4.4 0.4 - - - +
183B TYR* 4.2 17.8 + - - -
165D ALA* 3.9 17.7 + - - +
168D CYS* 3.9 14.8 - - - -
169D ASN* 3.2 26.8 + - - +
174D CYS 2.7 23.4 + - - +
175D LYS 3.8 2.7 - - - +
177D LEU* 1.3 71.5 - - - +
179D SER* 1.3 65.6 + - - +
181D TYR* 3.3 25.4 + - + +
182D ILE* 3.0 47.4 + - + +
207D PHE* 3.7 9.3 - - + -
219D MET* 3.7 16.5 - - + +
232D ARG* 4.1 4.4 - - - +
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLU* 2.9 45.1 + - - +
174B VAL 3.4 8.3 - - - -
175B SER* 2.6 37.0 + - - -
185B THR* 4.3 0.2 - - - -
175D LYS 3.0 17.7 + - - -
176D LYS 3.8 3.6 - - - -
178D ARG* 1.3 80.9 - - - +
180D SER* 1.3 57.0 + - - +
183D SER* 2.8 27.5 + - - -
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLU* 3.5 10.7 + - - -
176D LYS 2.9 18.5 + - - -
177D LEU* 3.6 12.6 - - - -
178D ARG 3.1 0.2 - - - -
179D SER* 1.3 77.3 - - - +
181D TYR* 1.3 60.7 + - - +
183D SER* 3.2 3.4 + - - -
184D ILE* 3.2 38.6 + - - +
203D ALA* 4.6 4.5 - - - +
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Residues in contact with TYR 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 4.7 2.3 + - - -
177D LEU 3.3 13.5 + - - -
178D ARG* 3.3 31.9 + - + +
180D SER* 1.3 74.6 - - - +
182D ILE* 1.3 77.5 + - + +
184D ILE* 4.6 0.2 - - - -
185D CYS* 2.8 43.4 + - + +
203D ALA* 3.6 33.1 - - + +
204D LEU* 3.6 26.7 - - + +
207D PHE* 3.7 38.6 - + + -
208D PHE* 6.0 0.2 - + - -
219D MET* 4.5 4.0 - - - +
236D THR* 2.6 43.6 + - + +
237D ILE* 4.5 3.8 - - - -
238D LEU* 4.9 3.1 - - + -
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B SER* 3.6 30.1 - - - +
183B TYR* 3.5 52.5 - - + +
184B HIS 4.6 0.4 - - - +
185B THR* 4.2 7.6 - - + -
178D ARG* 3.0 51.3 + - + +
179D SER 3.8 3.4 - - - +
181D TYR* 1.3 94.5 - - + +
183D SER* 1.3 57.4 + - - +
186D ASN* 2.9 35.6 + - + +
238D LEU* 3.8 5.0 - - + +
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLU* 2.9 27.7 + - - -
185B THR* 3.5 27.4 - - - -
187B HIS* 5.6 2.7 - - - -
179D SER 2.8 13.7 + - - -
180D SER* 3.2 6.4 + - - -
182D ILE* 1.3 77.1 - - - +
184D ILE* 1.3 65.8 + - - +
186D ASN* 4.2 2.3 - - - +
187D ARG* 3.4 44.2 + - - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D SER* 3.2 26.0 + - - +
181D TYR* 4.0 3.4 - - - +
183D SER* 1.3 81.9 + - - +
185D CYS* 1.3 61.3 + - - +
186D ASN 3.4 0.5 + - - -
187D ARG* 3.5 30.0 + - - +
195D CYS* 4.4 4.7 - - - +
196D ASN* 4.5 6.3 + - + +
199D LYS* 3.7 42.0 - - + +
200D CYS* 3.5 29.4 - - + +
203D ALA* 3.9 16.6 - - + -
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Residues in contact with CYS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D TYR* 2.8 36.6 + - - +
184D ILE* 1.3 74.3 - - - +
186D ASN* 1.3 58.2 + - - +
187D ARG 3.5 0.2 - - - -
194D ARG* 3.9 2.4 + - - -
195D CYS* 3.4 10.2 - - - +
200D CYS* 2.1 59.0 - - - -
204D LEU* 4.3 8.7 - - - -
237D ILE 4.7 2.2 - - - -
238D LEU* 3.8 25.0 - - + +
241D CYS* 3.3 23.0 - - - +
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Residues in contact with ASN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 3.0 43.2 + - + +
184B HIS* 4.8 2.2 - - - +
185B THR* 5.3 4.5 - - + +
182D ILE* 2.9 20.4 + - + +
183D SER* 4.2 4.3 - - - +
185D CYS* 1.3 78.8 - - - +
187D ARG* 1.3 57.8 + - - +
188D GLU* 3.3 2.8 + - - +
194D ARG* 3.0 38.4 + - - +
238D LEU* 4.0 8.3 - - + +
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Residues in contact with ARG 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 5.6 8.3 + - - -
183D SER* 3.4 41.0 + - - +
184D ILE* 3.5 22.0 + - - +
185D CYS 3.5 2.0 - - - -
186D ASN* 1.3 74.6 - - - +
188D GLU* 1.3 73.2 + - - +
189D ILE* 3.5 9.2 + - + +
194D ARG 3.4 8.0 - - - +
195D CYS* 3.5 12.5 - - - +
196D ASN 4.4 0.7 + - - -
199D LYS* 5.6 3.2 - - - +
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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
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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