Contacts of the helix formed by residues 168 - 183 (chain X) in PDB entry 5A31
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 168 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X ILE* 4.2 9.2 - - + -
166X GLN 4.1 9.6 - - - +
167X ARG* 1.3 75.0 - - - +
169X PRO* 1.3 79.7 - - - +
170X LYS* 3.3 22.6 + - - +
171X ILE* 3.1 31.8 + - + +
172X ASN* 2.9 26.1 + - - -
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Residues in contact with PRO 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ARG 4.7 0.7 - - - +
168X THR* 1.3 86.0 - - - +
170X LYS* 1.3 65.9 + - - +
172X ASN* 3.0 6.7 + - - +
173X MET* 2.9 20.3 + - - +
195X VAL* 3.2 20.5 - - + +
198X GLN* 4.3 32.5 - - + -
199X CYS* 6.6 0.2 - - + -
47Y ALA* 4.4 16.2 - - + -
49Y LEU* 4.3 12.6 - - + -
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Residues in contact with LYS 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLU* 5.1 14.5 - - - +
140X TYR* 3.7 40.4 + - + +
168X THR* 3.2 19.6 + - - +
169X PRO* 1.3 81.0 - - + +
171X ILE* 1.3 75.9 + - + +
173X MET* 3.3 4.7 + - + +
174X MET* 3.1 24.1 + - - +
46Y ALA 5.1 4.6 + - - -
47Y ALA* 3.2 35.3 + - + +
48Y GLY* 5.4 2.7 - - - -
49Y LEU* 3.9 14.1 - - + +
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Residues in contact with ILE 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X ILE* 3.6 33.2 - - + +
137X GLU* 5.8 0.7 - - - -
140X TYR* 3.9 29.4 - - + -
159X LEU* 3.8 29.0 - - + +
162X ILE* 4.4 2.5 - - + -
167X ARG* 3.8 29.2 - - + -
168X THR* 3.1 35.5 + - + +
170X LYS* 1.3 94.8 - - + +
172X ASN* 1.3 59.4 + - - +
174X MET* 3.3 2.3 + - - +
175X LEU* 2.9 27.5 + - + +
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Residues in contact with ASN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X SER 5.0 1.2 + - - -
167X ARG* 3.2 41.9 + - - +
168X THR 2.9 22.5 + - - -
169X PRO* 3.0 4.6 + - - +
171X ILE* 1.3 77.9 - - - +
173X MET* 1.3 56.6 + - - +
175X LEU* 3.3 7.5 + - - +
176X ALA 2.8 25.5 + - - -
191X SER* 3.3 22.2 - - - +
194X GLU* 3.7 32.1 + - - +
195X VAL* 3.5 17.6 - - + +
198X GLN* 5.4 3.0 - - - +
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Residues in contact with MET 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140X TYR* 5.7 3.6 - - - +
169X PRO 2.9 15.0 + - - +
170X LYS* 3.7 6.1 - - - +
171X ILE 3.3 0.4 - - - -
172X ASN* 1.3 74.0 - - - +
174X MET* 1.3 77.6 + - + +
176X ALA* 3.2 7.7 + - - +
177X ASN* 3.1 48.4 + - - +
192X TYR* 4.9 11.4 - - + -
195X VAL* 3.4 15.9 - - + +
204X ASP* 5.5 0.9 - - + -
205X ALA* 5.6 1.6 - - + +
49Y LEU* 3.8 25.8 - - + -
50Y HIS 5.5 0.9 - - - +
51Y SER* 5.2 8.3 - - - +
52Y ASN* 3.0 40.4 - - - +
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Residues in contact with MET 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X TYR* 3.6 35.4 - - + +
143X ALA* 3.4 36.8 - - + -
144X GLU* 4.2 13.9 - - - -
147X THR* 4.5 13.2 - - + +
159X LEU* 3.7 14.4 - - + -
170X LYS 3.1 15.8 + - - +
171X ILE 3.9 2.2 - - - +
173X MET* 1.3 82.2 - - + +
175X LEU* 1.3 63.4 + - - +
177X ASN* 3.2 11.9 + - + +
178X LEU* 3.1 34.0 + - + +
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Residues in contact with LEU 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ILE* 4.6 17.7 - - + +
159X LEU* 4.3 33.3 - - + +
160X ASP* 4.9 2.7 - - - +
167X ARG* 3.3 40.2 - - - +
171X ILE 2.9 18.3 + - - +
172X ASN* 3.3 6.7 - - - +
174X MET* 1.3 76.5 - - - +
176X ALA* 1.3 61.7 + - - +
178X LEU* 3.2 4.6 + - + +
179X TYR* 3.0 64.0 + - + +
191X SER* 3.7 10.8 - - - +
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Residues in contact with ALA 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172X ASN 2.8 17.0 + - - +
173X MET* 3.2 9.8 + - - +
175X LEU* 1.3 73.1 - - - +
177X ASN* 1.3 63.1 + - - +
179X TYR 3.3 1.4 + - - -
180X LYS* 3.0 22.2 + - - +
188X SER* 3.3 16.5 + - - +
191X SER* 3.5 19.3 - - - -
192X TYR* 3.5 36.1 - - + -
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Residues in contact with ASN 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173X MET* 3.1 49.1 + - - +
174X MET* 3.2 10.1 + - + +
176X ALA* 1.3 76.4 - - - +
178X LEU* 1.3 65.1 + - + +
180X LYS* 3.4 13.9 + - - +
181X LYS* 3.1 22.5 + - - +
192X TYR* 3.0 21.7 + - - -
51Y SER* 6.3 0.4 - - - -
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Residues in contact with LEU 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X THR* 4.2 23.3 - - + +
152X ASP* 4.1 28.0 - - + +
155X ALA* 3.7 28.0 - - + -
156X ILE* 4.2 20.3 - - + +
159X LEU* 4.4 11.7 - - + -
174X MET* 3.1 32.7 + - + +
175X LEU* 3.2 7.2 + - + +
177X ASN* 1.3 77.2 - - + +
179X TYR* 1.3 59.9 + - - +
181X LYS* 3.3 7.6 + - + +
182X ALA* 2.9 28.2 + - - +
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Residues in contact with TYR 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ILE* 4.0 30.8 - - + +
160X ASP* 4.0 20.1 + - - -
175X LEU* 3.0 54.9 + - + +
176X ALA 3.3 3.6 + - - +
178X LEU* 1.3 76.6 - - - +
180X LYS* 1.3 49.4 + - - +
182X ALA* 3.1 4.0 + - - +
183X GLY 2.7 29.3 + - - -
184X GLN* 2.8 30.7 + - + +
187X PRO* 3.3 43.6 - - + +
188X SER* 3.1 20.4 - - - +
190X THR* 6.1 0.4 - - + -
191X SER* 4.7 0.4 - - - -
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Residues in contact with LYS 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176X ALA 3.0 8.9 + - - +
177X ASN* 3.6 17.7 + - - +
179X TYR* 1.3 73.1 - - - +
181X LYS* 1.3 64.3 + - - +
183X GLY* 3.0 15.3 + - - +
184X GLN 4.9 0.9 - - - +
188X SER* 2.9 27.5 + - - +
192X TYR* 2.9 31.6 + - + +
204X ASP 5.6 0.2 + - - -
208X GLY* 4.2 12.7 - - - -
211X SER* 4.5 8.6 + - - +
212X LEU* 4.0 21.5 - - + -
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Residues in contact with LYS 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735H LYS* 4.4 5.5 + - - -
152X ASP* 3.4 27.7 + - - +
177X ASN 3.1 9.9 + - - +
178X LEU* 3.5 11.4 - - + +
180X LYS* 1.3 79.6 - - - +
182X ALA* 1.3 60.5 + - - +
183X GLY* 3.4 0.7 + - - -
370X SER* 3.2 45.3 + - - +
371X ASN* 6.0 0.7 - - + -
402X LEU* 5.6 10.7 - - + +
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Residues in contact with ALA 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734H PRO* 3.6 10.6 - - - +
735H LYS* 2.9 24.0 + - - +
152X ASP* 5.5 3.6 + - + -
153X LYS* 6.5 0.9 - - - -
156X ILE* 4.5 13.5 - - + -
178X LEU 2.9 14.3 + - - +
179X TYR* 3.1 10.1 + - - +
181X LYS* 1.3 77.4 - - - +
183X GLY* 1.3 59.1 + - - +
184X GLN* 3.5 22.9 + - + +
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Residues in contact with GLY 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731H GLN* 4.7 3.3 - - - +
734H PRO* 4.4 11.9 - - - +
735H LYS* 4.8 2.2 - - - -
179X TYR 2.7 9.1 + - - -
180X LYS* 3.0 14.8 + - - -
181X LYS 4.5 0.4 - - - -
182X ALA* 1.3 76.6 - - - +
184X GLN* 1.3 60.6 + - - +
185X GLU* 3.4 14.0 + - - +
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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
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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