Contacts of the helix formed by residues 159 - 178 (chain s) in PDB entry 5JPQ
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 ASP 159 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78s ARG* 5.9 0.9 + - - -
133s PRO* 4.5 8.5 - - - +
134s SER* 2.9 37.7 + - - +
156s ASP* 3.6 13.1 + - + +
157s GLN 2.8 1.4 + - - -
158s ASN* 1.3 84.6 - - - +
160s ARG* 1.3 52.8 + - - +
161s ASP* 2.7 20.6 + - - -
162s PHE* 3.4 8.4 + - - +
163s LEU* 3.2 41.4 + - + +
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Residues in contact with ARG 160 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156s ASP 4.0 1.4 + - - -
157s GLN* 2.9 37.4 + - - +
158s ASN 3.5 1.0 - - - -
159s ASP* 1.3 74.7 - - - +
161s ASP* 1.3 60.8 + - - +
164s GLU* 2.8 67.1 + - - +
186s PHE* 3.1 56.1 - - + +
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Residues in contact with ASP 161 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158s ASN 3.7 17.4 - - - +
159s ASP* 2.7 6.4 + - - +
160s ARG* 1.3 80.8 - - - +
162s PHE* 1.3 66.5 - - + +
163s LEU 3.2 0.3 + - - -
164s GLU* 3.4 5.0 + - - +
165s GLU* 3.9 16.4 - - - +
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Residues in contact with PHE 162 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81s ILE* 4.2 30.1 - - + -
85s GLU* 4.7 2.2 - - - -
93s PHE* 4.9 4.9 - + - -
130s LEU 4.4 8.5 - - - -
131s LEU 4.3 0.7 - - - -
133s PRO* 3.1 46.7 - - + -
159s ASP* 3.4 9.6 + - - +
161s ASP* 1.3 81.3 - - + +
163s LEU* 1.3 86.1 + - + +
165s GLU* 4.0 4.1 + - - +
166s LYS* 3.2 57.8 + - + +
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Residues in contact with LEU 163 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131s LEU* 3.2 37.2 - - + +
134s SER* 4.3 15.5 - - - +
155s LEU* 3.7 38.1 - - + -
156s ASP 5.0 1.8 - - - +
159s ASP* 3.2 36.2 + - + +
161s ASP 3.2 0.8 - - - -
162s PHE* 1.3 94.1 - - + +
164s GLU* 1.3 66.2 + - - +
165s GLU 3.2 2.2 - - - -
166s LYS* 4.1 3.7 - - + +
167s LEU* 3.0 26.2 + - - +
170s ILE* 5.9 2.8 - - + +
186s PHE* 4.6 6.3 - - + -
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Residues in contact with GLU 164 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160s ARG* 2.8 67.1 + - + +
161s ASP 3.4 2.2 + - - +
163s LEU* 1.3 76.9 - - - +
165s GLU* 1.3 59.7 + - + +
167s LEU* 3.0 31.4 - - + +
168s ASP* 4.5 2.8 - - - +
186s PHE* 4.2 14.2 - - + -
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Residues in contact with GLU 165 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91s ILE* 5.1 6.9 - - + +
161s ASP 3.9 15.6 - - - +
162s PHE* 4.0 3.2 + - - +
163s LEU 3.2 0.4 - - - -
164s GLU* 1.3 75.1 - - + +
166s LYS* 1.3 88.5 + - + +
167s LEU 3.0 2.3 + - - -
168s ASP* 3.3 18.9 + - - +
169s ALA 4.8 0.5 + - - -
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Residues in contact with LYS 166 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85s GLU* 2.5 37.1 + - - -
91s ILE* 3.4 23.0 - - + +
93s PHE* 3.1 30.7 - - + -
162s PHE* 3.2 53.2 - - + +
163s LEU* 3.6 5.1 + - + +
165s GLU* 1.3 93.4 + - + +
167s LEU* 1.3 52.3 + - - +
168s ASP 2.8 1.8 + - - -
169s ALA* 2.7 32.8 + - - +
170s ILE* 3.0 19.3 + - + -
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Residues in contact with LEU 167 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155s LEU* 5.1 4.0 - - + -
163s LEU 3.0 14.5 + - - +
164s GLU* 3.0 31.4 - - + +
165s GLU 3.0 0.2 - - - -
166s LYS* 1.3 74.3 - - - +
168s ASP* 1.3 66.4 + - - +
170s ILE* 4.0 9.7 - - - +
171s THR* 2.9 26.3 + - - +
184s PHE* 3.4 49.8 - - + +
186s PHE* 4.7 15.7 - - + -
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Residues in contact with ASP 168 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50s ILE* 4.5 17.1 - - + +
164s GLU 4.5 3.3 - - - +
165s GLU* 3.3 15.4 - - - +
166s LYS 2.8 2.4 + - - -
167s LEU* 1.3 84.9 - - - +
169s ALA* 1.3 66.3 + - - +
171s THR* 3.5 7.4 - - - -
172s HIS* 3.1 23.4 + - - +
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Residues in contact with ALA 169 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50s ILE* 3.4 33.0 - - + +
60s ALA* 4.6 4.3 - - + -
91s ILE* 4.4 11.2 - - + -
93s PHE* 3.6 20.0 - - + -
165s GLU 4.8 0.4 + - - -
166s LYS 2.7 16.8 + - - +
168s ASP* 1.3 71.6 - - - +
170s ILE* 1.3 55.2 + - - +
172s HIS* 2.8 5.7 + - - +
173s ILE* 2.7 41.5 + - + +
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Residues in contact with ILE 170 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93s PHE* 3.6 23.5 - - + -
127s LEU* 4.1 9.9 - - + -
130s LEU* 3.2 43.6 - - + +
131s LEU* 3.3 24.0 - - + +
163s LEU* 5.9 2.2 - - + +
166s LYS* 3.0 15.5 + - + +
167s LEU* 4.0 8.1 - - - +
169s ALA* 1.3 78.2 - - - +
171s THR* 1.3 66.4 + - - +
173s ILE* 2.9 9.1 + - - +
174s TYR* 2.8 25.6 + - + +
182s VAL* 5.6 0.2 - - + -
184s PHE* 3.7 24.9 - - + -
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Residues in contact with THR 171 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167s LEU* 2.9 16.6 + - - +
168s ASP* 3.5 11.6 - - - -
169s ALA 3.2 0.2 - - - -
170s ILE* 1.3 82.4 - - - +
172s HIS* 1.3 60.2 + - - +
174s TYR* 3.3 5.9 + - - +
175s LYS* 3.0 54.5 + - + +
180s ARG 4.7 0.3 - - - +
182s VAL* 3.3 32.7 + - - +
184s PHE* 4.0 2.9 - - - -
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Residues in contact with HIS 172 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48s PHE* 4.4 15.7 - - + +
49s GLN 3.2 33.1 + - - -
50s ILE* 4.4 12.8 - - + -
51s ASN 5.7 1.8 - - - -
168s ASP 3.1 9.5 + - - +
169s ALA* 2.8 11.7 + - - +
171s THR* 1.3 81.1 - - - +
173s ILE* 1.3 54.8 + - + +
175s LYS* 3.7 11.7 + - + +
176s THR* 2.5 46.1 + - + +
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Residues in contact with ILE 173 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48s PHE* 3.3 47.1 - - + -
60s ALA* 5.8 4.0 - - + +
61s VAL 5.8 0.7 - - - -
62s LEU* 3.9 21.8 - - + +
93s PHE* 3.0 40.4 - - + -
130s LEU* 4.7 9.6 - - + -
169s ALA* 2.7 29.1 + - + +
170s ILE* 2.9 5.3 + - - +
172s HIS* 1.3 73.0 - - + +
174s TYR* 1.3 61.8 + - - +
176s THR* 2.9 7.1 + - - -
177s VAL* 2.8 37.7 + - + +
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Residues in contact with TYR 174 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123s TYR 2.5 24.8 + - - -
124s ASP* 3.7 7.4 + - - -
126s LEU* 3.6 18.4 - - + -
127s LEU* 3.2 57.8 - - + +
130s LEU* 4.5 8.1 - - + -
151s TYR* 5.6 0.4 - + - -
170s ILE* 2.8 15.4 + - + +
171s THR 3.5 3.8 - - - +
173s ILE* 1.3 78.1 - - - +
175s LYS* 1.3 59.6 + - - +
177s VAL* 4.4 2.0 - - - -
178s THR* 2.8 54.6 + - + -
180s ARG* 3.6 32.8 + - + -
182s VAL* 3.2 28.5 - - + -
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Residues in contact with LYS 175 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171s THR* 3.0 41.8 + - + +
172s HIS* 4.0 14.1 - - + +
174s TYR* 1.3 75.9 - - - +
176s THR* 1.3 61.5 + - - +
179s THR* 3.7 17.3 - - - +
180s ARG 3.7 21.5 - - - +
181s GLU* 4.0 26.8 + - - +
182s VAL 4.7 0.2 - - - +
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Residues in contact with THR 176 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48s PHE* 3.9 26.7 - - + -
172s HIS* 2.5 39.2 + - + +
173s ILE* 2.9 9.0 + - - -
175s LYS* 1.3 80.1 - - - +
177s VAL* 1.3 66.2 + - - +
178s THR 4.6 0.7 - - - +
179s THR* 5.6 1.0 - - - +
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Residues in contact with VAL 177 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46s LYS* 5.6 4.7 - - - +
48s PHE* 4.8 7.6 - - + -
62s LEU* 5.2 4.7 - - + -
64s TYR* 4.9 11.9 - - - +
123s TYR* 2.8 25.5 + - + +
126s LEU* 4.0 28.5 - - + -
173s ILE* 2.8 37.1 + - + +
174s TYR* 4.4 0.9 - - - +
176s THR* 1.3 77.1 - - - +
178s THR* 1.3 71.0 + - - +
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Residues in contact with THR 178 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123s TYR* 3.2 40.5 + - + -
126s LEU* 4.3 2.3 - - - +
174s TYR* 2.8 41.1 + - + -
175s LYS 4.5 0.7 - - - -
177s VAL* 1.3 82.4 - - - +
179s THR* 1.3 81.7 + - - +
180s ARG* 3.0 48.2 - - + +
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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
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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