Contacts of the helix formed by residues 154 - 171 (chain R) in PDB entry 5GJQ
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 154 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153R ASP* 1.3 92.7 + - - +
155R ASP* 1.3 58.2 + - - +
156R LEU 3.1 0.9 - - - -
157R ILE* 2.6 41.5 + - - +
158R THR* 3.3 4.9 + - - -
187R TYR* 3.9 33.5 - - - +
191R ILE* 5.4 4.7 - - - -
37Y HIS* 5.7 11.0 - - + -
39Y TRP 6.0 1.3 - - - -
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Residues in contact with ASP 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153R ASP* 4.1 3.8 + - - +
154R ASN* 1.3 78.9 - - - +
156R LEU* 1.3 53.6 + - - +
157R ILE 2.5 13.2 + - - -
158R THR* 2.8 23.8 + - - +
159R ARG* 3.0 23.0 + - + +
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Residues in contact with LEU 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R LYS* 4.2 22.4 - - - +
121R LEU* 5.1 9.6 - - + -
144R LEU 4.7 8.3 - - - +
145R LEU* 4.7 1.9 - - - -
147R ILE* 5.7 0.2 - - + -
148R GLY* 4.2 16.6 - - - +
153R ASP* 3.9 26.9 + - + +
155R ASP* 1.3 76.2 - - - +
157R ILE* 1.3 55.9 + - + +
159R ARG* 4.5 3.3 - - - +
160R ASN* 3.3 24.6 - - - +
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Residues in contact with ILE 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R LEU* 3.8 25.4 - - + +
148R GLY* 3.5 10.5 - - - +
149R LEU* 3.4 39.0 - - + +
153R ASP 5.0 2.5 - - - +
154R ASN* 2.6 24.5 + - - +
155R ASP 2.5 4.9 + - - -
156R LEU* 1.3 74.8 - - + +
158R THR* 1.3 53.1 + - - +
159R ARG 3.0 1.8 - - - -
160R ASN* 2.7 26.4 + - - +
161R THR* 2.7 30.1 + - - +
187R TYR* 4.7 27.8 - - + -
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Residues in contact with THR 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R ASN 3.3 3.8 + - - -
155R ASP* 2.8 23.4 + - - -
157R ILE* 1.3 78.1 - - - +
159R ARG* 1.3 53.1 + - - +
161R THR* 4.0 6.5 - - - -
162R GLU* 2.7 46.7 + - - +
187R TYR* 5.6 8.5 - - - -
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Residues in contact with ARG 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155R ASP* 3.0 22.6 + - + +
156R LEU* 4.9 2.0 - - - +
157R ILE 2.9 1.0 + - - -
158R THR* 1.3 79.7 - - - +
160R ASN* 1.3 63.7 + - - +
162R GLU* 3.7 8.0 - - - +
163R LYS* 3.5 17.2 + - - +
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Residues in contact with ASN 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R VAL* 4.8 13.4 - - + +
144R LEU* 5.0 9.4 - - - -
145R LEU* 4.2 24.2 - - + +
156R LEU* 3.3 20.9 - - - +
157R ILE 2.7 7.1 + - - +
159R ARG* 1.3 81.8 - - - +
161R THR* 1.3 58.9 + - - +
162R GLU 3.0 0.9 - - - -
163R LYS* 2.9 12.1 + - + +
164R ALA* 2.9 31.2 + - - +
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Residues in contact with THR 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R LEU* 5.4 2.3 - - - +
157R ILE* 2.7 33.7 + - - +
158R THR* 4.0 8.7 - - - -
160R ASN* 1.3 71.7 - - - +
162R GLU* 1.3 62.0 + - - +
164R ALA* 4.4 4.3 - - - +
165R LYS* 2.9 29.2 + - - +
180R LEU* 5.4 12.0 - - - +
184R GLN* 4.0 31.9 + - - +
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Residues in contact with GLU 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R THR* 2.7 33.5 + - - +
159R ARG* 3.7 10.3 - - - +
160R ASN 3.0 0.2 - - - -
161R THR* 1.3 81.9 - - - +
163R LYS* 1.3 68.8 + - - +
165R LYS* 3.0 12.7 - - - +
166R SER* 3.0 18.9 + - - -
184R GLN* 5.7 1.4 + - - -
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Residues in contact with LYS 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R VAL* 4.3 16.8 - - + -
159R ARG 3.5 9.5 + - - +
160R ASN* 2.9 16.2 + - - +
162R GLU* 1.3 76.4 - - - +
164R ALA* 1.3 56.1 + - - +
166R SER* 2.3 40.9 + - - -
167R LEU* 3.0 10.0 + - + +
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Residues in contact with ALA 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138R LEU* 5.3 3.4 - - + +
141R VAL* 4.8 11.5 - - + +
142R PHE* 4.0 35.0 - - + -
160R ASN 2.9 17.0 + - - +
161R THR* 4.4 2.5 - - - +
163R LYS* 1.3 72.2 - - - +
165R LYS* 1.3 64.6 + - - +
167R LEU* 3.1 11.2 + - - +
168R ILE* 2.8 32.1 + - + +
180R LEU* 4.4 9.4 - - + -
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Residues in contact with LYS 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161R THR 2.9 23.2 + - - +
162R GLU* 3.0 20.2 - - - +
163R LYS 3.0 0.4 - - - -
164R ALA* 1.3 77.2 - - - +
166R SER* 1.3 55.4 + - - +
168R ILE* 3.7 4.8 - - - +
169R GLU* 2.8 63.5 + - + +
180R LEU* 5.8 6.0 - - + +
184R GLN* 5.8 4.5 - - - +
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Residues in contact with SER 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R GLU 3.0 9.1 + - - -
163R LYS* 2.3 34.9 + - - -
165R LYS* 1.3 71.4 - - - +
167R LEU* 1.3 68.0 + - - +
169R GLU* 3.0 15.7 + - - +
170R GLU* 2.9 25.2 + - - +
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Residues in contact with LEU 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134R LEU* 4.6 11.8 - - + +
137R ARG* 4.6 20.9 - - - +
138R LEU* 3.2 33.2 - - + -
141R VAL* 5.8 0.9 - - + -
163R LYS* 3.0 19.1 + - + +
164R ALA* 3.6 8.7 - - - +
166R SER* 1.3 84.2 + - - +
168R ILE* 1.3 58.0 + - - +
170R GLU* 2.6 28.2 - - - +
171R GLY 3.8 5.0 + - - -
172R GLY* 4.6 1.7 + - - -
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Residues in contact with ILE 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134R LEU* 5.4 2.2 - - + -
138R LEU* 5.3 6.1 - - + -
142R PHE* 5.3 6.3 - - + -
164R ALA* 2.8 26.1 + - + +
165R LYS* 3.7 4.9 - - - +
167R LEU* 1.3 80.6 - - + +
169R GLU* 1.3 64.0 + - + +
170R GLU 3.1 1.8 - - - -
171R GLY 2.8 25.5 - - - +
172R GLY* 4.7 3.8 - - - -
173R ASP 4.2 15.0 - - - +
176R ARG* 3.9 35.4 - - + -
177R ARG* 2.9 53.0 + - + +
180R LEU* 5.6 4.5 - - + -
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Residues in contact with GLU 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165R LYS* 2.8 48.9 + - + +
166R SER* 3.5 13.9 - - - +
168R ILE* 1.3 79.8 - - + +
170R GLU* 1.3 62.4 + - - +
171R GLY 4.9 0.2 - - - +
177R ARG* 4.7 8.8 + - - +
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Residues in contact with GLU 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R LEU* 5.2 8.7 - - + -
166R SER 2.9 9.7 + - - +
167R LEU* 2.6 40.2 - - - +
169R GLU* 1.3 80.2 - - - +
171R GLY* 1.3 64.3 + - - +
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Residues in contact with GLY 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R LEU 4.4 0.9 - - - -
168R ILE 2.8 20.3 + - - +
169R GLU 4.9 0.2 - - - +
170R GLU* 1.3 87.8 - - - +
172R GLY* 1.3 66.5 + - - +
173R ASP 3.8 0.3 + - - -
177R ARG* 4.3 7.3 + - - -
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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