Contacts of the helix formed by residues 148 - 167 (chain o) 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 THR 148 (chain o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8o PHE* 4.6 1.8 - - - -
146o GLY 5.0 2.7 - - - +
147o MET* 1.3 78.2 - - - +
149o LYS* 1.3 65.3 + - - +
150o GLU* 3.6 14.3 + - - +
151o GLU* 2.7 44.9 + - - +
152o CYS* 3.0 22.0 + - - -
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Residues in contact with LYS 149 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8o PHE* 3.8 44.4 - - + -
13o VAL* 4.4 0.4 - - + +
148o THR* 1.3 75.6 - - - +
150o GLU* 1.3 80.2 + - - +
152o CYS* 3.2 4.2 + - - +
153o LEU* 2.9 40.0 + - + +
178o ALA* 3.8 22.9 - - + -
185o GLU* 2.4 43.1 + - - +
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Residues in contact with GLU 150 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148o THR* 3.7 13.9 + - - +
149o LYS* 1.3 100.5 + - - +
151o GLU* 1.3 56.1 + - + +
153o LEU* 3.2 12.6 + - + +
154o GLN* 2.9 29.5 + - - +
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Residues in contact with GLU 151 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144o ARG* 3.0 33.0 + - - +
146o GLY 4.2 1.6 - - - +
147o MET* 3.2 10.5 - - + +
148o THR* 2.7 54.0 + - - +
150o GLU* 1.3 74.7 - - + +
152o CYS* 1.3 59.9 + - - +
154o GLN* 3.4 6.5 + - - +
155o PHE* 2.9 28.3 + - - +
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Residues in contact with CYS 152 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6o VAL* 3.7 25.6 - - + -
7o GLN 4.6 0.9 - - - -
8o PHE* 3.8 22.4 - - - -
13o VAL* 3.6 20.0 - - + -
147o MET* 3.6 20.0 - - - -
148o THR 3.0 18.3 + - - -
149o LYS 3.5 8.3 - - - +
151o GLU* 1.3 75.3 - - - +
153o LEU* 1.3 57.6 + - - +
155o PHE* 3.2 7.3 - - - +
156o THR* 2.9 36.7 + - - +
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Residues in contact with LEU 153 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13o VAL* 3.6 31.9 - - + -
149o LYS* 2.9 28.8 + - - +
150o GLU* 3.2 14.6 + - + +
152o CYS* 1.3 74.6 - - - +
154o GLN* 1.3 58.2 + - - +
156o THR* 3.1 5.1 + - - -
157o ALA* 2.9 30.3 + - - +
176o LEU* 3.9 25.1 - - + +
178o ALA* 4.3 18.2 - - + +
185o GLU* 5.8 2.9 - - + +
187o GLN* 3.3 29.6 - - + +
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Residues in contact with GLN 154 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150o GLU 2.9 16.2 + - - +
151o GLU* 3.8 5.6 - - - +
153o LEU* 1.3 76.8 - - - +
155o PHE* 1.3 57.5 + - - +
157o ALA* 3.5 7.2 - - - +
158o ASN* 2.9 59.4 + - - +
189o LEU* 6.0 0.3 - - - +
195o PRO* 4.2 11.9 - - - +
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Residues in contact with PHE 155 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4o MET* 3.5 15.3 - - + -
6o VAL* 3.7 29.2 - - + -
125o PHE* 5.2 1.6 - + - -
138o TYR* 4.2 13.6 - + - -
139o VAL* 3.3 26.5 - - + -
142o THR* 3.5 40.6 - - + -
143o TYR* 3.9 20.9 - + + -
147o MET* 4.1 21.5 - - + -
151o GLU 2.9 15.5 + - - +
152o CYS* 3.2 10.5 - - - +
154o GLN* 1.3 76.6 - - - +
156o THR* 1.3 58.0 + - + +
158o ASN* 3.3 7.0 + - - +
159o ALA* 3.0 26.0 + - - +
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Residues in contact with THR 156 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4o MET* 3.8 22.7 - - + +
6o VAL* 3.6 26.7 - - + -
13o VAL* 3.5 24.8 - - + +
15o GLY* 5.3 2.2 - - - -
152o CYS 2.9 13.7 + - - +
153o LEU 3.1 9.5 + - - -
155o PHE* 1.3 71.9 - - + +
157o ALA* 1.3 70.2 + - - +
160o LEU* 2.9 33.3 + - - +
176o LEU* 3.1 23.1 - - - +
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Residues in contact with ALA 157 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153o LEU 2.9 14.9 + - - +
154o GLN* 3.5 12.8 - - - +
156o THR* 1.3 83.9 + - - +
158o ASN* 1.3 62.7 + - - +
160o LEU* 4.8 0.2 - - - -
161o ALA* 3.0 23.7 + - - +
174o ILE* 3.5 13.4 - - - +
176o LEU* 4.1 6.7 - - + -
189o LEU* 3.6 28.5 - - + -
195o PRO* 4.3 10.8 - - + +
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Residues in contact with ASN 158 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138o TYR* 3.2 27.1 + - + +
154o GLN* 2.9 38.1 + - - +
155o PHE* 3.3 2.3 + - - +
157o ALA* 1.3 76.4 - - - +
159o ALA* 1.3 63.4 + - - +
161o ALA* 3.0 5.6 + - - +
162o LEU* 2.9 26.7 + - - +
195o PRO* 3.2 30.7 - - - +
197o PHE* 4.4 15.2 - - + -
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Residues in contact with ALA 159 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4o MET* 3.5 33.2 - - + -
135o ILE* 3.7 15.9 - - + +
138o TYR* 4.0 21.7 - - + -
139o VAL* 5.4 0.7 - - + -
155o PHE 3.0 13.6 + - - +
156o THR 3.9 0.2 - - - +
158o ASN* 1.3 76.8 - - - +
160o LEU* 1.3 63.3 + - - +
162o LEU* 3.1 7.6 + - - +
163o ALA* 3.0 24.8 + - - +
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Residues in contact with LEU 160 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2o THR* 3.7 40.6 - - + +
4o MET* 4.0 24.0 - - + -
15o GLY* 3.3 12.8 - - - +
16o ALA* 3.3 33.2 - - - +
17o ASP 4.8 1.3 - - - +
135o ILE* 5.2 0.7 - - + -
156o THR* 2.9 22.4 + - - +
157o ALA 3.9 2.2 - - - +
159o ALA* 1.3 76.7 - - - +
161o ALA* 1.3 63.0 + - - +
163o ALA* 3.9 2.0 - - - +
164o MET* 2.9 35.0 + - - +
174o ILE* 3.9 23.1 - - + -
176o LEU* 4.4 2.7 - - + -
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Residues in contact with ALA 161 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157o ALA 3.0 15.5 + - - +
158o ASN* 3.0 11.4 + - - +
160o LEU* 1.3 77.9 - - - +
162o LEU* 1.3 55.7 + - - +
164o MET* 3.4 5.8 + - - +
165o GLU* 2.9 29.5 + - - +
174o ILE* 3.9 5.7 - - + +
194o ILE* 3.7 18.4 - - + -
195o PRO* 3.6 25.6 - - + +
197o PHE* 4.9 3.4 - - + -
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Residues in contact with LEU 162 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137a GLY* 4.0 22.9 - - - +
140a ASP* 4.0 16.3 - - + +
141a ALA* 4.2 3.1 - - + -
135o ILE* 4.1 9.6 - - + -
138o TYR* 3.6 48.7 - - + -
158o ASN 2.9 18.8 + - - +
159o ALA* 3.1 6.5 + - - +
161o ALA* 1.3 71.8 - - - +
163o ALA* 1.3 67.6 + - - +
165o GLU* 3.1 16.4 + - + +
166o ARG* 3.1 18.4 + - - +
197o PHE* 3.5 36.8 - - + -
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Residues in contact with ALA 163 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2o THR* 3.6 35.0 - - + +
131o GLY 3.9 11.4 - - - +
134o TYR* 4.7 2.4 - - - -
135o ILE* 3.6 22.3 - - + +
159o ALA 3.0 11.4 + - - +
160o LEU 3.9 2.0 - - - +
162o LEU* 1.3 76.4 - - - +
164o MET* 1.3 56.2 + - - +
166o ARG* 3.1 4.9 + - - +
167o ASP* 2.7 39.0 + - - +
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Residues in contact with MET 164 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2o THR* 5.0 2.7 - - - +
17o ASP* 3.8 20.6 - - + -
160o LEU* 2.9 28.0 + - - +
161o ALA* 3.6 6.3 - - - +
163o ALA* 1.3 76.4 - - - +
165o GLU* 1.3 63.8 + - - +
167o ASP 3.3 15.1 - - - +
170o SER* 3.5 15.7 - - - +
171o GLY* 3.5 41.6 - - - +
172o GLY 3.6 19.5 - - - +
173o VAL* 4.0 1.1 - - - +
174o ILE* 3.5 32.3 - - + -
194o ILE* 4.5 9.0 - - + -
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Residues in contact with GLU 165 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140a ASP* 5.8 0.9 - - - +
34g ALA* 4.1 12.1 - - - +
37g ARG* 3.8 24.2 + - - +
184g TYR* 2.5 53.8 + - - -
161o ALA 2.9 14.4 + - - +
162o LEU* 3.1 12.8 + - + +
164o MET* 1.3 78.8 - - - +
166o ARG* 1.3 64.4 + - + +
167o ASP 4.8 0.9 - - - +
199o VAL* 5.3 0.7 - - - +
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Residues in contact with ARG 166 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125a PHE* 4.7 10.7 - - - -
136a TYR* 3.4 40.7 - - + -
137a GLY* 5.6 0.9 - - - +
140a ASP* 2.9 40.5 + - - +
33g LEU* 3.5 17.5 - - + +
34g ALA* 3.1 46.2 + - - +
35g ARG* 3.0 28.1 + - - +
37g ARG* 3.2 35.2 - - - +
134o TYR* 4.2 15.3 - - + -
162o LEU 3.1 13.0 + - - +
163o ALA 3.1 3.6 + - - +
165o GLU* 1.3 85.2 - - + +
167o ASP* 1.3 60.1 + - - +
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Residues in contact with ASP 167 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32g SER* 4.1 11.7 + - - -
34g ALA* 5.8 0.4 - - - -
19o ARG* 4.9 0.2 + - - -
130o SER* 2.5 31.7 + - - -
131o GLY* 3.2 12.0 + - - -
134o TYR* 3.6 21.0 + - + -
163o ALA 2.7 19.6 + - - +
164o MET 3.3 7.1 - - - +
165o GLU 4.8 1.0 - - - +
166o ARG* 1.3 73.2 - - - +
168o GLY* 1.3 65.4 + - - +
169o SER* 3.4 11.8 + - - -
170o SER* 2.6 46.6 + - - +
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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