Contacts of the helix formed by residues 147 - 166 (chain p) 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 GLU 147 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8p TYR* 4.1 2.7 - - - -
9p LYS* 4.4 8.9 - - - +
10p ASP* 4.0 16.8 - - - +
143p ARG* 6.0 0.9 - - - +
145p ASP* 4.1 11.8 - - - +
146p MET* 1.3 81.4 - - - +
148p GLU* 1.3 68.2 + - - +
149p GLU 3.4 2.5 - - - +
150p GLU* 3.3 15.6 + - + +
151p ALA* 3.0 20.4 + - - +
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Residues in contact with GLU 148 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8p TYR* 3.5 34.8 + - + +
10p ASP* 5.7 1.0 + - - +
13p VAL* 4.8 0.2 - - - +
147p GLU* 1.3 75.5 + - - +
149p GLU* 1.3 67.9 + - + +
151p ALA* 3.1 4.5 + - - +
152p LYS* 2.9 49.7 + - + +
177p VAL* 3.8 18.1 - - + +
179p SER* 5.4 0.5 - - - -
182p LYS* 2.6 37.1 + - - -
184p ASP* 3.8 5.7 - - - +
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Residues in contact with GLU 149 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147p GLU* 3.4 1.4 - - - +
148p GLU* 1.3 87.6 - - + +
150p GLU* 1.3 58.4 + - - +
152p LYS* 2.8 40.8 + - - +
153p ASN* 3.0 28.4 + - - +
189p TYR* 4.7 5.9 + - - -
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Residues in contact with GLU 150 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141p LYS 5.4 1.2 - - - +
143p ARG* 2.7 45.7 + - - +
146p MET* 3.9 16.1 - - + +
147p GLU* 3.3 24.7 + - + +
148p GLU 3.2 0.2 - - - -
149p GLU* 1.3 77.4 - - - +
151p ALA* 1.3 58.8 + - - +
153p ASN* 3.2 7.7 + - - +
154p LEU* 2.9 27.1 + - + +
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Residues in contact with ALA 151 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6p VAL* 4.0 6.5 - - + -
8p TYR* 3.8 24.0 - - + -
13p VAL* 3.9 14.6 - - + -
146p MET* 3.7 19.5 - - + +
147p GLU 3.0 13.4 + - - +
148p GLU 3.5 8.5 - - - +
150p GLU* 1.3 78.5 - - - +
152p LYS* 1.3 57.8 + - - +
154p LEU* 3.2 1.4 + - - +
155p VAL* 2.9 35.5 + - - +
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Residues in contact with LYS 152 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13p VAL* 4.2 13.7 - - + -
148p GLU* 2.9 36.5 + - + +
149p GLU* 2.8 36.1 + - - +
150p GLU 3.3 0.2 - - - -
151p ALA* 1.3 74.4 - - - +
153p ASN* 1.3 61.1 + - - +
155p VAL* 4.0 0.2 - - - +
156p SER* 2.9 29.3 + - - -
175p LEU* 3.9 11.9 - - + +
177p VAL* 3.9 20.1 - - + +
184p ASP* 5.3 3.4 + - - -
186p LEU* 3.8 22.4 - - - +
189p TYR* 3.6 32.7 + - - +
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Residues in contact with ASN 153 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149p GLU 3.0 14.5 + - - +
150p GLU* 3.4 11.0 - - - +
152p LYS* 1.3 78.5 - - - +
154p LEU* 1.3 57.5 + - - +
156p SER* 2.7 20.8 + - - -
157p GLU* 3.0 41.5 + - - +
189p TYR* 4.4 5.1 + - - +
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Residues in contact with LEU 154 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6p VAL* 4.7 2.5 - - + -
137p VAL* 4.0 14.3 - - + +
138p PHE* 3.8 24.2 - - + -
141p LYS* 3.4 47.3 - - + +
142p PHE* 4.0 14.6 - - + -
146p MET* 3.6 25.1 - - + -
150p GLU* 2.9 14.5 + - + +
151p ALA* 3.2 10.3 + - - +
153p ASN* 1.3 77.9 + - - +
155p VAL* 1.3 64.6 + - + +
157p GLU* 3.1 8.8 + - + +
158p ALA* 3.0 21.5 + - - +
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Residues in contact with VAL 155 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4p ALA* 4.6 6.3 - - + +
5p GLY 5.0 0.2 - - - -
6p VAL* 3.6 31.4 - - + +
13p VAL* 3.7 20.6 - - + +
15p GLY* 3.8 21.5 - - - +
138p PHE* 4.3 13.5 - - + -
151p ALA 2.9 19.9 + - - +
152p LYS 4.0 1.8 - - - +
154p LEU* 1.3 74.6 - - + +
156p SER* 1.3 65.6 + - - +
158p ALA* 3.1 3.6 + - - +
159p ILE* 3.0 31.2 + - + +
175p LEU* 3.5 24.7 - - + -
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Residues in contact with SER 156 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152p LYS 2.9 15.6 + - - -
153p ASN* 2.7 28.1 + - - -
155p VAL* 1.3 78.3 - - - +
157p GLU* 1.3 55.8 + - - +
159p ILE 3.6 0.2 + - - -
160p ALA* 3.0 28.8 + - - +
173p ILE* 3.5 24.7 - - - +
175p LEU* 4.5 1.5 - - - +
189p TYR* 3.8 26.5 - - - -
190p THR* 5.4 1.8 - - - -
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Residues in contact with GLU 157 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152g GLU* 3.0 11.0 - - + +
137p VAL* 3.9 9.4 - - + +
141p LYS* 2.3 46.5 + - - +
153p ASN* 3.0 38.9 + - - +
154p LEU* 3.3 8.2 - - - +
155p VAL 3.1 0.2 - - - -
156p SER* 1.3 75.8 + - - +
158p ALA* 1.3 59.9 + - - +
160p ALA* 3.3 7.5 + - + +
161p ALA* 2.9 26.7 + - - +
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Residues in contact with ALA 158 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4p ALA* 4.5 2.2 - - + -
134p ALA* 3.6 34.6 - - + +
137p VAL* 3.7 14.1 - - + +
138p PHE* 3.6 33.4 - - + -
154p LEU 3.0 6.4 + - - +
155p VAL 3.6 5.2 - - - +
157p GLU* 1.3 74.4 - - - +
159p ILE* 1.3 62.2 + - - +
161p ALA* 3.1 5.0 + - - +
162p GLY* 3.0 18.4 + - - -
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Residues in contact with ILE 159 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2p THR* 3.4 27.8 - - + +
3p ILE 4.0 1.3 - - - -
4p ALA* 3.6 20.6 - - + +
15p GLY* 3.5 30.5 - - - +
16p ALA 3.7 6.5 - - - +
17p ASP* 3.7 29.2 - - + +
155p VAL* 3.0 20.9 + - + +
156p SER 3.9 4.7 - - - +
158p ALA* 1.3 71.7 - - - +
160p ALA* 1.3 61.8 + - - +
162p GLY* 3.3 2.2 + - - +
163p ILE* 2.9 26.1 + - + +
173p ILE* 4.0 22.2 - - + -
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Residues in contact with ALA 160 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156p SER 3.0 19.0 + - - +
157p GLU* 3.5 8.7 - - + +
158p ALA 3.1 0.2 - - - -
159p ILE* 1.3 76.2 - - - +
161p ALA* 1.3 63.8 - - - +
163p ILE* 3.0 7.4 + - - +
164p PHE* 2.9 47.7 + - + -
173p ILE* 4.0 11.6 - - + +
192p PRO* 6.1 0.4 - - + -
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Residues in contact with ALA 161 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148g PRO* 4.5 6.7 - - + +
133p ALA* 3.7 18.6 - - + +
137p VAL* 3.6 27.1 - - + -
157p GLU 2.9 7.5 + - - +
158p ALA 3.3 9.9 - - - +
160p ALA* 1.3 73.7 - - - +
162p GLY* 1.3 57.2 + - - +
164p PHE* 5.3 0.2 - - - -
165p ASN* 2.7 46.6 + - - +
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Residues in contact with GLY 162 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2p THR* 3.6 25.1 - - - -
130p GLY* 3.9 17.0 - - - -
133p ALA* 3.7 4.9 - - - +
158p ALA 3.0 10.7 + - - -
159p ILE 3.6 2.9 - - - -
160p ALA 3.2 0.2 - - - -
161p ALA* 1.3 76.1 - - - +
163p ILE* 1.4 54.3 + - - +
166p ASP* 2.8 37.4 + - - +
169p SER* 3.8 0.6 - - - -
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Residues in contact with ILE 163 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213f ASP* 3.6 34.8 - - + +
17p ASP* 3.9 18.6 - - + -
159p ILE 2.9 19.2 + - - +
160p ALA* 3.0 9.2 + - - +
162p GLY* 1.4 70.5 - - - +
164p PHE* 1.3 70.2 + - + +
166p ASP 3.3 17.3 - - - +
169p SER* 3.7 8.4 - - - +
170p GLY* 3.7 13.5 - - - +
171p SER 3.5 18.8 - - - +
172p ASN 3.5 17.3 - - - +
173p ILE* 3.7 21.1 - - + -
192p PRO* 4.8 2.9 - - + -
193p ASN* 3.9 10.3 - - - +
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Residues in contact with PHE 164 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35f ILE* 4.4 5.4 - - - +
38f ARG* 3.2 30.8 + - - +
212f LYS* 3.8 33.1 - - + +
213f ASP* 5.3 1.0 - - - +
160p ALA* 2.9 40.2 + - + +
161p ALA* 5.3 0.7 - - - -
163p ILE* 1.3 84.9 - - + +
165p ASN* 1.3 67.2 + - - +
166p ASP 4.9 0.2 - - - -
192p PRO* 3.9 32.3 - - + -
193p ASN* 3.3 29.2 - - - -
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Residues in contact with ASN 165 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33f PHE 3.7 9.2 - - - +
34f SER* 4.4 9.0 - - - -
35f ILE* 4.6 8.5 + - - -
38f ARG* 4.6 0.7 + - - -
148g PRO* 3.7 43.2 + - + +
151g ARG* 2.5 41.5 + - - +
133p ALA* 4.6 4.7 - - + -
161p ALA* 2.7 34.8 + - - +
162p GLY 3.8 0.2 - - - -
164p PHE* 1.3 87.1 - - - +
166p ASP* 1.3 58.0 + - - +
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Residues in contact with ASP 166 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33f PHE* 3.7 20.7 - - - +
35f ILE* 6.1 0.2 - - - -
213f ASP* 3.9 1.9 - - - +
129p SER* 2.4 41.0 + - - +
130p GLY* 3.3 15.6 + - - -
133p ALA* 6.2 0.4 - - + -
162p GLY* 2.8 15.0 + - - +
163p ILE 3.3 10.3 - - - +
164p PHE 5.2 0.2 - - - -
165p ASN* 1.3 81.2 - - - +
167p LEU* 1.3 70.6 + - - +
168p GLY* 3.1 8.7 + - - -
169p SER* 2.9 36.7 + - - +
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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