Contacts of the helix formed by residues 146 - 159 (chain E) in PDB entry 4GDK
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 GLN 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144E GLU 4.3 0.2 + - - -
145E MET* 1.3 81.2 - - - +
147E LYS* 1.3 67.4 + - - +
148E LYS* 3.1 10.1 - - + +
149E ASP* 3.1 28.6 + - - +
150E HIS* 3.6 7.3 + - - -
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Residues in contact with LYS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLN* 1.3 77.3 + - - +
148E LYS* 1.3 62.8 + - + +
150E HIS* 3.4 16.3 + - + +
151E LYS* 3.1 37.6 + - + +
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Residues in contact with LYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLN* 3.1 5.9 - - + +
147E LYS* 1.3 80.1 - - + +
149E ASP* 1.3 63.3 + - - +
151E LYS* 3.5 8.1 + - - +
152E GLN* 3.0 28.3 + - - +
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Residues in contact with ASP 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E MET* 3.9 18.3 - - + +
146E GLN* 3.1 26.8 + - - +
148E LYS* 1.3 79.9 - - - +
150E HIS* 1.3 66.2 + - - +
152E GLN* 3.2 7.5 + - - +
153E LEU* 3.1 26.7 + - - +
168E ILE* 3.9 28.8 - - + +
171E LYS* 3.6 23.2 + - - -
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Residues in contact with HIS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLY 3.4 26.3 + - - -
122E GLU* 5.4 1.1 - - - -
126E MET* 3.6 35.3 - - + +
130E LYS* 5.2 0.7 - - - -
142E ILE* 3.1 35.5 + - + +
143E ASN* 5.7 1.6 - - - -
145E MET* 4.0 30.8 - - + +
146E GLN 3.6 4.9 + - - -
147E LYS* 3.4 16.1 + - + +
149E ASP* 1.3 77.3 - - - +
151E LYS* 1.3 62.1 + - + +
153E LEU* 3.4 10.3 + - + +
154E TRP* 3.2 21.3 + - - +
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Residues in contact with LYS 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ASP* 5.3 3.0 + - - -
122E GLU* 2.8 38.8 + - - +
147E LYS* 3.1 29.4 + - + +
148E LYS* 3.6 11.7 - - - +
149E ASP 3.2 0.4 - - - -
150E HIS* 1.3 80.3 - - + +
152E GLN* 1.3 57.3 + - - +
154E TRP* 3.3 9.7 + - + +
155E MET* 2.9 44.2 + - + +
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Residues in contact with GLN 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E LYS 3.0 17.1 + - - +
149E ASP* 3.2 6.6 + - - +
151E LYS* 1.3 73.6 - - - +
153E LEU* 1.3 60.7 + - - +
155E MET* 3.9 7.3 - - - +
156E GLY* 2.9 28.9 + - - -
164E GLN* 3.0 50.4 + - + +
165E PHE* 4.6 0.2 - - - -
167E ALA* 4.1 10.7 - - - +
168E ILE* 3.7 25.1 - - + +
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Residues in contact with LEU 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PHE* 4.2 3.2 - - + -
126E MET* 5.2 3.4 - - + -
129E MET* 3.9 27.6 - - + -
142E ILE* 5.4 2.7 - - + -
145E MET* 4.7 7.6 - - - -
149E ASP 3.1 17.7 + - - +
150E HIS* 3.5 18.2 - - + +
152E GLN* 1.3 75.9 - - - +
154E TRP* 1.3 63.6 + - - +
157E LEU* 3.3 9.4 + - - +
165E PHE* 3.1 53.1 - - + +
168E ILE* 3.7 14.6 - - + -
169E ASN* 3.6 33.9 - - + +
172E LEU* 4.3 8.7 - - + -
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Residues in contact with TRP 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 3.8 26.5 - - + -
118E LYS* 3.7 17.7 + - + -
121E ILE* 3.5 27.8 - - + -
122E GLU* 3.5 56.9 + - + +
125E PHE* 3.9 32.0 - + + -
126E MET* 5.3 1.8 - - - -
150E HIS 3.2 9.2 + - - +
151E LYS* 3.6 12.8 - - + +
152E GLN 3.2 0.2 - - - -
153E LEU* 1.3 78.3 - - - +
155E MET* 1.3 67.2 + - + +
157E LEU* 3.1 20.0 + - + +
158E GLN* 2.8 51.3 + - - +
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Residues in contact with MET 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LYS* 2.9 32.7 + - + +
152E GLN* 3.9 2.9 - - - +
154E TRP* 1.3 84.7 - - + +
156E GLY* 1.3 55.2 + - - +
158E GLN* 4.3 8.5 - - - +
159E ASN* 2.7 54.9 + - - +
164E GLN* 3.5 26.2 - - - +
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Residues in contact with GLY 156 (chain E).
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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12E TRP* 3.3 11.2 - - - -
152E GLN 2.9 16.8 + - - -
153E LEU 4.0 2.2 - - - -
155E MET* 1.3 78.1 - - - +
157E LEU* 1.3 56.1 + - - +
160E ASP 3.1 5.9 + - - -
161E ARG 2.9 36.6 + - - -
164E GLN* 3.4 16.7 + - - -
165E PHE* 4.0 6.5 - - - -
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Residues in contact with LEU 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TRP* 3.8 10.6 - - + -
42E VAL* 3.7 29.2 - - + +
43E SER* 4.2 16.7 + - - -
44E TYR* 3.9 15.5 - - + -
47E LEU* 4.2 9.1 - - + +
125E PHE* 3.6 36.3 - - + -
153E LEU 3.3 11.2 + - - +
154E TRP* 3.1 25.6 + - + +
156E GLY* 1.3 76.0 - - - +
158E GLN* 1.3 64.7 + - - +
160E ASP* 3.4 10.7 + - - +
165E PHE* 4.2 2.2 - - + -
261E PRO* 3.8 16.8 - - + -
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Residues in contact with GLN 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 3.9 30.3 + - + +
48E VAL* 6.0 1.6 - - - +
118E LYS* 4.1 29.5 - - - +
154E TRP* 2.8 47.6 + - + +
155E MET* 4.0 8.6 - - - +
157E LEU* 1.3 79.8 - - - +
159E ASN* 1.3 68.2 + - - +
160E ASP* 3.3 1.8 + - - +
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Residues in contact with ASN 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E MET* 2.7 50.1 + - - +
158E GLN* 1.3 85.4 + - - +
160E ASP* 1.3 71.8 + - - +
161E ARG* 3.3 26.4 - - + +
164E GLN* 4.3 3.8 + - - +
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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