Contacts of the helix formed by residues 142 - 153 (chain G) in PDB entry 4GEK
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 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119G ARG* 2.8 46.9 + - + +
138G LEU* 3.8 15.1 - - + +
139G GLU* 2.9 41.5 + - - +
141G SER* 1.3 85.5 - - - +
143G ARG* 1.3 64.0 + - - +
144G GLN 3.4 2.2 + - - -
145G ALA* 3.6 10.5 + - - +
146G LEU* 3.4 19.9 + - - +
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Residues in contact with ARG 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G LEU* 3.1 48.7 + - + +
136G GLN* 3.2 19.1 + - - +
138G LEU* 2.9 25.9 + - + -
139G GLU 3.6 8.3 - - - +
140G PRO* 3.1 35.6 + - - +
142G GLU* 1.3 75.3 - - - +
144G GLN* 1.3 67.1 + - - +
146G LEU* 3.3 4.2 + - - +
147G LEU* 3.1 24.5 + - - +
164G GLU* 5.5 0.8 + - - -
207G LEU* 2.8 31.9 + - - +
208G THR* 4.7 0.2 - - - +
209G ASP* 2.9 36.9 + - - -
214G HIS* 5.7 0.2 - - - -
217G ARG* 3.9 19.5 - - - +
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Residues in contact with GLN 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G PRO 4.5 1.8 + - - -
141G SER 4.9 4.3 + - - +
142G GLU 3.4 0.4 - - - -
143G ARG* 1.3 79.4 - - - +
145G ALA* 1.3 57.1 + - - +
147G LEU* 3.1 3.7 + - - +
148G ASP* 2.8 64.6 + - - +
217G ARG* 3.1 58.9 + - - +
220G LYS* 3.9 29.7 - - + +
221G ALA* 3.5 9.5 - - - +
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G SER 5.4 1.9 + - - +
142G GLU* 3.6 12.3 + - - +
143G ARG 3.4 0.8 - - - -
144G GLN* 1.3 77.5 - - - +
146G LEU* 1.3 62.7 + - - +
148G ASP* 3.4 11.4 + - - +
149G LYS* 3.0 23.5 + - - +
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Residues in contact with LEU 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 4.4 8.3 - - + -
118G ILE* 3.5 51.4 - - + +
119G ARG* 5.1 3.8 - - + -
121G ILE* 5.8 0.2 - - + -
123G ILE* 5.7 0.2 - - + -
131G LEU* 4.1 12.8 - - + -
135G LEU* 3.9 14.8 - - + -
138G LEU* 3.8 16.8 - - + -
142G GLU 3.4 9.5 + - - +
143G ARG 3.3 8.6 + - - +
144G GLN 3.2 0.6 - - - -
145G ALA* 1.3 78.1 - - - +
147G LEU* 1.3 58.1 + - - +
149G LYS* 3.2 19.4 + - - +
150G ILE* 2.9 49.2 + - + +
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Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 4.0 21.3 - - + -
135G LEU* 4.2 20.0 - - + -
143G ARG 3.1 15.3 + - - +
144G GLN* 3.7 6.7 - - - +
146G LEU* 1.3 76.3 - - - +
148G ASP* 1.3 63.4 + - - +
150G ILE* 3.3 5.4 + - + +
151G TYR* 2.9 24.4 + - - +
160G LEU* 3.8 28.5 - - + -
162G LEU* 4.6 6.5 - - + -
214G HIS* 5.4 0.7 - - - +
217G ARG* 3.6 35.9 - - + +
218G LEU* 4.2 15.9 - - + -
221G ALA* 3.7 15.0 - - + +
223G PHE* 4.3 2.5 - - + -
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Residues in contact with ASP 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G GLN* 2.8 56.7 + - - +
145G ALA* 3.6 8.8 - - - +
147G LEU* 1.3 72.2 - - - +
149G LYS* 1.3 61.5 + - - +
151G TYR* 3.3 2.6 + - - +
152G GLN* 3.0 31.9 + - + +
220G LYS* 4.3 4.8 - - - +
221G ALA* 3.2 20.7 - - - +
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Residues in contact with LYS 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ILE 2.9 21.0 + - - -
119G ARG* 3.1 21.8 + - - +
120G ASP 3.8 1.2 - - - -
121G ILE* 2.8 31.7 + - - +
122G ALA* 4.7 3.8 - - - -
123G ILE* 4.0 19.7 - - + +
145G ALA 3.0 16.1 + - - +
146G LEU* 3.2 23.8 + - - +
148G ASP* 1.3 75.2 - - - +
150G ILE* 1.3 64.0 + - - +
152G GLN* 3.4 6.3 + - - +
153G GLY* 2.9 21.3 + - - -
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Residues in contact with ILE 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 3.7 20.6 - - + -
123G ILE* 4.3 14.2 - - + +
129G VAL* 3.9 35.7 - - + -
131G LEU* 3.6 31.2 - - + -
146G LEU* 2.9 31.9 + - + +
147G LEU* 3.3 9.6 + - + +
149G LYS* 1.3 75.9 - - - +
151G TYR* 1.3 64.4 + - - +
153G GLY 3.1 2.1 + - - -
154G LEU* 2.9 33.7 + - + +
160G LEU* 4.2 15.0 - - + -
223G PHE* 4.4 0.9 - - + -
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Residues in contact with TYR 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G LEU 2.9 16.6 + - - +
148G ASP 3.3 2.2 + - - +
150G ILE* 1.3 78.4 - - - +
152G GLN* 1.3 81.0 + - + +
154G LEU* 3.4 5.3 + - - +
221G ALA 3.3 25.1 - - - +
222G GLY* 3.1 22.4 - - - -
223G PHE* 3.6 42.1 - + + -
224G GLU* 2.6 28.8 + - - -
242G LYS* 2.8 64.0 + - + +
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Residues in contact with GLN 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G ASP* 3.0 22.7 + - + +
149G LYS* 3.8 6.7 - - - +
151G TYR* 1.3 100.2 - - + +
153G GLY* 1.3 59.9 + - - +
154G LEU 3.8 1.0 - - - +
221G ALA 4.8 1.9 - - - +
242G LYS* 3.5 12.9 + - - +
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Residues in contact with GLY 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ILE* 3.3 32.6 - - - +
124G GLU* 5.0 0.4 - - - -
125G ASN 3.6 9.4 + - - -
126G ALA* 3.3 19.9 + - - +
149G LYS 2.9 13.2 + - - -
150G ILE 3.1 2.9 + - - -
152G GLN* 1.3 74.7 - - - +
154G LEU* 1.3 63.8 + - - +
155G ASN* 3.6 1.4 + - - +
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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