Contacts of the helix formed by residues 142 - 153 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ARG* 2.8 48.1 + - + +
138A LEU* 3.8 14.7 - - + +
139A GLU* 2.8 46.7 + - + +
141A SER* 1.4 82.0 - - - +
143A ARG* 1.3 63.2 + - - +
144A GLN 3.4 1.6 - - - -
145A ALA* 3.6 10.6 + - - +
146A LEU* 3.4 20.4 + - - +
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.1 46.5 + - + +
136A GLN* 3.2 18.5 + - - +
138A LEU* 2.8 26.9 + - + -
139A GLU 3.6 5.6 - - - +
140A PRO* 3.1 40.3 + - - +
142A GLU* 1.3 75.9 - - - +
144A GLN* 1.4 66.4 + - - +
146A LEU* 3.2 4.3 + - - +
147A LEU* 3.1 28.0 + - - +
164A GLU* 5.5 0.6 + - - -
207A LEU* 2.8 32.0 + - - +
208A THR* 4.7 0.2 - - - +
209A ASP* 2.9 42.7 + - - -
217A ARG* 3.9 17.3 - - - +
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PRO 4.5 1.6 + - - -
141A SER 4.8 5.0 + - - +
142A GLU 3.4 0.2 - - - -
143A ARG* 1.4 79.9 - - - +
145A ALA* 1.4 52.0 + - - +
147A LEU* 3.2 3.1 + - - +
148A ASP* 2.8 69.9 + - - +
217A ARG* 3.0 58.0 + - - +
220A LYS* 3.8 31.2 - - - +
221A ALA* 3.5 9.7 - - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER 5.3 1.7 + - - +
142A GLU* 3.6 11.9 + - - +
143A ARG 3.4 0.6 - - - -
144A GLN* 1.4 77.4 - - - +
146A LEU* 1.3 63.7 + - - +
148A ASP* 3.4 11.3 + - - +
149A LYS* 3.0 23.8 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.4 8.1 - - + -
118A ILE* 3.5 50.5 - - + +
119A ARG* 5.1 4.0 - - + -
121A ILE* 5.3 0.2 - - + -
123A ILE* 5.7 0.2 - - + -
131A LEU* 4.0 13.7 - - + -
135A LEU* 3.9 14.1 - - + -
138A LEU* 3.8 17.9 - - + -
142A GLU 3.4 10.2 + - - +
143A ARG 3.2 8.8 + - - +
144A GLN 3.2 0.6 - - - -
145A ALA* 1.3 80.3 - - - +
147A LEU* 1.3 57.2 + - - +
149A LYS* 3.2 19.6 + - - +
150A ILE* 2.9 47.7 + - + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.9 21.8 - - + -
135A LEU* 4.1 22.2 - - + -
143A ARG 3.1 16.3 + - - +
144A GLN* 3.7 5.4 - - - +
146A LEU* 1.3 72.5 - - - +
148A ASP* 1.4 66.3 + - - +
150A ILE* 3.3 5.2 + - + +
151A TYR* 3.0 19.9 + - - +
160A LEU* 3.9 28.0 - - + -
162A LEU* 4.7 6.5 - - + -
214A HIS* 5.9 0.7 - - - +
217A ARG* 3.7 33.2 - - + +
218A LEU* 4.3 15.3 - - + -
221A ALA* 3.5 21.0 - - + +
223A PHE* 4.3 2.9 - - + -
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLN* 2.8 58.7 + - - +
145A ALA* 3.6 9.5 - - - +
146A LEU 3.2 0.2 - - - -
147A LEU* 1.4 70.8 - - - +
149A LYS* 1.3 57.6 + - - +
151A TYR* 3.3 2.6 + - - +
152A GLN* 3.0 37.6 + - + +
220A LYS* 4.2 3.5 - - - +
221A ALA* 3.2 20.5 - - - +
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE 2.9 20.4 + - - -
119A ARG* 3.2 21.6 + - - +
120A ASP 3.9 1.2 - - - -
121A ILE* 2.7 30.6 + - - +
122A ALA* 4.7 4.7 - - - -
123A ILE* 4.0 19.5 - - + +
145A ALA 3.0 16.3 + - - +
146A LEU* 3.2 24.0 + - - +
148A ASP* 1.3 76.8 - - - +
150A ILE* 1.3 56.7 + - - +
152A GLN* 3.4 6.6 + - - +
153A GLY* 2.9 26.3 + - - -
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.8 21.1 - - + -
123A ILE* 4.3 14.6 - - + +
129A VAL* 3.9 33.9 - - + -
131A LEU* 3.7 29.6 - - + -
146A LEU* 2.9 32.3 + - + +
147A LEU* 3.3 10.3 + - + +
149A LYS* 1.3 75.3 - - - +
151A TYR* 1.3 66.9 + - - +
153A GLY 3.2 0.9 + - - -
154A LEU* 3.0 34.1 + - + +
160A LEU* 4.2 15.7 - - + -
223A PHE* 4.3 0.7 - - + -
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU 3.0 15.3 + - - +
148A ASP 3.3 1.5 + - - +
150A ILE* 1.3 79.3 - - - +
152A GLN* 1.4 76.1 + - + +
154A LEU* 3.4 2.9 + - - +
221A ALA 3.2 26.0 - - - +
222A GLY* 3.2 21.7 + - - -
223A PHE* 3.6 42.4 - + + -
224A GLU* 2.6 27.6 + - - -
242A LYS* 2.8 65.3 + - + +
246A ALA* 3.8 12.1 - - - +
247A ALA* 5.1 3.3 + - - -
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASP* 3.0 22.3 + - + +
149A LYS* 3.8 7.0 - - - +
151A TYR* 1.4 100.0 - - - +
153A GLY* 1.4 58.9 + - - +
154A LEU 3.7 0.9 - - - +
221A ALA 4.7 2.1 - - - +
242A LYS* 3.4 14.9 + - - +
247A ALA* 5.5 3.8 + - - -
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.2 32.8 - - - +
125A ASN 3.7 9.7 + - - -
126A ALA* 3.3 18.2 + - - +
149A LYS 2.9 15.4 + - - -
150A ILE 3.2 1.7 + - - -
152A GLN* 1.4 73.0 - - - +
154A LEU* 1.3 66.0 + - - +
155A ASN* 3.6 1.2 + - - +
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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