Contacts of the helix formed by residues 145 - 153 (chain A) in PDB entry 1EE8
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 PRO 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ALA 3.9 1.3 - - - +
144A ARG* 1.3 92.5 - - + +
146A LEU* 1.3 68.9 + - - +
147A LYS* 4.5 1.6 - - + +
148A ALA* 2.9 29.5 + - + +
149A LEU* 3.4 4.2 + - - +
175A PRO 3.8 11.9 - - - +
176A PHE* 3.9 18.6 - - + +
177A ARG 3.5 9.0 - - - +
178A PRO* 4.4 0.2 - - + -
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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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139A LEU* 4.1 15.5 - - + -
144A ARG 3.4 1.0 + - - -
145A PRO* 1.3 71.2 - - - +
147A LYS* 1.3 64.7 + - - +
149A LEU* 3.0 15.8 + - - +
150A LEU* 3.2 11.4 + - + +
168A LEU* 3.6 25.1 - - + -
173A LEU* 4.2 9.6 - - + -
174A SER 3.7 19.1 - - - +
175A PRO* 3.5 1.2 + - + +
177A ARG* 2.8 19.3 + - + +
179A ALA* 3.8 19.7 - - - +
182A LEU* 3.6 35.9 - - + -
190A LEU* 3.6 23.8 - - + -
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Residues in contact with LYS 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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145A PRO* 5.5 1.1 - - + -
146A LEU* 1.3 79.9 - - - +
148A ALA* 1.3 57.6 + - - +
150A LEU* 2.9 20.9 + - - +
151A LEU* 3.0 25.1 + - + +
161A ASN* 3.0 28.8 + - - +
164A ALA* 4.2 15.0 - - + -
165A ASP* 2.6 32.1 + - - +
168A LEU* 3.9 19.5 - - + -
175A PRO* 3.1 19.6 + - + +
176A PHE* 6.1 0.4 - - + -
253A ARG* 5.4 1.7 - - - +
254A GLY 3.1 9.3 + - - -
255A THR* 2.8 36.1 + - + +
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Residues in contact with ALA 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 ARG* 3.8 32.2 + - + +
145A PRO* 2.9 29.3 + - + +
147A LYS* 1.3 76.9 - - - +
149A LEU* 1.3 59.4 + - - +
151A LEU* 3.3 10.2 + - - +
152A ASP* 3.0 22.9 + - - +
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Residues in contact with LEU 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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138A GLY 3.5 15.5 - - - +
139A LEU* 3.6 17.7 - - + -
142A SER* 3.1 43.3 - - - +
144A ARG* 3.6 32.1 - - + +
145A PRO 3.4 1.9 + - - +
146A LEU 3.0 13.1 + - - +
148A ALA* 1.3 79.1 - - - +
150A LEU* 1.3 64.9 + - - +
152A ASP* 3.7 16.3 + - - +
153A GLN 4.6 0.5 + - - -
155A LEU* 3.7 33.6 - - + +
156A ALA 5.0 0.5 + - - -
179A ALA* 3.3 18.2 - - + -
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Residues in contact with LEU 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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135A PHE* 4.4 14.1 - - + -
139A LEU* 5.3 2.2 - - + -
146A LEU* 3.2 13.4 + - + +
147A LYS 2.9 8.1 + - - +
149A LEU* 1.3 79.6 - - - +
151A LEU* 1.3 61.5 + - - +
152A ASP 3.5 0.4 + - - -
153A GLN 4.4 0.4 + - - -
156A ALA* 4.0 12.9 - - + +
159A VAL* 3.4 25.7 - - + +
164A ALA* 4.1 22.9 - - + +
167A ALA* 5.1 3.1 - - + -
168A LEU* 3.6 42.4 - - + -
190A LEU* 4.1 24.2 - - + -
194A LEU* 4.2 22.9 - - + -
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Residues in contact with LEU 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 LYS* 3.0 27.1 + - + +
148A ALA* 3.3 9.2 + - - +
149A LEU 3.2 0.2 - - - -
150A LEU* 1.3 78.9 - - - +
152A ASP* 1.3 66.1 + - - +
153A GLN* 3.2 16.3 + - - +
159A VAL 4.1 6.1 - - - +
160A GLY* 3.6 19.5 - - - +
161A ASN* 3.8 11.7 - - - +
164A ALA* 3.5 31.2 - - + -
253A ARG* 3.6 35.0 - - + +
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Residues in contact with ASP 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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117A LEU* 5.1 6.8 - - - +
120A ARG* 5.8 0.9 + - - -
144A ARG* 3.0 34.5 + - - -
148A ALA 3.0 7.6 + - - +
149A LEU* 3.8 16.0 - - - +
150A LEU 3.5 0.8 - - - -
151A LEU* 1.3 77.1 - - - +
153A GLN* 1.3 67.4 + - - +
154A ARG* 3.0 43.5 + - + +
155A LEU* 4.4 3.5 - - + +
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Residues in contact with GLN 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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51A GLY* 4.6 1.6 - - - -
52A LYS* 3.0 41.1 + - - +
117A LEU* 5.0 13.7 - - + +
121A LEU* 3.7 26.1 - - + +
122A GLY 2.9 19.4 + - - -
149A LEU 4.6 0.6 + - - -
150A LEU 4.4 1.2 + - - -
151A LEU 3.2 15.2 + - - +
152A ASP* 1.3 77.4 - - - +
154A ARG* 1.3 58.8 + - - +
155A LEU 3.1 3.2 - - - +
156A ALA 3.4 26.1 + - - +
157A ALA* 3.6 7.8 + - - -
158A GLY* 2.7 27.4 + - - -
159A VAL 3.8 7.4 + - - +
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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