Contacts of the helix formed by residues 138 - 148 (chain A) in PDB entry 5V89
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 ASN 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.0 21.7 - - + +
135A GLU* 3.3 21.5 - - + +
136A PRO 3.0 2.9 + - - +
137A GLU* 1.3 76.6 + - - +
139A VAL* 1.3 72.6 + - - +
140A VAL* 2.9 40.3 + - + +
141A MET* 3.0 20.7 + - + +
142A LEU* 3.8 3.1 + - - +
184A ARG* 4.6 9.6 + - - +
223A LEU* 3.9 9.6 - - - +
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Residues in contact with VAL 139 (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 ASN* 1.3 78.9 + - - +
140A VAL* 1.3 67.0 + - + +
142A LEU* 3.0 20.8 + - + +
143A VAL* 3.2 11.4 + - - +
184A ARG* 5.6 4.7 - - + +
187A LEU* 3.7 38.8 - - + -
223A LEU* 3.5 43.3 - - + +
224A LEU* 4.3 14.6 - - + +
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Residues in contact with VAL 140 (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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134A VAL* 4.2 18.2 - - + -
138A ASN* 2.9 24.1 + - + +
139A VAL* 1.3 81.7 - - - +
141A MET* 1.3 64.9 + - + +
143A VAL* 3.3 6.0 + - - +
144A LEU* 2.9 27.8 + - - +
180A LEU* 3.7 45.5 - - + +
183A LEU* 3.7 17.0 - - + -
184A ARG* 3.8 24.0 - - + +
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Residues in contact with MET 141 (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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125A MET* 4.0 22.4 - - + -
128A PHE* 4.1 9.4 - - + -
129A CYS* 3.5 26.7 - - - -
132A ILE* 4.1 22.4 - - - -
134A VAL* 4.1 8.1 - - + -
135A GLU 4.0 13.0 - - - +
136A PRO* 3.7 20.4 - - + +
138A ASN* 3.0 11.4 + - + +
140A VAL* 1.3 79.3 - - + +
142A LEU* 1.3 63.0 + - + +
144A LEU* 3.7 17.9 - - + +
145A ALA* 3.0 27.7 + - - +
156A PHE* 4.5 4.8 - - + -
180A LEU* 6.2 0.4 - - - -
203A PHE* 5.2 0.9 - - - -
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Residues in contact with LEU 142 (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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136A PRO 6.1 0.4 - - - +
138A ASN 4.4 2.7 - - - +
139A VAL* 3.0 17.2 + - + +
141A MET* 1.3 78.4 - - + +
143A VAL* 1.3 60.2 + - - +
145A ALA* 3.3 5.9 + - - +
146A TRP* 3.0 28.6 + - - +
153A MET* 4.7 2.9 - - + -
196A ILE* 4.7 12.5 - - + +
199A TYR* 4.0 5.3 - - + -
200A ALA* 4.6 5.6 - - + -
203A PHE* 3.8 25.8 - - + -
220A MET* 3.9 26.5 - - + +
223A LEU* 4.1 26.2 - - + -
224A LEU* 4.0 33.9 - - + -
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Residues in contact with VAL 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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139A VAL 3.2 14.5 + - - +
140A VAL* 3.6 8.7 - - - +
142A LEU* 1.3 73.9 - - - +
144A LEU* 1.3 65.8 + - - +
146A TRP* 3.2 22.3 + - + +
147A LYS* 2.9 22.2 + - - +
183A LEU* 3.4 43.7 - - + +
186A PHE* 4.2 9.4 - - + -
187A LEU* 3.9 31.9 - - + -
196A ILE* 4.1 9.2 - - + -
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Residues in contact with LEU 144 (chain A).
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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128A PHE* 3.7 35.7 - - + -
132A ILE* 5.2 1.3 - - + -
140A VAL 2.9 17.1 + - - +
141A MET* 3.7 18.8 - - - +
143A VAL* 1.3 76.1 - - - +
145A ALA* 1.3 63.4 + - - +
147A LYS* 3.1 4.6 + - - +
148A LEU* 2.9 43.5 + - + +
156A PHE* 4.1 14.6 - - + -
165A MET* 4.4 4.0 - - + -
168A LEU* 3.9 19.1 - - + -
176A LEU* 4.2 14.8 - - + -
180A LEU* 6.0 1.8 - - + -
183A LEU* 4.1 17.6 - - + +
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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 MET 3.0 16.5 + - - +
142A LEU 3.7 4.3 - - - +
143A VAL 3.3 0.2 - - - -
144A LEU* 1.3 76.4 - - - +
146A TRP* 1.3 62.8 + - - +
148A LEU 3.0 2.4 + - - +
149A ASP 2.9 18.0 + - - -
150A ALA* 3.0 14.3 + - + -
156A PHE* 4.0 18.8 - - + -
199A TYR* 3.3 8.7 - - + +
203A PHE* 3.4 35.9 - - + -
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Residues in contact with TRP 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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142A LEU 3.0 16.6 + - - +
143A VAL* 3.5 15.7 - - + +
145A ALA* 1.3 77.6 - - - +
147A LYS* 1.3 76.7 + - + +
149A ASP* 3.0 19.6 + - - +
186A PHE* 3.6 40.2 - + - -
192A ASN* 4.0 11.4 - - - -
195A LEU* 4.0 38.5 + - + +
196A ILE* 3.5 29.8 - - + -
199A TYR* 3.5 45.4 - + + -
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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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143A VAL 2.9 15.1 + - - +
144A LEU* 3.6 8.1 - - - +
146A TRP* 1.3 91.4 - - + +
148A LEU* 1.3 61.1 + - + +
149A ASP* 3.2 1.8 + - - +
164A GLY* 3.9 11.3 - - - -
167A SER* 4.4 12.5 + - - +
168A LEU* 4.1 32.1 - - + +
182A TYR* 5.3 2.3 + - - -
183A LEU* 4.1 16.6 - - + -
186A PHE* 3.8 32.3 - - + -
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Residues in contact with LEU 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 LEU* 2.9 36.3 + - + +
145A ALA* 3.0 7.1 + - - +
147A LYS* 1.3 77.0 - - - +
149A ASP* 1.3 68.8 + - - +
150A ALA 3.2 2.9 + - - +
156A PHE* 3.9 38.6 - - + -
160A GLU* 3.5 38.0 - - + +
161A TRP* 4.0 20.2 - - + +
163A LYS* 6.1 0.3 - - - +
164A GLY* 3.7 25.1 + - - +
165A MET* 4.1 16.8 - - + +
168A LEU* 4.4 3.4 - - + -
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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