Contacts of the helix formed by residues 189 - 199 (chain A) in PDB entry 5DFV
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 ASP 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A CYS* 3.9 0.4 - - - -
157A CYS 4.9 0.4 - - - -
158A GLY 4.2 2.7 - - - -
159A SER* 3.4 6.1 - - - +
160A SER* 2.7 48.7 + - - +
185A LEU 3.8 3.0 + - - +
186A PHE 4.6 10.8 - - - +
187A LYS 3.5 3.8 + - - -
188A GLU* 1.3 77.0 - - - +
190A CYS* 1.3 70.0 + - - +
191A HIS* 3.3 21.8 + - - +
192A GLN* 3.6 16.3 + - + +
193A LYS* 3.5 21.8 + - - +
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Residues in contact with CYS 190 (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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127A TYR* 3.6 32.8 - - + -
150A PHE 5.5 0.2 - - - -
151A HIS* 3.7 11.2 - - - -
154A LEU* 5.1 5.4 - - + -
156A CYS* 2.0 48.5 - - - -
157A CYS 3.8 2.0 - - - -
158A GLY 3.1 21.4 + - - +
189A ASP* 1.3 72.6 + - - +
191A HIS* 1.3 62.0 + - - +
192A GLN 3.1 1.8 - - - -
193A LYS* 3.0 1.9 + - - +
194A ILE* 2.8 41.6 + - + +
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Residues in contact with HIS 191 (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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124A LYS* 3.4 44.8 + - + +
127A TYR* 4.4 8.3 - + - -
128A ASP* 2.6 43.3 + - - -
159A SER* 3.2 18.0 + - - -
160A SER* 5.3 0.4 - - - +
161A THR* 3.5 29.0 - - + +
189A ASP* 3.7 11.9 - - - +
190A CYS* 1.3 77.7 - - - +
192A GLN* 1.3 56.9 + - - +
194A ILE* 3.5 0.8 + - + +
195A ASP* 3.1 30.7 + - - +
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Residues in contact with GLN 192 (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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189A ASP* 3.6 23.2 + - + +
190A CYS 3.1 0.6 - - - -
191A HIS* 1.3 76.8 - - - +
193A LYS* 1.3 63.4 + - + +
195A ASP* 3.4 16.0 + - - +
196A ASP* 3.0 63.8 + - - +
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Residues in contact with LYS 193 (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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154A LEU* 3.4 37.9 + - + +
155A ASP* 3.1 26.3 + - - +
156A CYS* 4.1 7.9 - - - -
187A LYS 5.4 5.6 + - - -
188A GLU* 5.9 3.0 - - - +
189A ASP 3.5 13.6 + - - +
190A CYS 3.0 7.0 + - - +
192A GLN* 1.3 76.9 - - + +
194A ILE* 1.3 61.2 + - - +
196A ASP* 3.3 11.3 + - - +
197A LEU* 2.9 25.1 + - - +
202A HIS* 3.4 32.3 - - + +
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Residues in contact with ILE 194 (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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120A ALA* 3.7 22.9 - - - +
123A VAL* 4.0 25.6 - - + +
124A LYS* 3.8 33.4 - - + +
127A TYR* 4.4 14.1 - - + -
150A PHE* 4.9 2.9 - - + -
154A LEU* 4.1 19.1 - - + -
190A CYS* 2.8 28.9 + - + +
191A HIS* 3.7 4.5 - - - +
193A LYS* 1.3 74.0 - - - +
195A ASP* 1.3 65.8 + - - +
197A LEU* 3.2 15.4 + - + +
198A PHE* 3.3 26.9 + - + -
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Residues in contact with ASP 195 (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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116A LYS* 4.9 2.9 + - - +
120A ALA* 4.3 10.1 - - - +
124A LYS* 2.8 34.0 + - - -
191A HIS 3.1 14.6 + - - +
192A GLN* 3.4 24.8 - - - +
193A LYS 3.3 0.2 - - - -
194A ILE* 1.3 75.5 - - - +
196A ASP* 1.3 60.7 + - - +
198A PHE* 3.2 6.7 + - - +
199A SER* 2.9 35.5 + - - +
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Residues in contact with ASP 196 (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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192A GLN* 3.0 44.0 + - - +
193A LYS* 3.7 12.0 - - - +
194A ILE 3.2 0.2 - - - -
195A ASP* 1.3 74.0 - - - +
197A LEU* 1.3 65.2 + - - +
199A SER* 4.4 2.7 - - - +
200A GLY* 3.2 4.2 + - - -
201A LYS* 3.1 57.9 + - + +
202A HIS* 3.7 24.5 + - + +
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Residues in contact with LEU 197 (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 VAL* 6.5 0.7 - - + -
154A LEU* 4.4 15.3 - - + -
193A LYS 2.9 14.4 + - - +
194A ILE* 3.2 12.3 + - + +
196A ASP* 1.3 79.3 - - - +
198A PHE* 1.3 70.6 + - + +
199A SER 3.5 0.5 + - - -
200A GLY* 3.6 4.0 + - - -
202A HIS* 3.4 4.9 - - + -
123B VAL* 6.3 0.9 - - + -
146B VAL* 4.6 1.4 - - - +
149B THR* 3.4 33.2 - - + +
150B PHE* 3.3 54.5 - - + -
153B THR* 3.8 21.1 - - + +
154B LEU* 5.6 4.7 - - + -
197B LEU* 5.6 10.1 - - + -
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Residues in contact with PHE 198 (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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116A LYS* 4.0 25.0 - - + +
119A ILE* 3.3 33.9 - - + -
120A ALA* 4.0 22.2 - - + -
123A VAL* 3.8 24.5 - - + -
194A ILE* 3.3 27.0 + - + +
195A ASP 3.2 6.5 + - - +
197A LEU* 1.3 90.1 - - + +
199A SER* 1.3 58.2 + - - +
200A GLY 3.5 0.7 - - - -
123B VAL* 3.9 15.9 - - + -
126B PHE* 3.4 54.9 - + + -
142B ASN* 5.0 1.7 + - - -
146B VAL* 3.8 8.3 - - - +
150B PHE* 4.2 7.6 - + - -
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Residues in contact with SER 199 (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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116A LYS* 2.9 25.9 + - - +
195A ASP* 2.9 20.6 + - - +
196A ASP 3.5 1.5 + - - -
197A LEU 3.3 0.2 - - - -
198A PHE* 1.3 76.0 - - - +
200A GLY* 1.3 64.8 + - - +
201A LYS* 3.5 32.6 + - - +
142B ASN* 3.4 21.1 - - - +
146B VAL* 4.2 1.8 - - - -
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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