Contacts of the helix formed by residues 128 - 138 (chain A) in PDB entry 6R4F
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.2 11.3 - - - +
127A THR* 1.3 72.0 + - - +
129A TYR* 1.3 62.7 + - - +
130A LYS 3.2 3.4 - - - +
131A ASP* 3.2 21.1 + - + +
132A LEU* 3.1 34.2 + - - +
180A GLN 2.7 28.3 + - - -
182A GLU* 2.8 49.0 + - - +
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Residues in contact with TYR 129 (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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99A HIS* 4.1 26.0 + + - -
126A ILE* 3.4 26.6 + - + +
127A THR 3.1 6.2 + - - -
128A ASN* 1.3 77.5 + - - +
130A LYS* 1.3 88.8 + - + +
132A LEU* 4.0 6.5 - - - -
133A LYS* 3.2 38.9 + - + +
146A GLU 4.2 14.2 + - - -
147A THR 4.4 5.6 - - - -
148A ASP* 3.5 41.3 - - + -
151A THR* 3.9 12.7 - - + +
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Residues in contact with LYS 130 (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 THR 5.5 3.1 - - - +
128A ASN* 3.2 1.2 - - - +
129A TYR* 1.3 106.9 - - + +
131A ASP* 1.3 66.3 + - - +
133A LYS* 3.5 5.4 + - - +
134A LYS* 3.4 34.8 + - - +
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Residues in contact with ASP 131 (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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128A ASN* 3.2 22.0 + - + +
130A LYS* 1.3 79.4 - - - +
132A LEU* 1.3 65.8 + - + +
134A LYS* 3.1 17.2 + - - +
135A PHE* 3.1 21.2 + - - +
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Residues in contact with LEU 132 (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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126A ILE* 4.0 7.9 - - + -
128A ASN* 3.1 33.9 + - - +
129A TYR* 4.1 5.6 - - - +
131A ASP* 1.3 76.8 - - + +
133A LYS* 1.3 62.9 + - - +
135A PHE* 3.1 11.5 + - + +
136A LEU* 3.0 33.3 + - + +
151A THR* 4.4 16.4 - - - +
155A LEU* 4.5 13.5 - - + -
180A GLN* 3.7 29.4 - - + +
181A LEU* 3.7 28.9 - - + -
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Residues in contact with LYS 133 (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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129A TYR* 3.2 34.8 + - + +
130A LYS* 3.8 6.3 - - - +
131A ASP 3.3 0.2 - - - -
132A LEU* 1.3 79.0 - - - +
134A LYS* 1.3 56.8 + - + +
137A GLU* 3.0 59.0 + - - +
143A PHE* 3.7 46.8 - - + +
145A SER 4.3 13.1 + - - -
146A GLU* 5.4 3.8 - - - +
151A THR* 3.9 5.8 - - + +
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Residues in contact with LYS 134 (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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130A LYS* 3.4 22.9 + - - +
131A ASP* 3.1 19.5 + - - +
133A LYS* 1.3 76.5 - - + +
135A PHE* 1.3 66.5 + - - +
137A GLU* 3.2 13.1 + - - +
138A SER* 2.9 25.1 + - - -
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Residues in contact with PHE 135 (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 ASP 3.1 11.6 + - - +
132A LEU* 3.1 14.3 + - + +
134A LYS* 1.3 75.6 - - - +
136A LEU* 1.3 71.9 + - + +
138A SER* 2.5 24.5 + - - -
139A LYS* 3.3 24.1 - - - +
155A LEU* 4.9 7.4 - - + -
158A TYR* 3.3 52.3 - + - -
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Residues in contact with LEU 136 (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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132A LEU* 3.0 22.2 + - + +
135A PHE* 1.3 82.3 - - + +
137A GLU* 1.3 60.1 + - - +
139A LYS* 2.9 16.9 + - - -
140A GLY 3.2 0.5 + - - -
141A TYR* 3.1 39.8 + - + -
143A PHE* 3.9 15.5 - - + -
151A THR* 3.7 11.4 - - - +
154A LYS* 3.6 30.1 - - + +
155A LEU* 3.7 23.8 - - + +
158A TYR* 3.7 35.2 - - + -
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Residues in contact with GLU 137 (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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133A LYS* 3.0 57.0 + - - +
134A LYS* 3.7 11.3 - - - +
136A LEU* 1.3 75.4 - - - +
138A SER* 1.3 58.5 + - - +
140A GLY* 3.0 19.4 + - - -
141A TYR 3.3 21.3 - - - +
142A ASP* 5.1 3.6 - - - +
143A PHE* 3.8 12.3 + - + +
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Residues in contact with SER 138 (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 LYS 2.9 12.1 + - - -
135A PHE* 2.5 31.6 + - - -
137A GLU* 1.3 75.9 - - - +
139A LYS* 1.3 64.2 + - - +
140A GLY 3.3 1.0 + - - -
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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