Contacts of the helix formed by residues 124 - 137 (chain A) in PDB entry 6DC0
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 ILE 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A PHE 3.6 1.2 + - - -
123A PRO* 1.3 70.4 - - + +
125A LYS* 1.3 83.6 + - + +
126A HIS 3.1 1.4 + - - -
127A TYR* 3.3 28.3 + - + -
128A GLN* 4.5 2.6 + - - +
151A LEU* 4.6 8.7 - - + -
152A GLY 3.5 15.7 - - - +
153A GLU 3.3 16.8 - - - +
154A THR* 2.9 39.0 + - + +
155A LYS 3.4 28.3 - - - +
156A ALA* 3.7 8.1 - - + +
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Residues in contact with LYS 125 (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 PRO* 3.0 5.7 + - + +
124A ILE* 1.3 94.5 - - + +
126A HIS* 1.3 77.7 + - + +
128A GLN* 5.1 3.0 + - - +
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Residues in contact with HIS 126 (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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122A PHE* 4.9 3.1 - - + -
123A PRO* 2.9 21.9 + - + +
125A LYS* 1.3 94.6 - - + +
127A TYR* 1.3 66.3 + - - +
128A GLN 3.3 3.5 + - - -
129A ASP* 3.8 10.7 + - + +
130A LYS* 3.7 23.7 + - - +
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Residues in contact with TYR 127 (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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122A PHE* 4.0 22.7 - - + -
123A PRO 3.2 4.9 + - - +
124A ILE* 3.3 23.7 + - + +
126A HIS* 1.3 77.0 - - - +
128A GLN* 1.3 94.1 + - + +
130A LYS* 3.2 13.9 + - - +
131A ILE* 3.3 43.3 + - + +
149A VAL* 4.1 17.9 - - + +
151A LEU* 3.6 24.8 - - + +
156A ALA* 3.4 32.5 - - + -
158A VAL* 4.8 4.0 - - + -
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Residues in contact with GLN 128 (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 ILE 4.5 2.9 + - - +
125A LYS 5.1 2.4 + - - +
126A HIS* 3.3 1.6 - - - +
127A TYR* 1.3 115.3 + - + +
129A ASP* 1.3 67.7 + - - +
131A ILE* 3.4 8.2 + - - +
132A ARG* 3.3 23.5 + - - +
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Residues in contact with ASP 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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126A HIS* 3.8 8.0 + - + +
128A GLN* 1.3 78.7 - - - +
130A LYS* 1.3 68.0 + - - +
132A ARG* 3.4 33.6 + - - +
133A PRO* 3.9 3.6 - - - +
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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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122A PHE* 3.7 37.5 - - + -
126A HIS* 3.7 20.8 + - + +
127A TYR 3.2 10.5 + - - +
129A ASP* 1.3 79.5 - - - +
131A ILE* 1.3 60.7 + - - +
133A PRO* 3.4 12.6 - - - +
134A TYR* 4.2 5.9 - - - -
227A GLU* 3.9 47.4 - - + +
228A ASP* 4.9 11.0 - - - -
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Residues in contact with ILE 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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122A PHE* 4.8 3.1 - - + -
127A TYR* 3.3 36.4 + - + +
128A GLN* 3.7 11.2 - - - +
129A ASP 3.3 0.2 - - - -
130A LYS* 1.3 79.9 - - + +
132A ARG* 1.3 65.7 + - - +
133A PRO* 3.2 4.5 - - - -
134A TYR* 3.1 23.1 + - + +
135A ILE* 3.0 32.6 + - + +
146A ILE* 3.6 28.5 - - + -
149A VAL* 4.3 9.4 - - + -
158A VAL* 4.2 23.3 - - + -
160A PHE* 6.0 0.2 - - + -
227A GLU* 5.5 1.3 - - - +
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Residues in contact with ARG 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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128A GLN* 3.3 20.0 + - + +
129A ASP* 3.4 27.8 + - - +
131A ILE* 1.3 74.8 - - - +
133A PRO* 1.3 68.7 - - + +
135A ILE* 3.2 11.8 + - + +
136A GLN* 3.1 43.7 + - - +
231A ILE* 3.5 44.3 - - + +
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Residues in contact with PRO 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 ASP 3.9 4.0 - - - +
130A LYS 3.4 12.3 - - - +
131A ILE 3.2 5.2 - - - -
132A ARG* 1.3 95.2 - - + +
134A TYR* 1.3 56.7 + - + +
136A GLN 3.3 0.7 + - - +
137A LEU* 2.9 33.4 + - - +
201A ILE* 3.6 10.6 - - + +
226A LEU* 3.8 33.4 - - + +
227A GLU 5.3 2.7 - - - +
229A THR* 3.8 21.1 - - - +
231A ILE* 3.7 21.7 - - + -
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Residues in contact with TYR 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 4.2 11.2 - - - -
131A ILE* 3.1 24.6 + - + +
133A PRO* 1.3 76.8 - - + +
135A ILE* 1.3 58.2 + - + +
137A LEU* 3.0 24.3 - - - +
143A ILE* 5.7 0.2 - - + -
144A THR 3.2 26.5 - - - -
145A GLY* 4.5 2.0 - - - -
146A ILE* 3.8 32.1 - - + +
160A PHE* 3.5 24.2 - + - -
225A SER* 3.6 6.1 - - - -
226A LEU* 2.9 48.3 + - + +
227A GLU* 2.7 30.9 + - - -
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Residues in contact with ILE 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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128A GLN 5.4 0.2 - - - +
131A ILE* 3.0 56.5 - - + +
132A ARG* 3.2 10.8 + - + +
134A TYR* 1.3 82.0 - - + +
136A GLN* 1.3 78.7 + - - +
137A LEU 3.4 4.5 + - - +
146A ILE* 5.2 1.1 - - + -
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Residues in contact with GLN 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 ARG* 3.1 35.3 + - - +
133A PRO 3.3 4.0 + - - +
135A ILE* 1.3 110.4 - - - +
137A LEU* 1.3 58.7 - - - +
138A PRO* 3.5 8.1 - - - +
199A SER* 4.7 8.9 - - - +
201A ILE* 4.3 12.1 - - + -
231A ILE* 3.8 23.4 - - + +
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Residues in contact with LEU 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 PRO 2.9 17.2 + - - +
134A TYR* 3.0 18.4 - - - +
135A ILE 3.8 4.0 - - - +
136A GLN* 1.3 78.1 - - - +
138A PRO* 1.3 75.9 - - + +
139A SER* 3.7 1.6 + - - -
143A ILE* 3.8 35.7 - - + -
195A HIS* 3.7 19.3 - - + +
196A CYS* 3.8 26.9 - - - -
199A SER* 3.5 29.4 - - - +
201A ILE* 3.7 11.0 - - + -
226A LEU* 3.9 11.7 - - + -
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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