Contacts of the helix formed by residues 120 - 126 (chain D) in PDB entry 6ACQ
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 SER 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B ARG* 3.6 26.0 - - - -
92D MET* 3.8 4.4 - - - +
116D THR* 5.7 0.2 - - - -
118D SER 4.3 0.2 + - - -
119D LEU* 1.3 70.8 - - - +
121D ILE* 1.3 62.9 + - - +
122D THR* 3.3 3.8 + - - -
123D GLU* 3.1 29.8 + - - +
124D VAL* 3.1 25.4 + - - +
181D GLU* 2.5 29.3 + - - -
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D SER* 4.5 8.7 - - - +
116D THR* 4.1 23.6 - - + +
119D LEU 3.4 4.0 + - - +
120D SER* 1.3 71.2 - - - +
122D THR* 1.3 58.7 + - - +
124D VAL* 3.2 8.1 + - - +
125D ALA* 2.9 27.5 + - + +
134D VAL* 4.0 10.8 - - + +
135D ILE* 3.8 29.6 - - - +
136D GLY* 3.5 22.7 - - - -
152D ILE* 3.6 30.3 - - + -
154D GLY* 3.9 16.6 - - - +
181D GLU* 3.3 10.5 + - + +
185D PHE* 5.4 3.8 - - + -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LYS* 3.5 19.9 - - - +
265B ARG* 3.6 7.3 - - + +
266B ALA* 3.3 38.6 - - + +
120D SER* 3.5 5.2 - - - -
121D ILE* 1.3 77.7 - - - +
123D GLU* 1.3 62.1 + - - +
125D ALA* 3.4 8.7 + - - +
126D SER* 3.3 16.8 + - - -
154D GLY* 4.5 3.1 - - - -
155D ILE* 3.1 27.6 + - + +
156D ALA* 6.1 0.7 - - + +
181D GLU* 2.7 26.2 + - - -
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ARG* 3.2 48.6 + - + +
92D MET* 3.9 28.4 - - + +
96D LYS* 3.7 28.8 + - - +
120D SER* 3.1 17.7 + - - +
122D THR* 1.3 79.1 - - - +
124D VAL* 1.3 63.4 + - - +
126D SER* 3.1 17.3 - - - -
127D ALA 4.0 1.6 + - - -
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D MET* 3.6 26.5 - - + -
95D LYS* 4.3 24.0 - - + +
96D LYS* 4.4 7.4 - - + -
99D PHE* 3.5 46.2 - - + -
114D SER* 5.9 3.4 - - - +
116D THR* 6.5 0.9 - - + -
119D LEU* 5.4 1.6 - - + -
120D SER 3.1 12.9 + - - +
121D ILE* 3.5 10.1 - - - +
123D GLU* 1.3 74.8 - - - +
125D ALA* 1.3 56.8 + - - +
126D SER 3.0 1.6 - - - -
127D ALA* 2.8 32.2 + - - +
128D THR* 4.1 3.1 - - - +
134D VAL* 4.8 2.0 - - + -
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ILE* 2.9 17.0 + - + +
122D THR* 3.6 9.2 - - - +
124D VAL* 1.3 76.9 - - - +
126D SER* 1.3 57.3 + - - +
127D ALA 3.0 0.2 - - - -
128D THR* 2.8 32.7 + - - +
131D PRO* 4.0 22.1 - - + +
134D VAL* 3.6 35.4 - - + -
154D GLY* 6.3 0.9 - - - -
156D ALA* 5.8 2.2 - - + -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ARG 2.7 25.4 + - - -
266B ALA* 3.2 21.0 + - - -
267B GLY* 4.7 0.7 - - - -
96D LYS* 5.7 2.5 - - - -
122D THR 3.3 2.4 + - - -
123D GLU* 3.1 16.6 - - - -
125D ALA* 1.3 78.3 - - - +
127D ALA* 1.3 57.6 + - - +
128D THR 3.2 5.7 - - - +
129D LYS* 4.8 5.0 + - - -
131D PRO* 5.8 2.5 - - - -
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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