Contacts of the helix formed by residues 122 - 130 (chain D) in PDB entry 6AHU
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 GLN 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ASP* 4.0 4.4 + - - -
121D THR* 1.3 81.7 - - + +
123D PRO* 1.3 68.3 - - - +
124D GLN* 3.1 3.6 - - + +
125D MET* 2.9 55.5 + - + +
126D ILE* 3.4 5.9 + - - +
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Residues in contact with PRO 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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120D ASP* 5.3 8.5 - - - +
121D THR 4.1 4.5 - - - +
122D GLN* 1.3 86.7 - - - +
124D GLN* 1.3 62.3 + - + +
125D MET 3.2 0.2 - - - -
126D ILE* 3.6 10.3 + - + +
127D GLN* 3.4 12.3 + - - +
191D PHE* 4.8 11.4 - - + -
243J SER* 3.0 34.7 + - - +
245J VAL* 4.9 15.9 - - + -
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Residues in contact with GLN 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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122D GLN* 3.1 3.0 - - + -
123D PRO* 1.3 79.7 - - + +
125D MET* 1.3 61.7 + - - +
126D ILE 3.4 0.2 - - - -
127D GLN* 3.4 25.3 + - - +
128D ALA* 3.3 22.9 + - - +
98J ARG* 2.6 58.1 + - - +
236J LYS* 3.9 17.4 + - - +
237J THR* 4.4 5.8 - - + +
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Residues in contact with MET 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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114D CYS* 4.7 26.0 - - + +
121D THR* 5.8 3.4 - - - -
122D GLN* 2.9 42.4 + - + +
124D GLN* 1.3 77.8 - - - +
126D ILE* 1.3 61.9 + - + +
128D ALA* 3.8 4.6 - - + +
129D LYS* 3.0 61.5 + - + +
9K GLU* 5.8 0.9 - - - +
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Residues in contact with ILE 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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110D ILE* 6.3 3.1 - - + -
114D CYS* 3.7 35.2 - - + -
116D GLY 4.9 3.1 - - - +
117D LEU* 5.0 4.3 - - + -
121D THR 4.2 4.9 - - - +
122D GLN 3.4 15.4 + - - +
123D PRO* 3.6 7.6 + - + +
124D GLN 3.4 0.4 - - - -
125D MET* 1.3 79.4 - - + +
127D GLN* 1.3 60.1 + - - +
128D ALA 3.4 0.3 + - - -
129D LYS* 3.6 4.5 + - + +
130D LEU* 3.4 36.8 + - + +
188D THR* 5.8 4.0 - - + +
191D PHE* 4.1 49.4 - - + -
243J SER* 4.7 6.7 - - - +
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Residues in contact with GLN 127 (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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123D PRO 3.4 9.9 + - - +
124D GLN* 3.4 31.2 - - - +
126D ILE* 1.3 77.8 - - - +
128D ALA* 1.3 60.1 + - + +
130D LEU* 4.2 3.8 - - - -
131D LEU* 3.5 19.4 + - - +
237J THR* 3.0 42.1 + - - +
238J ALA* 3.9 8.5 - - + +
241J ILE* 2.9 50.4 - - + +
242J ILE* 3.5 2.9 - - - -
243J SER* 3.1 28.2 + - - +
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Residues in contact with ALA 128 (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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124D GLN 3.3 17.9 + - - +
125D MET* 3.2 7.3 + - + +
126D ILE 3.2 0.6 - - - -
127D GLN* 1.3 78.9 - - + +
129D LYS* 1.3 67.2 + - + +
130D LEU 3.3 1.8 - - - -
131D LEU* 3.4 31.3 + - + +
132D LYS* 4.5 7.8 + - - -
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Residues in contact with LYS 129 (chain D).
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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113D LEU* 3.8 25.2 - - + +
114D CYS* 6.2 2.2 - - + -
125D MET* 3.0 52.2 + - + +
126D ILE* 3.6 5.6 + - + +
128D ALA* 1.3 77.3 - - + +
130D LEU* 1.3 61.7 + - + +
131D LEU 3.2 2.6 + - - -
132D LYS* 3.8 10.4 + - - +
133D ALA* 3.3 5.7 + - - +
9K GLU* 3.6 42.8 + - + +
13K ARG* 2.8 30.9 + - - +
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Residues in contact with LEU 130 (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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106D TRP* 5.3 7.9 - - + +
110D ILE* 4.5 24.5 - - + -
113D LEU* 5.8 3.4 - - + -
126D ILE* 3.4 30.4 + - + +
127D GLN* 4.2 2.9 - - - +
128D ALA 3.3 0.8 - - - -
129D LYS* 1.3 76.2 - - + +
131D LEU* 1.3 63.7 + - - +
132D LYS 3.4 0.2 - - - -
133D ALA* 3.8 26.9 + - + +
135D LEU* 4.7 14.9 - - + +
186D VAL* 5.8 4.0 - - + -
188D THR* 5.1 8.7 - - + +
193D SER* 3.7 29.2 - - - +
195D ILE* 5.8 4.7 - - + -
200D PHE* 5.5 0.3 - - - -
207D ARG* 5.3 0.9 + - - -
241J ILE* 3.7 21.9 - - + +
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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