Contacts of the helix formed by residues 154 - 164 (chain B) in PDB entry 1A6Y
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 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 4.0 15.5 - - + -
134B TYR* 2.9 41.1 - - + +
135B LYS* 4.6 15.4 - - - +
150B ARG 5.5 1.6 - - - -
151B ASN* 4.6 12.1 + - - +
152B ARG 3.6 2.8 + - - +
153B CYS* 1.3 68.4 - - - +
155B GLN* 1.3 57.1 + - - +
157B ARG* 2.4 35.5 + - - +
158B PHE 3.1 8.1 + - - -
621D C 3.3 16.6 + - - -
622D T 3.0 28.3 + - - +
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 6.0 0.4 - - - +
134B TYR* 4.1 29.2 + - + +
135B LYS 3.0 28.7 + - - +
136B ARG* 4.2 8.1 - - - +
137B CYS* 4.4 8.7 - - + +
141B GLU* 3.3 23.2 - - - +
153B CYS* 4.1 11.4 - - - -
154B GLN* 1.3 76.6 - - - +
156B CYS* 1.3 57.3 + - - +
158B PHE* 3.6 11.1 + - - +
159B LYS* 3.0 32.6 + - - +
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Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B CYS* 3.6 0.9 - - - -
141B GLU* 3.2 39.0 - - - -
143B CYS* 3.5 23.6 - - + +
145B ILE* 4.4 6.9 - - + +
153B CYS* 3.4 6.5 + - - +
154B GLN 2.5 5.7 + - - -
155B GLN* 1.3 75.5 - - - +
157B ARG* 1.3 59.2 + - - +
159B LYS* 3.5 9.7 + - + +
160B LYS* 2.9 26.9 + - - +
451B ZN 2.3 34.5 - - - -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.1 15.0 - - + -
120B GLY 3.3 0.6 - - - -
121B CYS* 3.2 37.0 - - - +
124B PHE* 3.3 46.5 - - + +
145B ILE* 3.8 16.3 - - + +
150B ARG* 3.3 37.9 + - - +
151B ASN* 3.2 19.1 + - - +
153B CYS 3.3 9.2 + - - +
154B GLN* 2.4 24.2 + - - +
156B CYS* 1.3 64.9 - - - +
158B PHE* 1.3 52.9 + - - +
160B LYS* 2.6 24.6 + - - +
161B CYS* 2.6 20.8 + - - -
622D T 4.4 5.7 + - - -
623D G 2.8 29.3 + - - -
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 3.6 18.7 - + + -
125B PHE* 3.8 20.6 - + - -
128B SER* 4.0 23.1 - - - -
129B ILE* 3.9 21.5 - - + -
133B ILE 6.0 2.5 - - - -
134B TYR* 4.4 14.4 - + + -
154B GLN 3.1 5.0 + - - +
155B GLN* 3.9 14.6 - - - +
157B ARG* 1.3 78.0 - - - +
159B LYS* 1.3 57.2 + - - +
161B CYS* 3.0 4.2 + - + -
162B LEU* 2.9 69.4 + - + +
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU* 3.3 54.3 + - + +
155B GLN* 3.0 23.9 + - - +
156B CYS* 3.6 8.5 - - - +
158B PHE* 1.3 77.6 - - - +
160B LYS* 1.3 57.8 + - - +
162B LEU* 4.3 9.4 - - - +
163B SER* 2.9 27.7 + - - -
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS 3.8 14.4 + - - -
103B VAL* 2.8 44.3 + - + +
145B ILE* 3.9 24.2 + - + +
156B CYS 2.9 13.8 + - - +
157B ARG* 2.6 23.5 + - - +
159B LYS* 1.3 72.2 - - - +
161B CYS* 1.3 63.3 + - - +
163B SER* 3.0 11.0 + - - +
164B VAL* 2.9 37.4 + - + +
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Residues in contact with CYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 3.7 29.2 - - - -
121B CYS* 4.5 5.6 - - - -
124B PHE* 4.5 11.9 - - - -
125B PHE* 3.4 33.7 - - + -
157B ARG 2.6 21.8 + - - -
158B PHE* 3.3 11.9 - - - +
160B LYS* 1.3 72.0 - - - +
162B LEU* 1.3 61.5 + - - +
164B VAL* 2.8 23.5 + - - +
165B GLY 3.2 4.9 + - - -
166B MET* 3.3 17.4 + - - -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.5 27.8 - - + -
129B ILE* 5.2 0.9 - - + -
158B PHE* 2.9 53.8 + - + +
159B LYS* 4.3 6.3 - - - +
161B CYS* 1.3 77.1 - - - +
163B SER* 1.3 61.7 + - - +
164B VAL 3.2 0.7 + - - -
165B GLY* 3.3 11.1 + - - -
166B MET 3.8 10.8 - - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS* 2.9 26.7 + - - -
160B LYS* 3.0 20.8 + - - +
162B LEU* 1.3 78.2 - - - +
164B VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 3.5 58.5 - - + +
103B VAL* 3.9 13.0 - - + -
115B VAL* 4.2 11.8 - - + +
160B LYS* 2.9 28.0 + - + +
161B CYS* 2.8 28.9 - - - +
163B SER* 1.3 83.7 - - - +
165B GLY* 1.3 56.9 + - - +
166B MET* 4.1 9.4 - - + -
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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