Contacts of the helix formed by residues 150 - 159 (chain W) in PDB entry 6AH0
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 150 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144W GLN 4.0 7.4 - - - -
145W GLY* 4.7 7.9 - - - -
147W GLY 3.0 14.7 + - - -
149W LYS* 1.3 79.7 - - - +
151W HIS* 1.3 61.9 + - - +
152W ALA 3.1 3.4 - - - -
153W TYR* 2.8 21.8 + - - -
154W ILE* 3.0 11.4 + - - -
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Residues in contact with HIS 151 (chain W).
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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143W PHE* 5.0 5.4 - - - +
144W GLN 3.2 9.6 + - - +
149W LYS 4.0 2.0 + - - -
150W SER* 1.3 70.0 - - - +
152W ALA* 1.3 55.6 + - - +
154W ILE* 4.7 2.0 - - - +
155W HIS* 2.9 26.4 + - - -
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Residues in contact with ALA 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134W TYR 6.1 0.2 - - - -
143W PHE* 4.4 11.5 - - - +
144W GLN 2.9 16.0 + - - -
145W GLY* 4.5 6.5 - - - -
146W ARG 5.5 0.7 - - - +
151W HIS* 1.3 74.5 - - - +
153W TYR* 1.3 57.9 + - - +
155W HIS* 3.9 0.6 - - - +
156W SER* 3.0 24.4 + - - -
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Residues in contact with TYR 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145W GLY* 5.2 1.8 - - - -
146W ARG 4.9 8.2 + - - -
147W GLY 4.5 11.4 + - - -
148W LEU* 4.6 4.3 - - - +
150W SER 2.8 13.5 + - - -
152W ALA* 1.3 68.3 - - - +
154W ILE* 1.3 63.9 + - - +
156W SER* 3.0 12.8 + - - +
157W VAL* 3.1 10.4 + - - -
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Residues in contact with ILE 154 (chain W).
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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148W LEU 4.2 5.9 + - - -
150W SER 3.0 13.7 + - - -
151W HIS* 4.2 1.8 - - - +
153W TYR* 1.3 72.6 - - - +
155W HIS* 1.3 56.8 + - - +
157W VAL* 3.1 3.1 + - - -
158W GLN* 2.8 27.4 + - - -
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Residues in contact with HIS 155 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W HIS 2.9 20.1 + - - -
152W ALA* 3.9 1.1 - - - +
154W ILE* 1.3 74.9 - - - +
156W SER* 1.3 61.5 + - - +
158W GLN* 4.6 0.4 - - - +
159W PHE* 3.0 28.9 + - - +
161W HIS* 4.4 1.0 + - - -
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Residues in contact with SER 156 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152W ALA 3.0 16.8 + - - -
153W TYR 3.0 5.5 + - - -
155W HIS* 1.3 73.0 - - - +
157W VAL* 1.3 54.7 - - - +
160W SER* 3.2 8.0 + - - -
161W HIS 3.1 43.3 + - - -
162W HIS* 4.8 3.7 + - - +
175W LEU 5.7 3.8 - - - -
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Residues in contact with VAL 157 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810C PRO* 5.7 4.9 - - - +
153W TYR 3.1 7.5 + - - -
154W ILE* 3.1 6.4 + - - +
156W SER* 1.3 76.6 - - - +
158W GLN* 1.3 60.2 + - - +
159W PHE 3.3 2.1 + - - -
160W SER* 4.0 5.4 + - - -
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Residues in contact with GLN 158 (chain W).
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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154W ILE 2.8 17.2 + - - -
155W HIS* 5.3 0.7 - - - +
157W VAL* 1.3 72.0 - - - +
159W PHE* 1.3 56.2 + - - +
160W SER 3.7 0.9 - - - -
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Residues in contact with PHE 159 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W HIS* 3.0 15.1 + - - +
158W GLN* 1.3 79.1 - - - +
160W SER* 1.3 60.3 + - - +
161W HIS* 3.0 6.8 + - - -
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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