Contacts of the helix formed by residues 146 - 154 (chain t) in PDB entry 5JPQ
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 HIS 146 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126t GLY* 6.0 0.7 - - - -
137t VAL 5.0 0.9 - - - -
138t LEU* 3.4 29.8 - - + +
139t GLY* 2.8 42.3 + - - -
141t LYS 4.3 15.9 - - - +
142t GLU* 5.3 4.7 - - - -
144t SER* 3.1 7.5 + - - +
145t ARG* 1.3 77.2 - - - +
147t VAL* 1.3 56.5 + - - +
148t GLN 3.0 6.5 + - - -
149t LYS* 3.3 35.6 + - + +
150t ARG* 3.8 13.0 + - - +
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Residues in contact with VAL 147 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142t GLU 4.3 1.6 - - - +
143t LYS 3.6 16.2 - - - +
144t SER 2.8 22.9 - - - +
145t ARG* 2.8 1.7 - - - -
146t HIS* 1.3 77.2 - - - +
148t GLN* 1.3 59.9 + - + +
150t ARG* 3.5 44.1 - - - +
151t VAL* 2.9 25.6 + - + +
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Residues in contact with GLN 148 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145t ARG* 3.1 44.2 + - - +
146t HIS 3.0 0.8 - - - -
147t VAL* 1.3 79.3 - - + +
149t LYS* 1.3 66.7 + - + +
150t ARG 2.8 6.8 + - - -
151t VAL* 2.9 19.5 + - + +
152t LYS* 2.9 42.8 + - - +
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Residues in contact with LYS 149 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123t LEU* 3.1 30.7 + - - +
124t HIS* 4.4 17.4 - - - +
125t TYR 3.4 20.2 - - - +
126t GLY* 4.8 2.7 - - - +
138t LEU* 4.2 10.5 - - + -
145t ARG 4.9 4.5 - - - +
146t HIS* 3.3 45.7 + - + +
148t GLN* 1.3 78.6 - - + +
150t ARG* 1.3 56.5 + - - +
152t LYS* 4.1 5.9 - - - +
153t ARG* 2.8 32.0 + - - +
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Residues in contact with ARG 150 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138t LEU* 5.6 10.8 - - + -
142t GLU* 3.0 45.1 + - - +
146t HIS* 3.8 12.3 + - - +
147t VAL* 3.5 39.2 - - - +
148t GLN 2.8 0.6 - - - -
149t LYS* 1.3 76.1 - - - +
151t VAL* 1.3 58.1 + - + +
153t ARG* 2.8 13.2 + - - +
154t THR* 2.7 40.7 + - - +
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Residues in contact with VAL 151 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147t VAL* 2.9 27.6 - - + +
148t GLN* 2.9 12.5 + - + +
150t ARG* 1.3 75.4 - - + +
152t LYS* 1.3 65.1 + - + +
154t THR* 3.7 7.8 + - - +
155t LYS* 3.5 13.9 + - - +
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Residues in contact with LYS 152 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124t HIS* 2.9 59.4 + - + +
125t TYR* 3.9 21.3 - - + -
148t GLN* 2.9 45.0 + - - +
149t LYS* 4.1 7.3 - - - +
151t VAL* 1.3 75.7 - - + +
153t ARG* 1.3 59.9 + - - +
155t LYS* 2.7 38.0 + - + +
157t GLN* 3.7 6.2 - - - +
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Residues in contact with ARG 153 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125t TYR* 4.0 24.6 - - - +
127t ILE* 3.7 21.2 - - + +
136t THR* 3.0 29.9 + - - +
138t LEU* 3.0 35.5 - - - +
149t LYS 2.8 21.2 + - - +
150t ARG* 2.8 12.6 + - - +
152t LYS* 1.3 73.6 - - - +
154t THR* 1.3 60.5 + - - +
155t LYS 3.1 0.9 + - - -
156t ALA* 3.9 5.9 + - - -
157t GLN* 4.0 12.4 + - - +
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Residues in contact with THR 154 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150t ARG* 2.7 22.6 + - - +
151t VAL* 4.0 8.5 - - - +
153t ARG* 1.3 69.0 - - - +
155t LYS* 1.3 51.6 + - - +
156t ALA* 2.3 25.7 + - - +
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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