Contacts of the helix formed by residues 164 - 173 (chain J) in PDB entry 5T0G
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 GLY 164 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161J ILE 5.0 0.2 - - - -
162J GLY 3.2 1.2 + - - -
163J ARG* 1.3 73.3 - - - +
165J ALA* 1.3 64.1 + - - +
166J LYS* 3.3 2.5 - - - -
167J SER* 2.4 34.7 + - - -
168J VAL* 3.1 12.8 + - - +
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Residues in contact with ALA 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J ALA* 3.8 9.3 - - - +
161J ILE* 3.7 29.4 - - + +
162J GLY 3.3 16.4 + - - +
164J GLY* 1.3 73.2 - - - +
166J LYS* 1.3 60.2 - - - +
168J VAL* 4.6 2.5 - - - +
169J ARG* 2.9 32.7 + - - +
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Residues in contact with LYS 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLY* 4.4 0.6 - - - -
165J ALA* 1.3 78.2 - - - +
167J SER* 1.3 58.6 + - - +
169J ARG* 3.8 4.9 - - - +
170J GLU* 2.9 28.9 + - - +
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Residues in contact with SER 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLY* 2.4 36.5 + - - -
166J LYS* 1.3 80.0 - - - +
168J VAL* 1.3 64.9 + - - +
170J GLU* 3.3 15.0 + - - +
171J PHE* 3.3 11.4 + - - +
197J GLU* 5.0 10.0 + - - +
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Residues in contact with VAL 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J THR* 6.3 2.2 - - - -
33J VAL* 4.0 25.6 - - + -
159J ASN 4.9 0.2 - - - +
160J ALA* 4.3 13.0 - - + -
161J ILE 5.4 4.3 - - - +
163J ARG 5.1 3.8 - - - +
164J GLY 3.1 16.9 + - - +
165J ALA* 4.2 4.0 - - - +
167J SER* 1.3 75.5 + - - +
169J ARG* 1.3 62.3 + - - +
171J PHE* 2.8 25.7 + - + +
172J LEU* 3.0 25.6 + - + +
194J ALA* 4.5 15.3 - - + +
197J GLU* 4.7 4.9 - - - +
198J VAL* 4.0 26.7 - - + -
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Residues in contact with ARG 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J ALA* 3.8 11.5 - - + +
165J ALA 2.9 20.0 + - - +
166J LYS* 3.8 6.3 - - - +
168J VAL* 1.3 75.7 - - - +
170J GLU* 1.3 63.9 + - - +
172J LEU* 3.2 25.8 + - - +
173J GLU* 3.7 5.4 + - - +
56K SER* 6.1 0.2 - - - +
58K LEU* 4.3 21.8 - - + +
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Residues in contact with GLU 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J LYS 2.9 14.8 + - - +
167J SER* 3.4 13.7 - - - +
168J VAL 3.1 0.2 - - - -
169J ARG* 1.3 76.5 - - - +
171J PHE* 1.3 60.7 + - - +
173J GLU* 3.3 24.6 + - - +
174J LYS 4.6 0.7 + - - -
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Residues in contact with PHE 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J SER 3.3 7.6 + - - +
168J VAL* 2.8 12.6 + - + +
170J GLU* 1.3 74.6 - - - +
172J LEU* 1.3 70.2 + - + +
173J GLU 3.1 3.1 + - - -
174J LYS* 3.4 22.7 + - + +
175J ASN* 3.6 14.5 + - + -
190J LEU* 5.2 4.3 - - + -
193J LYS* 3.3 35.7 - - + -
194J ALA* 3.7 25.4 - - + +
197J GLU* 4.5 19.5 - - + -
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Residues in contact with LEU 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J VAL* 5.9 1.6 - - + -
158J ALA* 3.8 29.8 - - + +
159J ASN 4.3 7.6 - - - +
160J ALA* 3.6 30.3 - - + -
168J VAL* 3.0 19.5 + - + +
169J ARG* 3.2 13.1 + - + +
171J PHE* 1.3 83.1 - - + +
173J GLU* 1.3 59.6 + - - +
174J LYS 3.2 0.2 - - - -
175J ASN* 2.8 42.1 + - + +
176J TYR* 3.0 20.8 + - + -
194J ALA* 4.8 6.5 - - + -
58K LEU* 4.6 16.2 - - + -
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Residues in contact with GLU 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J ARG 3.7 4.8 + - - +
170J GLU* 3.3 17.7 + - - +
171J PHE 3.1 1.0 - - - -
172J LEU* 1.3 78.0 - - - +
174J LYS* 1.3 59.5 + - - +
175J ASN 3.6 0.2 + - - -
176J TYR* 3.9 14.7 + - - +
177J THR* 4.8 4.9 + - - +
57K PRO* 6.6 0.7 - - + -
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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