Contacts of the helix formed by residues 171 - 179 (chain J) in PDB entry 5GJQ
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 171 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167J LEU* 3.2 26.4 + - + +
169J VAL 3.0 0.4 - - - -
170J LYS* 1.3 97.4 - - + +
172J PRO* 1.4 58.0 - - - +
173J GLU* 2.7 23.4 + - + +
174J LEU* 2.7 28.0 + - + +
175J PHE* 4.2 0.9 + - - -
92R GLU 3.9 14.2 + - - -
93R LYS* 4.2 12.5 + - - +
94R ASN* 4.0 4.7 - - - -
95R LEU* 3.1 53.0 + - - +
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Residues in contact with PRO 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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168J PRO* 3.1 24.0 - - + +
169J VAL* 2.6 27.4 - - + +
170J LYS 3.8 2.5 - - - +
171J HIS* 1.4 71.9 - - - +
173J GLU* 1.3 52.9 - - - +
174J LEU 3.1 0.4 + - - -
175J PHE* 3.4 5.9 + - + +
176J GLU* 2.8 56.4 + - - +
182J GLN* 3.9 10.8 - - - +
288J ASN* 5.0 11.4 - - - +
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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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171J HIS* 2.7 14.1 + - + +
172J PRO* 1.3 73.3 - - - +
174J LEU* 1.3 51.4 + - - +
176J GLU* 3.6 15.3 + - - +
177J ALA* 2.4 51.4 + - + +
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Residues in contact with LEU 174 (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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407I LEU* 3.5 24.2 - - + +
410I ARG* 5.0 11.2 - - - +
412I MET* 5.9 5.5 - - - +
167J LEU* 3.3 44.0 - - + -
171J HIS* 2.7 28.6 + - + +
173J GLU* 1.3 74.2 - - - +
175J PHE* 1.3 64.6 + - + +
177J ALA* 3.7 5.5 - - + +
178J LEU* 3.1 28.3 + - + +
93R LYS 5.0 10.1 - - - +
94R ASN* 5.4 1.3 - - + -
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Residues in contact with PHE 175 (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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404I LEU* 4.6 8.5 - - + -
407I LEU* 3.1 28.7 - - + -
163J GLU 3.4 24.0 - - - -
167J LEU* 3.2 42.0 - - + -
168J PRO* 3.6 18.4 - - + -
171J HIS 4.9 1.6 - - - -
172J PRO* 3.4 6.5 + - + +
174J LEU* 1.3 82.1 - - + +
176J GLU* 1.3 61.6 + - - +
177J ALA 3.3 0.2 - - - -
178J LEU* 4.4 0.7 - - - -
179J GLY 3.0 6.9 + - - -
180J ILE* 3.0 63.3 + - + +
182J GLN* 4.1 25.8 - - + -
183J PRO* 4.4 4.3 - - + -
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Residues in contact with GLU 176 (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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172J PRO* 2.8 44.3 + - + +
173J GLU* 3.6 11.1 + - - +
175J PHE* 1.3 79.6 - - + +
177J ALA* 1.3 61.0 + - - +
179J GLY* 3.2 13.4 + - - -
180J ILE 5.0 2.7 - - - +
182J GLN* 4.1 11.5 - - + +
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Residues in contact with ALA 177 (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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412I MET* 3.2 30.3 - - + +
173J GLU* 2.4 45.7 + - + +
174J LEU* 3.7 7.9 - - + +
176J GLU* 1.3 72.2 - - - +
178J LEU* 1.3 58.5 + - - +
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Residues in contact with LEU 178 (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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372I MET* 2.9 29.6 - - + +
373I THR* 3.5 7.6 + - + +
403I GLY* 4.4 3.4 - - - +
406I ALA* 4.0 13.2 - - + -
407I LEU* 3.4 35.9 - - + -
411I ARG 3.2 21.5 - - - +
412I MET* 2.8 39.9 - - - +
413I LYS* 4.7 0.9 - - - -
414I VAL* 5.2 3.4 - - + -
174J LEU* 3.1 16.1 + - + +
175J PHE* 3.3 5.1 + - - +
176J GLU 3.1 0.4 - - - -
177J ALA* 1.3 79.1 - - - +
179J GLY* 1.3 59.5 + - - +
180J ILE* 4.2 17.3 - - + -
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Residues in contact with GLY 179 (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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368I HIS 4.8 4.2 - - - +
371I ARG* 3.0 23.3 - - - +
372I MET* 3.2 15.3 - - - +
175J PHE 3.0 3.4 + - - -
176J GLU* 3.2 12.5 + - - -
177J ALA 3.4 0.2 - - - -
178J LEU* 1.3 79.7 - - - +
180J ILE* 1.3 66.6 + - - +
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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