Contacts of the helix formed by residues 169 - 177 (chain G) in PDB entry 4UNA
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 ASP 169 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146G GLY 3.9 19.9 - - - +
147G VAL* 4.3 12.0 - - + +
148G ARG* 2.7 64.5 + - - +
166G SER* 3.0 12.3 + - - +
168G ARG* 1.3 78.5 - - - +
170G ARG* 1.3 64.0 + - - +
171G ILE 3.3 2.7 - - - -
172G LYS* 3.3 19.5 + - + +
173G PHE* 2.9 23.7 + - - +
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Residues in contact with ARG 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LEU 3.4 16.0 + - - -
123G LYS* 2.8 31.7 + - - +
125G LEU* 3.7 25.0 - - + +
166G SER 3.6 1.8 + - - -
167G LEU* 3.1 48.2 + - - +
168G ARG 3.4 1.4 + - - -
169G ASP* 1.3 77.1 - - - +
171G ILE* 1.3 67.4 + - + +
173G PHE* 3.2 1.8 + - - +
174G VAL* 2.9 43.9 + - + +
4H T 4.2 13.9 + - - -
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Residues in contact with ILE 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G ARG 5.3 0.4 + - - -
169G ASP 3.3 0.6 - - - -
170G ARG* 1.3 88.1 - - + +
172G LYS* 1.3 66.6 + - - +
174G VAL* 3.4 3.7 + - - -
175G HIS* 3.2 44.7 + - + +
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Residues in contact with LYS 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G LEU 3.5 17.5 - - - +
146G GLY* 2.9 35.4 + - - +
147G VAL* 4.1 4.9 - - + -
169G ASP* 3.3 22.2 + - + +
171G ILE* 1.3 80.2 - - - +
173G PHE* 1.3 57.8 + - - +
175G HIS* 5.1 1.8 - - - -
176G THR* 2.1 48.3 + - + +
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Residues in contact with PHE 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ILE* 4.3 7.4 - - + -
114G TYR* 3.9 33.0 - + - -
125G LEU* 4.0 22.4 - - + -
142G LEU* 3.9 22.2 - - + -
147G VAL* 4.1 18.4 - - + +
165G ILE* 3.9 23.3 - - + -
169G ASP 2.9 16.1 + - - +
170G ARG* 3.6 4.5 - - - +
171G ILE 3.1 0.2 - - - -
172G LYS* 1.3 76.1 - - - +
174G VAL* 1.3 69.5 + - + +
175G HIS 3.0 1.4 + - - -
176G THR* 4.3 0.4 - - - -
177G ILE* 3.1 66.6 + - + +
178G LEU* 3.6 21.1 + - + -
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Residues in contact with VAL 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LEU* 4.8 17.0 - - + -
125G LEU* 4.5 11.7 - - + -
170G ARG* 2.9 33.0 + - + +
171G ILE* 4.2 4.7 - - - +
173G PHE* 1.3 86.4 - - + +
175G HIS* 1.3 64.4 + - + +
178G LEU* 3.6 17.4 - - + +
179G SER* 2.7 42.9 + - - +
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Residues in contact with HIS 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G ILE* 3.2 35.6 + - + +
172G LYS* 4.6 1.6 - - - +
173G PHE 3.1 0.6 - - - -
174G VAL* 1.3 91.6 + - + +
176G THR* 1.3 63.4 + - + +
177G ILE 3.6 0.2 - - - -
179G SER* 3.5 38.8 + - - -
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Residues in contact with THR 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G MET* 6.3 2.9 - - + -
107G ILE* 3.4 29.5 - - + +
145G LEU* 5.5 5.2 + - - +
147G VAL* 5.2 1.9 - - - +
172G LYS* 2.1 45.3 + - + +
173G PHE* 4.3 0.9 - - - -
175G HIS* 1.3 79.5 - - + +
177G ILE* 1.3 65.7 + - - +
179G SER 4.8 3.8 - - - +
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Residues in contact with ILE 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ILE* 3.8 36.7 - - + +
110G ILE* 3.7 31.9 - - + -
111G LYS* 3.7 33.8 - - - +
142G LEU* 4.4 3.8 - - + -
145G LEU* 4.0 17.9 - - + -
147G VAL* 5.6 2.2 - - + -
173G PHE* 3.1 41.5 + - + +
176G THR* 1.3 83.6 - - - +
178G LEU* 1.3 75.9 + - + +
179G SER 3.2 4.9 + - - +
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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