Contacts of the helix formed by residues 170 - 177 (chain G) in PDB entry 6PB4
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 GLN 170 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472 A 2.7 41.1 + - - +
482 T 2.8 12.2 + - - +
167G ILE* 4.1 1.0 - - + +
168G THR* 3.1 27.0 - - + +
169G ARG* 1.3 77.4 - - - +
171G GLU* 1.3 79.4 + - + +
172G ILE* 3.4 2.1 - - - +
173G GLY* 3.2 4.8 + - - -
174G GLN* 3.1 29.2 + - - +
180G ARG* 5.9 0.7 - - + +
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Residues in contact with GLU 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ILE* 3.6 9.1 - - - +
63G TYR* 3.0 30.0 + - + +
89G LYS* 5.5 4.6 + - - -
167G ILE* 3.4 18.8 - - + +
170G GLN* 1.3 89.3 - - + +
172G ILE* 1.3 61.3 + - - +
173G GLY 3.0 1.1 - - - -
174G GLN* 3.5 19.7 - - - +
175G ILE* 2.8 49.4 + - + +
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Residues in contact with ILE 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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143G ILE* 3.3 35.2 - - + +
146G THR* 4.4 13.0 - - + -
147G LEU* 3.9 21.5 - - + -
150G LEU* 5.9 1.3 - - + -
167G ILE* 3.6 19.9 - - + +
169G ARG* 3.6 32.5 - - + +
171G GLU* 1.3 77.9 - - - +
173G GLY* 1.3 60.3 + - - +
175G ILE* 3.9 5.7 - - - +
176G VAL* 2.8 42.8 + - + +
178G CYS* 5.2 0.2 - - - -
183G VAL* 3.9 13.5 - - + -
187G LEU* 4.7 12.8 - - + -
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Residues in contact with GLY 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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57G LYS* 5.6 0.4 - - - -
169G ARG 5.1 2.7 - - - -
170G GLN 3.2 8.2 + - - -
171G GLU 3.0 0.4 - - - -
172G ILE* 1.3 82.3 - - - +
174G GLN* 1.3 62.4 + - - +
175G ILE 3.1 1.6 - - - -
177G GLY* 2.3 38.5 + - - -
178G CYS* 3.7 28.7 - - - -
183G VAL* 5.1 0.9 - - - -
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Residues in contact with GLN 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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57G LYS* 3.3 39.8 - - - +
58G GLU 3.9 10.2 - - - +
59G MET* 4.1 32.4 - - - +
60G ILE* 4.4 20.9 + - + +
170G GLN 3.1 15.3 + - - +
171G GLU* 3.3 28.0 + - - +
173G GLY* 1.3 77.0 - - - +
175G ILE* 1.3 62.5 + - + +
176G VAL 4.7 0.3 - - - -
177G GLY* 4.5 3.3 + - - -
178G CYS 5.7 1.2 + - - -
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Residues in contact with ILE 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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60G ILE* 5.7 6.1 - - + +
63G TYR* 4.8 18.4 - - + -
130G LYS* 6.1 5.4 - - + +
146G THR* 4.3 18.6 - - + +
150G LEU* 4.0 27.8 - - + -
171G GLU* 2.8 39.4 + - + +
172G ILE* 4.0 4.0 - - - +
174G GLN* 1.3 80.5 - - + +
176G VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 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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134G LEU* 4.8 14.4 - - - +
139G VAL* 4.3 9.9 - - + -
142G ARG* 3.7 36.0 + - + +
143G ILE* 3.7 34.1 - - + +
146G THR* 3.2 28.3 - - - +
172G ILE* 2.8 28.3 + - + +
173G GLY* 4.5 1.8 - - - -
174G GLN 4.7 0.2 - - - -
175G ILE* 1.3 79.1 - - - +
177G GLY* 1.3 63.4 + - - +
178G CYS* 4.5 2.9 - - - -
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Residues in contact with GLY 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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381 A 5.1 2.1 + - - -
57G LYS* 5.4 4.9 - - - -
139G VAL* 5.0 2.3 - - - +
142G ARG* 4.7 9.5 + - - -
173G GLY 2.3 23.4 + - - -
174G GLN* 4.9 3.6 - - - -
176G VAL* 1.3 75.8 - - - +
178G CYS* 1.3 64.7 + - - +
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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