Contacts of the helix formed by residues 162 - 172 (chain G) in PDB entry 4D1Q
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 ILE 162 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G LYS 3.0 17.2 + - - +
159G LYS* 4.1 8.1 - - - +
161G LEU* 1.3 94.6 - - + +
163G GLY* 1.3 67.9 + - - +
164G ARG 3.1 3.3 + - - -
165G GLU* 3.3 13.8 + - + +
166G ILE* 3.1 48.4 + - + +
207G LEU* 3.9 10.3 - - + -
235G PHE* 5.0 1.6 - - + -
599G PHE* 4.7 12.1 - - + -
603G PHE* 4.1 5.2 - - + -
607G PHE* 3.0 56.8 - - + -
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Residues in contact with GLY 163 (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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159G LYS 3.5 10.0 + - - -
160G ALA* 2.8 17.0 + - - -
162G ILE* 1.3 75.5 - - - +
164G ARG* 1.3 56.8 + - - +
166G ILE* 3.8 0.5 - - - +
167G LYS* 2.8 33.7 + - - +
235G PHE* 3.5 25.9 - - - +
236G ASN* 5.6 1.1 - - - -
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Residues in contact with ARG 164 (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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160G ALA 4.5 1.0 + - - -
161G LEU 4.4 8.4 + - - +
162G ILE 3.1 0.2 - - - -
163G GLY* 1.3 74.4 - - - +
165G GLU* 1.3 70.7 + - - +
166G ILE 2.9 0.7 + - - -
167G LYS* 3.5 4.9 - - - +
168G SER* 2.9 29.2 + - - -
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Residues in contact with GLU 165 (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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162G ILE* 3.3 18.5 + - + +
164G ARG* 1.3 84.4 - - + +
166G ILE* 1.3 57.5 + - + +
168G SER* 3.5 5.5 + - - -
169G ALA* 3.1 26.3 + - + +
198G TYR* 2.9 37.8 + - + +
200G GLU* 3.7 17.6 - - - +
205G ARG* 3.1 22.7 + - - -
607G PHE* 4.6 8.7 - - + -
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Residues in contact with ILE 166 (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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162G ILE* 3.1 43.7 + - + +
163G GLY 4.0 1.8 - - - +
164G ARG 3.1 0.6 - - - -
165G GLU* 1.3 76.2 - - + +
167G LYS* 1.3 69.3 + - - +
168G SER 3.0 1.6 - - - -
169G ALA* 3.4 4.1 + - - +
170G VAL* 3.0 24.2 + - + +
196G LEU* 3.4 26.0 - - + -
198G TYR* 4.2 15.3 - - + +
207G LEU* 4.0 7.2 - - + -
209G LEU* 4.0 24.2 - - + -
232G PHE* 5.4 2.0 - - + -
235G PHE* 4.6 16.6 - - + -
237G VAL* 4.4 15.5 - - + -
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Residues in contact with LYS 167 (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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163G GLY 2.8 24.2 + - - +
164G ARG* 3.5 6.1 - - - +
166G ILE* 1.3 69.0 - - - +
168G SER* 1.3 68.1 + - - +
170G VAL* 2.9 23.0 - - + +
171G GLU* 3.4 32.9 + - + +
235G PHE 4.7 4.7 - - - +
236G ASN* 3.8 31.3 + - + +
237G VAL* 4.1 17.6 - - + +
238G GLU* 5.2 5.5 - - - +
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Residues in contact with SER 168 (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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164G ARG* 2.9 20.6 + - - -
165G GLU* 3.5 8.2 + - - -
167G LYS* 1.3 78.9 - - - +
169G ALA* 1.3 57.5 + - - -
170G VAL 2.5 14.7 + - - -
171G GLU* 2.9 21.9 + - - +
172G LYS* 3.4 29.2 + - - +
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Residues in contact with ALA 169 (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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165G GLU* 3.1 15.7 + - + +
166G ILE 3.4 2.9 + - - +
168G SER* 1.3 78.4 + - - +
170G VAL* 1.3 56.3 + - - +
171G GLU 3.6 0.2 - - - -
172G LYS* 4.1 11.0 + - - +
174G GLY* 3.2 26.7 + - - -
175G ALA* 3.4 8.1 + - + -
198G TYR* 4.0 37.5 - - + -
199G HIS 5.6 2.2 - - - +
200G GLU* 5.9 1.8 - - - +
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Residues in contact with VAL 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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166G ILE* 3.0 16.0 + - + +
167G LYS* 2.9 19.7 - - + +
168G SER 2.5 6.9 + - - -
169G ALA* 1.3 72.6 - - - +
171G GLU* 1.3 72.6 + - + +
173G ASP* 3.6 10.4 + - - -
174G GLY 4.3 0.9 + - - -
175G ALA* 3.6 16.8 - - + +
196G LEU* 5.6 1.1 - - + -
232G PHE* 5.3 5.2 - - + -
237G VAL* 4.3 23.1 - - + -
239G ASP 5.1 2.2 - - - +
242G SER* 3.7 22.8 - - - +
243G ILE* 3.6 36.8 - - + -
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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
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167G LYS* 3.4 43.7 - - - +
168G SER* 2.9 17.4 + - - +
170G VAL* 1.3 77.9 - - + +
172G LYS* 1.3 63.0 + - + +
173G ASP* 2.7 27.1 + - - +
242G SER* 4.7 6.9 - - - -
461G LEU* 5.2 1.6 - - - +
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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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168G SER* 3.4 34.1 + - - +
169G ALA* 4.3 7.9 - - - +
170G VAL 3.4 0.2 - - - -
171G GLU* 1.3 82.5 + - + +
173G ASP* 1.3 56.1 + - - +
174G GLY* 2.7 18.8 + - - -
461G LEU* 4.1 20.1 - - + +
464G ILE* 3.7 38.6 + - + +
556G LYS* 5.2 5.2 - - - +
560G SER* 4.9 2.3 - - - -
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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