Contacts of the helix formed by residues 168 - 177 (chain G) in PDB entry 5XS0
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 168 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67F GLU* 5.6 0.2 - - - +
69F HIS* 3.8 28.2 + - + +
70F ARG* 4.8 6.2 + - - -
186F VAL* 4.4 1.9 - - - +
46G ARG* 4.0 19.5 + - - +
165G CYS* 2.9 17.9 + - + +
167G LEU* 1.3 76.5 - - - +
169G LYS* 1.3 62.6 + - - +
170G ASP* 3.4 20.8 + - - +
171G TYR* 3.2 19.7 + - + +
172G LEU* 3.0 28.4 + - - +
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Residues in contact with LYS 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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53F SER* 6.0 0.6 - - - -
65F TYR* 5.0 4.9 + - - -
67F GLU* 3.3 32.1 + - - +
69F HIS* 5.2 0.6 + - - -
167G LEU 4.4 7.4 - - - +
168G ASP* 1.3 74.4 + - - +
170G ASP* 1.3 61.9 + - - +
172G LEU* 3.1 17.8 + - + +
173G ARG* 2.9 33.3 + - + +
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Residues in contact with ASP 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ARG* 5.1 6.8 + - - -
183F PRO* 3.7 13.2 - - - +
184F LEU* 3.2 33.0 + - - +
186F VAL* 3.5 17.0 - - + +
168G ASP* 3.2 14.3 + - - +
169G LYS* 1.3 77.6 - - - +
171G TYR* 1.3 61.3 + - - +
173G ARG* 3.3 25.9 + - - +
174G SER* 2.9 31.7 + - - -
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Residues in contact with TYR 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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186F VAL* 3.7 10.0 - - - +
188F LEU* 3.5 31.0 - - + -
46G ARG* 3.5 27.8 - - + +
47G LEU* 2.4 36.5 + - - +
52G ILE* 3.6 15.2 - - - +
165G CYS* 3.3 30.3 - - + -
166G ILE* 4.2 17.7 - - + -
168G ASP* 3.2 25.0 + - + +
170G ASP* 1.3 77.4 - - - +
172G LEU* 1.3 62.0 + - + +
174G SER* 3.4 2.6 + - - -
175G LEU* 2.9 50.6 + - + +
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Residues in contact with LEU 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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62G LYS 6.0 1.8 - - - +
64G CYS* 3.7 35.0 - - + +
166G ILE* 3.9 24.9 - - + +
167G LEU 5.4 1.3 - - - -
168G ASP 3.0 18.3 + - - +
169G LYS* 3.1 19.5 + - + +
171G TYR* 1.3 85.6 - - + +
173G ARG* 1.3 58.1 + - + +
175G LEU* 3.1 7.4 + - + +
176G ASN* 2.7 44.2 + - - +
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Residues in contact with ARG 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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183F PRO* 3.8 19.9 + - - +
184F LEU 3.4 17.8 + - - -
185F GLU* 4.2 14.5 + - - +
169G LYS* 2.9 15.7 + - + +
170G ASP* 3.3 33.6 + - - +
172G LEU* 1.3 75.6 - - + +
174G SER* 1.3 62.3 + - - +
175G LEU 3.2 0.9 + - - -
176G ASN* 3.2 16.7 + - - +
177G LYS* 3.2 48.6 + - - +
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Residues in contact with SER 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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185F GLU* 3.9 10.7 - - - +
186F VAL* 2.6 43.0 + - - -
188F LEU* 3.4 25.3 - - - +
170G ASP 2.9 14.8 + - - -
171G TYR 3.9 1.6 - - - -
172G LEU 3.3 0.2 - - - -
173G ARG* 1.3 75.9 - - - +
175G LEU* 1.3 58.9 + - - +
177G LYS* 4.2 11.5 + - - +
178G LEU* 3.5 15.4 + - - +
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Residues in contact with LEU 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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188F LEU* 3.7 16.6 - - + -
47G LEU 4.7 0.4 - - - +
48G GLY 4.6 0.4 - - - -
49G PRO* 3.8 40.6 - - + +
52G ILE* 3.5 30.7 - - + -
64G CYS* 5.3 2.0 - - - -
171G TYR* 2.9 47.2 + - + +
172G LEU* 3.5 12.8 - - + +
173G ARG 3.1 0.4 - - - -
174G SER* 1.3 77.2 - - - +
176G ASN* 1.3 65.1 + - - +
177G LYS 3.3 0.2 - - - -
178G LEU* 3.3 20.1 + - + +
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Residues in contact with ASN 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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62G LYS* 3.0 38.8 + - - +
64G CYS* 5.8 3.6 - - - -
172G LEU* 2.7 37.5 + - - +
173G ARG* 3.2 8.2 + - - +
175G LEU* 1.3 73.3 - - - +
177G LYS* 1.3 59.4 + - + +
178G LEU 3.0 17.8 + - - +
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Residues in contact with LYS 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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185F GLU* 2.7 29.3 + - - +
173G ARG* 3.2 41.2 + - - +
174G SER* 4.5 8.7 - - - +
175G LEU 3.3 0.4 - - - -
176G ASN* 1.3 77.3 - - + +
178G LEU* 1.3 62.1 + - + +
179G PRO* 4.0 2.4 - - - +
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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