Contacts of the helix formed by residues 156 - 167 (chain G) in PDB entry 1GZ0
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 ASN 156 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82G GLU* 4.5 2.0 + - - -
154G VAL* 3.4 3.7 - - - +
155G THR* 1.3 79.6 - - + +
157G LEU* 1.3 65.0 + - - +
158G ALA* 2.9 15.1 + - - +
159G ARG* 2.7 65.6 + - + +
160G THR* 2.9 13.0 + - - -
162G ARG* 4.9 3.4 - - - +
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Residues in contact with LEU 157 (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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99G ILE* 3.7 28.0 - - + -
101G ASP* 3.3 32.1 - - + +
125G ILE* 4.3 18.4 - - + -
127G PRO* 4.3 27.0 - - + +
154G VAL* 3.4 11.7 + - + +
155G THR 3.9 1.8 + - - -
156G ASN* 1.3 72.1 + - - +
158G ALA* 1.3 56.5 + - - +
160G THR* 3.4 2.9 + - + -
161G MSE 2.9 45.4 + - + +
206G THR* 3.7 24.0 - - + +
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Residues in contact with ALA 158 (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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156G ASN* 2.9 7.9 + - - +
157G LEU* 1.3 74.5 - - - +
159G ARG* 1.3 61.0 - - - +
161G MSE 3.0 13.7 + - - +
162G ARG* 2.8 51.9 + - - +
205G LEU* 4.2 15.7 - - + +
206G THR* 5.7 0.7 - - - +
209G HIS* 3.9 22.0 - - + +
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Residues in contact with ARG 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G GLU* 4.0 20.8 + - - -
155G THR* 4.1 22.6 + - - +
156G ASN* 2.7 42.9 + - - +
158G ALA* 1.3 72.0 - - - +
160G THR* 1.3 65.4 + - - +
162G ARG* 3.1 26.5 + - + +
163G MSE 3.0 20.8 + - + +
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Residues in contact with THR 160 (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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82G GLU* 3.4 10.2 + - - +
85G LEU* 3.8 27.7 - - + +
125G ILE* 4.3 16.2 - - + -
154G VAL* 2.9 37.0 - - + +
156G ASN 2.9 7.0 + - - -
157G LEU* 3.5 11.0 - - + +
159G ARG* 1.3 77.8 - - - +
161G MSE 1.3 58.4 + - - +
163G MSE 3.1 13.5 + - + +
164G LEU* 2.9 33.5 + - + +
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Residues in contact with MSE 161 (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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99G ILE* 4.2 16.2 - - + -
157G LEU* 2.9 40.3 + - + +
158G ALA* 3.0 8.7 + - - +
160G THR* 1.3 77.2 - - - +
162G ARG* 1.3 62.6 + - - +
164G LEU* 3.0 9.8 + - + +
165G GLN* 2.9 29.7 + - - +
171G ILE* 3.7 30.1 - - + -
194G VAL* 4.2 6.3 - - + -
206G THR* 3.4 40.6 - - + +
209G HIS* 3.7 30.5 - - + +
210G CYS* 4.1 3.8 - - - -
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Residues in contact with ARG 162 (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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156G ASN* 4.2 4.2 + - - +
158G ALA* 2.8 46.3 + - - +
159G ARG* 3.3 27.7 - - + +
161G MSE 1.3 74.0 - - - +
163G MSE 1.3 51.9 + - - +
165G GLN* 3.1 16.2 + - - +
166G GLU* 2.7 41.7 + - - +
205G LEU* 5.1 1.8 - - - +
209G HIS* 3.6 22.4 + - + -
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Residues in contact with MSE 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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82G GLU* 5.5 1.1 - - + +
85G LEU* 4.1 21.8 - - + -
86G PRO* 4.1 36.8 - - + -
89G ILE* 3.6 25.6 - - - -
159G ARG* 3.0 12.0 + - + +
160G THR* 3.5 12.8 - - + +
162G ARG* 1.3 73.3 - - - +
164G LEU* 1.3 71.3 + - - +
166G GLU* 2.9 14.1 + - + +
167G GLU* 2.8 39.9 + - - +
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Residues in contact with LEU 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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85G LEU* 5.0 0.4 - - + -
89G ILE* 3.3 31.0 - - + -
97G LEU* 3.7 26.0 - - + -
99G ILE* 3.7 30.5 - - + -
125G ILE* 4.6 8.5 - - + -
160G THR* 2.9 27.7 + - + +
161G MSE 3.3 13.7 - - - +
163G MSE 1.3 80.0 - - - +
165G GLN* 1.3 60.9 + - - +
167G GLU* 3.4 5.0 + - - -
169G ILE* 2.8 42.5 + - + +
171G ILE* 4.3 6.7 - - + -
192G ALA* 4.5 6.7 - - + -
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Residues in contact with GLN 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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161G MSE 2.9 20.6 + - - +
162G ARG* 3.5 19.0 + - - +
164G LEU* 1.3 72.9 - - - +
166G GLU* 1.3 56.5 + - - +
167G GLU 2.8 5.2 - - - -
168G ASN* 2.7 25.3 + - - +
169G ILE 4.0 7.9 - - - +
171G ILE* 3.5 13.8 - - + +
209G HIS* 3.1 36.2 + - - +
210G CYS 4.6 0.2 - - - -
211G ASP* 3.3 34.3 + - - +
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Residues in contact with GLU 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 ARG* 2.7 24.7 + - - +
163G MSE 2.9 16.1 + - - +
165G GLN* 1.3 71.3 - - - +
167G GLU* 1.3 74.6 + - - +
168G ASN 3.3 1.4 + - - -
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Residues in contact with GLU 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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86G PRO* 5.6 6.0 - - + +
89G ILE* 4.6 22.7 - - + -
90G ALA* 6.2 0.4 - - - +
163G MSE 2.8 34.7 + - - +
164G LEU* 3.8 6.7 - - - +
165G GLN 2.8 0.6 - - - -
166G GLU* 1.3 103.3 - - - +
168G ASN* 1.3 58.7 - - - +
169G ILE* 3.5 3.6 + - + +
190G ARG* 2.7 33.5 + - - +
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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