Contacts of the helix formed by residues 165 - 170 (chain C) in PDB entry 1GZH
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 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C TYR* 3.4 1.6 - - - +
164C LYS* 1.3 79.7 - - + +
166C SER* 1.3 55.9 - - - +
167C GLN* 3.4 28.6 - - - +
168C HIS* 2.9 30.6 + - + +
169C MET* 2.8 34.7 + - - +
249C ARG* 4.2 4.3 - - - +
250C PRO* 3.4 32.7 - - + +
1861D ASP* 5.1 13.3 + - - +
1863D GLN* 5.8 1.8 - - - +
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Residues in contact with SER 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LYS 3.8 2.0 + - - -
165C GLN* 1.3 71.3 - - - +
167C GLN* 1.3 69.1 + - - +
168C HIS 2.9 1.8 + - - -
169C MET* 3.2 28.9 + - - +
170C THR* 4.7 5.5 + - - +
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Residues in contact with GLN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C GLN* 3.4 29.5 - - - +
166C SER* 1.3 86.5 + - - +
168C HIS* 1.3 84.4 + - + +
170C THR* 5.2 5.0 + - - +
1862D TRP 5.1 1.0 + - - +
1863D GLN* 3.3 43.2 + - + +
1864D PRO* 4.3 20.2 - - + -
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Residues in contact with HIS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TYR* 3.7 21.7 - - + -
165C GLN* 2.9 28.0 + - + +
166C SER 2.9 0.8 - - - -
167C GLN* 1.3 108.4 - - + +
169C MET* 1.3 53.6 + - - +
170C THR 3.3 2.7 - - - -
171C GLU* 2.7 40.6 + - + +
249C ARG* 3.2 48.6 + - + +
1844D ARG 5.4 1.3 + - - -
1847D LEU* 5.3 10.9 - - + +
1861D ASP* 5.3 6.3 - - + -
1862D TRP 5.1 10.1 + - - -
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Residues in contact with MET 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 3.4 45.0 - - + +
98C PRO 4.9 1.1 - - - +
100C GLN* 3.3 26.5 - - - +
162C ILE* 4.3 7.6 - - + +
163C TYR* 3.4 24.1 + - - +
164C LYS 4.3 5.6 - - - +
165C GLN 2.8 23.0 + - - +
166C SER* 3.2 23.3 + - - +
168C HIS* 1.3 71.6 - - - +
170C THR* 1.3 59.9 + - + +
171C GLU 3.1 5.0 + - - +
213C ARG* 2.9 21.1 + - - -
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C SER* 4.9 15.3 + - - +
96C SER* 6.6 0.2 - - - -
97C VAL* 5.0 11.2 - - + +
166C SER 5.2 4.9 - - - +
167C GLN 5.2 4.5 + - - +
168C HIS 3.1 1.7 + - - -
169C MET* 1.3 78.4 - - + +
171C GLU* 1.3 62.3 + - - +
172C VAL* 3.8 5.2 + - - +
213C ARG* 3.6 12.3 + - - +
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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