Contacts of the helix formed by residues 165 - 171 (chain C) in PDB entry 3IZ0
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 SER 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B GLU* 4.5 9.9 - - - -
152C PRO* 4.8 0.4 - - - -
163C ALA* 4.0 2.8 + - - +
164C LEU* 1.3 74.9 - - - +
166C LYS* 1.3 64.4 + - - +
167C SER* 3.7 8.4 + - - -
168C SER* 2.8 50.1 + - - -
169C MET* 3.5 7.7 + - - +
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Residues in contact with LYS 166 (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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196B GLU* 5.1 4.9 + - - +
148C GLU* 3.9 36.3 + - + +
149C GLU* 3.1 37.3 + - + +
152C PRO* 5.0 1.0 - - - +
164C LEU 3.8 1.0 + - - -
165C SER* 1.3 71.6 - - - +
167C SER* 1.3 62.9 + - - +
169C MET* 3.1 20.4 + - - +
170C TYR* 3.7 22.7 - - + -
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Residues in contact with SER 167 (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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196B GLU* 3.2 31.4 + - - -
263B PRO* 6.0 8.0 - - - +
264B ARG* 4.5 18.1 + - - -
165C SER* 3.2 6.4 + - - -
166C LYS* 1.3 76.4 - - - +
168C SER* 1.3 68.1 + - - +
169C MET 3.2 0.3 + - - -
170C TYR* 3.2 22.9 + - - +
171C THR* 3.3 16.0 + - - +
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 4.7 1.8 - - - +
165C SER* 2.8 40.2 + - - -
167C SER* 1.3 75.7 + - - +
169C MET* 1.3 71.7 + - - +
171C THR* 3.0 6.8 + - - -
172C VAL* 2.9 31.2 + - - -
177C THR* 4.1 14.4 - - - +
180C HIS* 6.0 0.9 - - - +
181C ILE* 4.1 13.6 - - - +
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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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122C VAL* 3.6 9.5 - - - +
125C PHE* 4.4 10.8 - - + -
147C PHE* 3.2 22.7 - - + +
148C GLU* 3.7 23.8 - - + +
151C VAL* 3.6 36.8 - - + -
152C PRO* 3.6 23.1 - - + -
164C LEU* 4.4 15.3 - - + -
165C SER 3.7 7.0 - - - +
166C LYS 3.3 9.6 - - - +
167C SER 3.1 0.8 - - - -
168C SER* 1.3 81.0 - - - +
170C TYR* 1.3 57.8 + - - +
171C THR 3.6 0.3 + - - -
172C VAL* 3.7 14.2 - - + +
181C ILE* 3.7 29.8 - - + -
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Residues in contact with TYR 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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406A HIS* 5.7 3.1 - - - +
263B PRO* 6.0 2.2 - - + -
122C VAL* 3.6 16.3 - - - +
147C PHE* 4.4 12.1 - + - -
148C GLU* 3.2 44.1 + - + +
166C LYS* 3.7 34.5 - - + -
167C SER* 3.2 16.2 + - - +
168C SER 3.2 0.6 - - - -
169C MET* 1.3 77.4 - - - +
171C THR* 1.3 68.7 + - + +
172C VAL 3.7 0.7 - - - -
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Residues in contact with THR 171 (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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406A HIS* 5.2 7.2 - - + -
263B PRO* 3.1 38.6 - - + +
122C VAL* 4.9 1.6 - - - -
167C SER* 3.3 15.0 + - - +
168C SER* 3.0 5.9 + - - -
170C TYR* 1.3 92.7 - - + +
172C VAL* 1.3 64.9 + - - +
173C GLY 3.1 3.1 - - - -
174C ALA* 2.8 32.1 + - - +
177C THR* 3.6 15.7 + - - +
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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