Contacts of the helix formed by residues 163 - 168 (chain B) in PDB entry 1ORZ
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 ALA 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.5 3.3 - - + +
107B MET* 3.6 26.0 - - + -
117B LEU* 4.7 5.8 - - + -
120B PHE* 3.8 34.0 - - + -
159B CYS* 6.1 0.6 - - - -
161B LEU* 3.2 4.5 - - - +
162B CYS* 1.3 82.4 - - - +
164B CYS* 1.3 65.9 + - - +
165B CYS* 3.2 7.1 - - - +
166B SER* 4.1 4.5 - - - +
167B THR* 3.2 22.9 + - - +
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Residues in contact with CYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ALA* 4.9 5.8 - - + -
83B ASN* 3.9 13.6 - - + -
84B THR* 5.0 2.2 - - - +
85B LEU* 5.7 0.2 - - + -
104B LEU* 4.3 4.5 - - - -
162B CYS* 3.1 18.6 - - + -
163B ALA* 1.3 79.2 - - - +
165B CYS* 1.3 72.3 + - - +
167B THR* 2.7 28.0 - - - +
168B SER* 2.8 13.2 + - - -
225B THR* 3.4 25.8 - - - +
226B CYS* 3.8 4.3 - - - -
227B PRO* 3.2 36.1 - - + -
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Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B CYS* 6.3 0.4 - - - -
162B CYS* 5.9 1.6 - - - -
163B ALA* 4.8 3.4 - - - -
164B CYS* 1.3 85.5 - - - +
166B SER* 1.3 76.6 + - - +
168B SER* 2.9 19.1 + - - -
169B CYS* 3.4 5.7 + - - +
182B PRO* 3.8 5.2 - - - -
183B ALA* 3.7 38.4 - - - -
222B CYS* 3.5 35.7 - - + +
225B THR* 3.4 14.1 - - + -
226B CYS* 5.6 2.7 - - + +
232B PRO* 4.8 6.5 - - + -
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET* 5.6 1.6 - - - -
120B PHE* 4.2 28.5 - - - -
163B ALA* 3.8 3.7 + - - -
164B CYS 3.5 0.4 - - - -
165B CYS* 1.3 84.7 - - - +
167B THR* 1.3 63.0 + - - +
169B CYS 3.0 11.6 + - - +
172B TYR* 3.3 51.7 - - - +
173B TRP* 4.7 0.2 - - - -
180B LEU 5.0 0.5 + - - -
181B GLY* 4.3 2.3 - - - -
182B PRO* 4.2 19.0 - - - +
183B ALA 5.0 0.4 - - - -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASN* 2.9 30.5 - - - +
104B LEU* 3.1 12.4 - - + +
105B PRO* 2.6 49.2 + - + +
107B MET* 4.6 8.4 - - - +
163B ALA 3.2 15.2 + - - +
164B CYS* 2.7 25.1 - - - +
166B SER* 1.3 78.6 - - - +
168B SER* 1.3 56.6 + - - +
172B TYR* 5.3 2.7 - - - -
173B TRP* 3.0 24.3 + - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 5.6 0.5 - - - +
83B ASN* 2.7 27.6 + - - +
105B PRO* 5.4 0.9 - - - -
164B CYS 2.8 10.1 + - - -
165B CYS* 2.9 13.8 + - - -
167B THR* 1.3 77.9 - - - +
169B CYS* 1.4 57.3 + - - +
170B PRO* 3.2 11.8 - - - +
173B TRP* 4.6 3.4 - - - -
221B ASN* 3.4 34.7 - - - +
225B THR* 3.8 9.7 - - - -
7C ASN* 5.6 0.4 - - - -
31C LEU* 6.0 1.6 - - - +
33C ILE* 5.5 0.2 - - - +
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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