Contacts of the helix formed by residues 169 - 175 (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 CYS 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B CYS 3.4 5.0 + - - +
166B SER 3.0 8.9 + - - -
167B THR 3.3 0.6 - - - -
168B SER* 1.4 78.1 - - - +
170B PRO* 1.3 67.3 - - + +
171B SER* 4.0 4.9 - - - +
172B TYR* 3.1 36.3 + - - +
173B TRP* 3.0 19.0 + - - -
179B TYR* 4.2 6.7 - - - -
182B PRO* 3.8 28.3 - - + -
219B ILE* 4.7 10.3 - - + -
221B ASN* 5.3 4.3 - - + -
222B CYS 5.7 2.5 - - - +
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Residues in contact with PRO 170 (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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168B SER 3.2 9.2 - - - +
169B CYS* 1.3 85.9 - - + +
171B SER* 1.3 66.1 + - - +
173B TRP* 2.9 42.7 + - + +
174B TRP* 3.0 26.0 + - + +
219B ILE* 4.0 2.7 - - + -
31C LEU* 5.5 2.9 - - + -
37C GLN* 3.0 42.0 - - - +
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Residues in contact with SER 171 (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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169B CYS* 3.2 5.9 - - - +
170B PRO* 1.3 76.2 - - - +
172B TYR* 1.3 61.8 + - - +
174B TRP* 3.3 11.4 + - - +
175B ASN* 3.0 24.6 + - - +
179B TYR* 3.7 14.6 - - - -
215B ARG* 2.9 45.4 + - - +
216B CYS* 5.1 2.2 - - - -
217B HIS* 4.4 14.7 + - - -
219B ILE* 4.6 6.3 - - - +
88D ASP* 5.4 3.3 + - - +
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Residues in contact with TYR 172 (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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105B PRO 6.1 0.2 - - - -
106B HIS* 4.8 6.7 - + + -
107B MET* 5.5 7.9 - - + -
119B ASN* 2.6 51.9 + - - +
120B PHE* 3.6 5.3 + + + -
123B GLN* 4.0 8.3 - - + -
166B SER* 3.3 32.8 - - - +
167B THR* 5.3 2.2 - - - -
169B CYS* 3.1 29.3 + - - +
170B PRO 3.0 0.2 - - - -
171B SER* 1.3 78.1 - - - +
173B TRP* 1.3 71.1 + + - +
175B ASN 4.3 0.9 - - - -
176B GLN* 3.3 55.0 + - + +
179B TYR* 3.9 20.1 - - - -
180B LEU 4.1 2.5 - - - -
181B GLY* 4.3 7.2 - - - -
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Residues in contact with TRP 173 (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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105B PRO* 3.8 6.7 - - + +
106B HIS* 2.7 63.6 + - + +
166B SER 4.7 1.1 - - - -
167B THR 3.0 23.6 + - - -
168B SER* 5.5 2.2 - - - -
169B CYS 3.0 26.3 + - - -
170B PRO* 2.9 28.9 + - + +
172B TYR* 1.3 82.4 - + + +
174B TRP* 1.3 79.7 + + + +
176B GLN* 4.1 1.6 - - - +
25C ARG* 3.4 26.9 - - - -
26C PRO* 4.3 20.6 - - + -
28C SER* 4.6 9.0 - - - -
31C LEU* 3.5 30.5 - - + -
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Residues in contact with TRP 174 (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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106B HIS* 5.9 2.5 - + - -
170B PRO* 3.0 26.8 + - + +
171B SER* 3.7 7.4 - - - +
173B TRP* 1.3 98.6 - + + +
175B ASN* 1.3 66.6 + - - +
176B GLN 3.9 1.2 + - - -
47C ARG* 5.3 0.8 - - - +
88D ASP* 3.3 66.9 + - + +
89D TYR* 4.0 40.9 + + - -
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Residues in contact with ASN 175 (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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171B SER* 3.0 9.7 + - - +
172B TYR* 3.4 5.4 - - - +
174B TRP* 1.3 85.0 - - - +
176B GLN* 1.3 64.4 + - - +
177B GLU 3.2 1.8 - - - +
178B GLN* 3.4 34.8 - - + +
179B TYR* 3.1 28.3 + - + +
211B MET* 3.6 26.2 - - - +
215B ARG* 4.0 5.3 - - - +
87D THR* 4.9 8.0 + - - +
88D ASP* 3.6 21.8 + - - -
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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