Contacts of the helix formed by residues 177 - 182 (chain D) in PDB entry 3O9Z
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 GLY 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D LYS 5.0 3.1 - - - -
170D VAL* 6.0 1.6 - - - -
172D GLU* 4.0 16.7 - - - +
175D SER* 2.9 14.0 + - - -
176D GLY* 1.3 79.1 - - - +
178D LEU* 1.3 60.9 + - - -
179D ALA 3.5 2.2 - - - -
180D THR 3.2 2.8 + - - -
181D ASN* 2.8 28.8 + - - +
293D ARG* 5.5 0.9 - - - -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D TYR* 3.8 15.5 - - + +
169D LYS 5.7 0.2 - - - -
177D GLY* 1.3 67.7 - - - -
179D ALA* 1.3 69.9 + - - +
181D ASN* 4.4 2.2 - - - +
182D ILE* 2.9 52.2 + - + +
183D GLY 3.2 2.6 + - - -
206D THR 5.2 1.1 - - - +
207D PRO 4.0 11.0 - - - +
208D THR 3.6 33.0 - - - +
209D VAL 3.7 7.4 - - - +
210D ASN* 3.9 25.1 + - + +
225D LEU* 4.5 8.5 - - + +
226D SER* 4.8 1.6 - - - -
227D ILE* 3.8 22.7 - - + -
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D GLY 3.5 0.6 - - - -
178D LEU* 1.3 74.6 - - - +
180D THR* 1.3 54.4 + - - +
183D GLY* 2.2 41.3 + - - +
187D PHE* 3.8 7.2 - - + -
210D ASN* 3.0 28.8 + - + +
223D TRP* 4.7 2.2 - - + -
225D LEU* 3.9 10.1 - - + -
289D ALA* 5.5 0.9 - - - +
292D LEU* 3.9 37.5 - - + +
293D ARG* 6.5 0.4 - - + -
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Residues in contact with THR 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PRO* 3.7 29.2 - - + -
105D LEU* 4.3 1.3 - - + -
175D SER 3.5 15.5 - - - +
176D GLY 3.3 11.0 + - - -
177D GLY 3.2 7.9 + - - -
178D LEU 3.1 0.4 - - - -
179D ALA* 1.3 76.7 - - - +
181D ASN* 1.3 68.6 + - - +
184D ILE* 3.1 36.1 + - + +
289D ALA* 3.5 18.2 + - + +
293D ARG* 2.7 34.2 + - - +
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Residues in contact with ASN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 2.9 26.3 + - - +
101D LYS* 2.8 26.0 + - - +
164D TYR* 3.2 27.1 + - - +
168D TRP* 3.7 6.4 - - - -
169D LYS* 3.6 22.6 - - - +
175D SER* 4.1 19.1 - - - +
177D GLY 2.8 20.6 + - - +
178D LEU 4.3 0.4 - - - +
180D THR* 1.3 75.5 - - - +
182D ILE* 1.3 58.9 + - - +
311D NAD 3.6 11.4 + - - -
312D AKG 3.1 25.7 + - - +
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D TYR* 3.6 36.6 - - + +
158D THR* 3.9 6.5 - - + -
160D ARG* 3.8 26.9 - - - +
164D TYR* 3.9 14.8 - - + +
178D LEU* 2.9 34.7 + - + +
181D ASN* 1.3 78.1 - - - +
183D GLY* 1.3 69.1 + - - +
184D ILE 2.7 5.2 + - - -
185D HIS* 3.6 21.1 - - - +
186D PHE* 5.1 1.9 - - - -
225D LEU* 5.1 10.3 - - + -
226D SER 5.3 2.7 - - - +
227D ILE* 3.9 14.6 - - + -
312D AKG 4.3 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