Contacts of the strand formed by residues 172 - 177 (chain M) in PDB entry 3AOI
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 ILE 172 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M ALA 4.4 0.2 - - - -
161M SER* 3.4 4.5 + - - -
162M ILE* 2.8 75.6 + - + +
164M PRO* 3.9 4.0 - - + -
170M PRO* 3.4 23.1 - - + +
171M TRP* 1.3 81.2 - - - +
173M ASP* 1.3 67.3 + - - +
174M LEU* 5.1 2.7 - - + -
184M MET* 3.8 22.9 - - + -
185M LYS 3.3 3.1 - - - +
186M VAL* 3.1 30.3 - - + -
258M TYR* 4.2 20.6 - - + +
303M PHE* 5.4 2.0 - - + -
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Residues in contact with ASP 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159M ILE* 4.4 15.6 - - + +
160M ALA 3.0 7.6 - - - +
161M SER* 4.2 11.9 + - - -
171M TRP* 3.0 36.0 + - - +
172M ILE* 1.3 76.9 - - - +
174M LEU* 1.3 78.2 + - - +
175M GLU* 6.1 1.8 - - + -
183M SER 4.2 0.7 - - - -
184M MET* 3.2 1.2 - - - +
185M LYS* 3.1 42.3 + - + +
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Residues in contact with LEU 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159M ILE* 3.2 10.2 - - - +
160M ALA* 2.7 44.1 + - + +
162M ILE* 4.8 9.9 - - + -
172M ILE* 5.1 2.7 - - + -
173M ASP* 1.3 95.7 - - - +
175M GLU* 1.3 60.3 + - - +
183M SER 3.2 1.6 - - - -
184M MET* 3.3 13.5 - - + -
193M LEU* 3.2 38.1 - - + -
303M PHE* 5.4 2.9 - - + -
306M THR* 2.7 46.4 - - + +
307M LEU* 4.2 5.2 - - + +
310M LEU* 4.1 13.4 - - + +
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Residues in contact with GLU 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M ASP* 3.5 18.4 - - - +
152M PRO* 5.0 5.2 - - - +
159M ILE* 3.9 19.0 - - + +
173M ASP* 5.8 1.6 - - + -
174M LEU* 1.3 74.4 - - - +
176M VAL* 1.3 64.0 - - - +
177M GLU* 2.5 42.1 - - - +
182M VAL* 3.3 0.8 - - - -
183M SER* 2.4 53.6 + - - +
185M LYS* 4.7 10.0 - - + +
190M LYS* 3.7 13.0 + - - -
193M LEU* 4.9 0.6 - - - +
310M LEU* 4.8 0.6 - - - +
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Residues in contact with VAL 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M ASP* 5.7 0.7 - - - +
154M ARG* 3.3 17.0 + - - +
157M ARG* 4.5 37.0 - - + +
158M TYR 5.0 4.0 - - - +
159M ILE* 5.0 1.0 - - + +
175M GLU* 1.3 75.1 - - - +
177M GLU* 1.3 64.0 + - - +
181M VAL 4.1 5.8 - - - +
182M VAL* 3.4 30.5 - - + -
217M LEU* 5.8 4.3 - - + -
310M LEU* 3.6 24.9 - - + +
311M PHE* 4.8 10.1 - - + -
314M THR* 5.1 0.4 - - - +
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Residues in contact with GLU 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M ASP* 5.3 0.2 - - - +
154M ARG* 3.2 5.7 + - - +
175M GLU* 2.5 58.8 - - - +
176M VAL* 1.3 75.6 - - - +
178M PRO* 1.3 81.1 - - + +
179M ASN* 4.7 5.8 - - + +
180M GLY 3.1 25.6 + - - +
181M VAL* 3.4 8.8 + - + +
183M SER* 3.4 19.1 - - - -
190M LYS* 3.5 11.0 + - - +
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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