Contacts of the strand formed by residues 160 - 164 (chain M) in PDB entry 6MUO
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 TYR 160 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M VAL* 3.7 13.5 - - + -
86M PHE 3.3 16.2 - - - +
87M GLN* 3.2 41.0 + - + +
153M VAL 4.4 0.3 - - - +
154M TYR* 3.2 14.8 - - - -
155M TYR* 3.7 10.7 + - + +
158M THR* 3.1 28.0 + - + +
159M PRO* 1.3 78.0 - - - +
161M ALA* 1.3 58.4 + - - +
162M PHE* 4.3 12.6 + - + -
191M MET* 4.5 11.6 - - - +
193M LEU* 5.8 0.9 - - + -
205M VAL* 3.6 36.3 + - + -
208M GLN* 5.3 4.9 + - - +
209M TYR* 3.4 40.4 + + + +
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Residues in contact with ALA 161 (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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84M ASP 3.5 1.4 - - - +
85M VAL* 3.4 5.2 - - - -
86M PHE* 2.8 47.4 + - + -
87M GLN* 5.6 0.2 - - - -
88M MET* 6.4 0.4 - - + -
152M VAL* 4.6 7.6 - - + -
153M VAL 3.5 5.6 - - - +
154M TYR* 3.8 19.7 - - + -
159M PRO 3.7 1.5 + - - +
160M TYR* 1.3 73.9 - - - +
162M PHE* 1.3 62.8 + - - +
163M THR* 3.6 9.1 + - - +
179M LEU* 4.6 14.1 - - + -
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Residues in contact with PHE 162 (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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83M TRP* 4.1 12.0 - - + -
84M ASP 3.4 2.7 - - - -
85M VAL* 3.8 33.0 - - + -
151M TYR 3.8 1.2 - - - +
152M VAL* 3.3 0.9 - - - -
153M VAL* 2.5 57.2 + - + +
155M TYR* 3.5 42.8 - + - -
160M TYR* 4.3 9.2 - - + -
161M ALA* 1.3 76.0 - - - +
163M THR* 1.3 60.1 + - - +
198M LEU* 4.9 18.8 - - + -
201M LEU* 4.2 26.7 - - + -
205M VAL* 4.1 24.7 - - + -
206M PHE* 4.2 9.2 - + - -
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Residues in contact with THR 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M TRP* 3.3 4.1 - - - -
84M ASP* 2.5 54.8 + - + +
86M PHE* 4.0 23.7 - - + -
150M THR* 4.5 4.7 - - + -
151M TYR 3.4 2.9 - - - +
152M VAL* 3.8 29.2 - - + +
161M ALA* 3.9 9.2 + - - +
162M PHE* 1.3 74.1 - - - +
164M SER* 1.3 75.4 + - - +
166M SER* 5.5 1.3 - - - +
175M LEU* 4.2 13.2 - - + +
179M LEU* 5.7 0.5 - - - +
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Residues in contact with SER 164 (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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81M LYS* 5.0 9.2 - - - -
82M VAL 3.6 7.4 - - - -
83M TRP* 3.5 14.8 - - - -
84M ASP* 5.2 0.7 - - - +
150M THR* 3.3 12.5 - - - +
151M TYR* 2.4 59.6 + - - -
163M THR* 1.3 88.4 - - - +
165M SER* 1.3 68.2 + - - +
166M SER* 3.6 2.9 + - - -
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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