Contacts of the strand formed by residues 145 - 150 (chain M) in PDB entry 4DKE
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 LYS 145 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144M ALA* 1.3 74.8 - - - +
146M VAL* 1.3 72.2 + - - +
147M GLN* 3.2 38.0 + - + +
195M GLU 3.6 3.0 - - - +
196M VAL* 3.7 1.7 - - - +
197M THR* 3.1 45.0 + - + +
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Residues in contact with VAL 146 (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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134M CYS* 4.9 0.2 - - - -
136M LEU* 4.0 29.6 - - + -
144M ALA 5.1 0.4 - - - +
145M LYS* 1.3 85.4 - - - +
147M GLN* 1.3 74.8 + - - +
148M TRP* 4.7 4.3 - - - +
161M GLU* 3.6 26.6 + - - +
175M LEU* 4.2 12.8 - - + -
177M SER* 3.8 19.7 - - - +
194M CYS* 3.8 28.5 - - - -
195M GLU 3.4 4.5 - - - +
196M VAL* 4.9 2.7 - - + -
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Residues in contact with GLN 147 (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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145M LYS* 3.2 30.0 + - + +
146M VAL* 1.3 80.8 - - - +
148M TRP* 1.3 65.3 + - - +
149M LYS* 3.9 1.5 + - + -
154M LEU* 3.7 38.5 - - + +
155M GLN 5.7 1.3 - - - +
194M CYS* 3.9 1.2 - - - -
195M GLU* 2.8 59.7 + - + +
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Residues in contact with TRP 148 (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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117M ILE* 3.7 10.8 - - + -
132M VAL* 3.6 43.3 - - + -
134M CYS* 3.7 26.5 - - + -
146M VAL* 4.7 3.5 - - + +
147M GLN* 1.3 76.0 - - - +
149M LYS* 1.3 59.5 + - - +
150M VAL* 5.9 0.2 - - + -
153M ALA 3.3 0.9 - - - +
154M LEU* 3.4 7.5 - - - +
155M GLN* 2.8 54.1 + - + +
159M SER* 3.2 23.3 + - - -
177M SER* 3.1 42.4 + - - -
179M LEU* 3.6 30.7 - - + +
192M TYR* 5.3 3.8 - - + -
193M ALA 3.5 24.7 - - - -
194M CYS* 4.5 7.2 - - + -
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Residues in contact with LYS 149 (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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147M GLN* 3.9 1.5 + - + +
148M TRP* 1.3 76.3 - - - +
150M VAL* 1.3 63.6 + - - +
151M ASP 3.8 0.7 + - - -
152M ASN* 3.8 37.2 + - - +
153M ALA 2.9 13.0 - - - +
154M LEU* 4.7 10.1 - - + -
191M VAL* 3.7 1.6 - - - +
192M TYR* 3.7 2.3 - - - -
193M ALA* 2.8 52.7 + - + +
195M GLU* 3.9 34.7 + - + +
206M THR* 5.9 0.7 - - + -
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Residues in contact with VAL 150 (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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148M TRP* 5.9 0.2 - - + -
149M LYS* 1.3 71.0 - - - +
151M ASP* 1.3 71.9 + - - +
153M ALA* 2.7 26.5 + - - +
155M GLN* 3.3 37.2 - - + +
179M LEU* 4.0 14.1 - - + -
181M LEU* 4.8 7.2 - - + -
185M ASP 5.4 0.9 - - - +
189M HIS* 3.8 29.4 - - + +
191M VAL 3.6 2.9 - - - -
192M TYR* 3.3 36.8 - - + +
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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