Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 5DK3
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 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA* 1.3 75.1 - - - +
150A VAL* 1.3 74.8 + - - +
151A GLN* 3.8 33.2 + - + +
165A GLU* 5.2 0.9 - - - -
199A GLU 3.6 0.7 - - - +
200A VAL* 3.4 6.9 - - - +
201A THR* 3.0 59.5 + - - +
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.8 34.1 - - + -
149A LYS* 1.3 80.7 - - - +
151A GLN* 1.3 72.7 + - - +
152A TRP* 4.1 13.7 - - + +
165A GLU* 3.7 24.5 + - - +
179A LEU* 3.9 7.6 - - + -
181A SER* 4.1 19.5 - - - +
198A CYS* 3.7 26.5 - - - -
199A GLU 3.3 3.8 - - - +
200A VAL* 4.6 1.1 - - + -
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS* 3.8 34.2 + - + +
150A VAL* 1.3 79.8 - - - +
152A TRP* 1.3 62.9 + - - +
153A LYS* 4.1 18.7 + - - +
158A LEU* 3.7 32.3 - - + +
197A ALA 3.7 0.5 - - - +
198A CYS* 3.6 3.6 - - - -
199A GLU* 2.8 54.6 + - + +
201A THR* 5.0 4.2 - - - +
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Residues in contact with TRP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.8 17.0 - - + -
136A VAL* 3.6 49.4 - - + -
137A VAL 3.8 4.9 - - - -
138A CYS* 3.6 34.1 - - + -
150A VAL* 4.1 9.8 - - + +
151A GLN* 1.3 73.0 - - - +
153A LYS* 1.3 61.8 + - - +
158A LEU* 3.6 8.3 - - - +
159A GLN* 2.9 49.3 + - + +
163A SER* 3.5 25.8 + - - -
181A SER* 2.9 26.5 + - - -
183A LEU* 3.7 27.4 - - + +
196A TYR* 5.3 0.9 - - + -
197A ALA 3.3 21.5 - - - -
198A CYS* 4.0 5.4 - - + -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 4.2 28.5 + - + +
152A TRP* 1.3 80.7 - - - +
154A VAL* 1.3 64.8 + - - +
155A ASP 4.0 0.4 - - - -
156A ASN* 4.2 21.5 - - - +
157A ALA 3.3 11.4 - - - +
158A LEU* 4.4 13.7 - - + +
195A VAL 3.7 2.3 - - - +
196A TYR* 3.7 1.7 - - - -
197A ALA* 3.0 48.3 + - + +
199A GLU* 2.7 35.8 + - + +
210A THR* 5.6 2.9 - - - -
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 1.3 76.3 - - - +
155A ASP* 1.3 67.5 + - - +
157A ALA* 3.0 24.7 + - - +
159A GLN* 3.6 28.5 - - - +
183A LEU* 3.8 17.5 - - + -
185A LEU* 4.6 6.5 - - + -
193A HIS* 3.4 44.1 + - + -
195A VAL 3.4 3.4 - - - +
196A TYR* 3.7 27.8 - - + -
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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