Contacts of the strand formed by residues 149 - 154 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ALA* 1.3 71.8 - - - +
150F VAL* 1.3 61.3 + - - +
151F GLN* 3.5 19.8 - - - +
165F GLU* 5.5 0.2 - - - -
199F GLU 3.7 1.4 - - - +
200F VAL* 3.6 5.9 - - - +
201F THR* 3.1 46.3 + - - +
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F CYS* 4.3 8.3 - - - -
140F LEU* 3.7 26.5 - - + -
148F ALA 4.1 3.8 + - - +
149F LYS* 1.3 75.0 - - - +
151F GLN* 1.3 64.0 + - - +
152F TRP* 4.3 7.3 + - + +
165F GLU* 3.3 28.6 + - - +
179F LEU* 3.8 13.9 - - + -
181F SER* 3.9 22.7 - - - +
198F CYS* 4.2 22.7 - - + -
199F GLU 3.6 5.4 - - - +
200F VAL* 4.5 2.2 - - + -
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Residues in contact with GLN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F LYS* 3.5 29.1 - - - +
150F VAL* 1.3 73.9 - - - +
152F TRP* 1.3 62.1 + - - +
153F LYS* 3.5 24.8 + - - +
158F LEU* 4.0 14.8 - - + -
198F CYS* 3.4 2.9 - - - -
199F GLU* 2.9 62.2 + - + +
201F THR* 4.0 12.4 + - - +
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Residues in contact with TRP 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ILE* 4.0 9.0 - - + -
136F VAL* 3.5 54.1 - - + -
137F VAL 4.1 0.9 - - - -
138F CYS* 3.5 29.6 - - + -
150F VAL* 4.3 7.0 + - + +
151F GLN* 1.3 74.6 - - - +
153F LYS* 1.3 61.6 + - - +
158F LEU* 3.7 6.5 - - - +
159F GLN* 3.0 49.2 + - + +
163F SER* 3.8 18.0 + - - -
181F SER* 2.9 30.4 + - - -
183F LEU* 3.7 31.2 - - + +
196F TYR* 5.0 1.6 - - + -
197F ALA 3.3 33.2 - - - -
198F CYS* 4.0 7.0 - - + -
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Residues in contact with LYS 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F GLN* 3.5 24.4 - - - +
152F TRP* 1.3 77.9 - - - +
154F VAL* 1.3 64.1 + - - +
155F ASP 4.1 0.6 + - - -
156F ASN* 4.1 24.9 - - - +
157F ALA 3.3 12.1 - - - +
158F LEU* 3.6 19.0 - - + +
195F VAL* 4.0 0.7 - - - +
196F TYR* 3.7 2.8 - - - -
197F ALA* 2.9 43.5 + - + +
199F GLU* 3.1 39.3 + - + +
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Residues in contact with VAL 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LYS* 1.3 76.4 - - - +
155F ASP* 1.4 63.2 + - - +
157F ALA* 2.9 31.6 + - - +
159F GLN* 3.5 33.4 - - + +
183F LEU* 4.1 10.5 - - + -
185F LEU* 5.0 3.8 - - + -
193F HIS* 3.3 48.5 + - + +
195F VAL 3.4 5.2 - - - +
196F TYR* 3.5 30.7 - - + -
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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