Contacts of the strand formed by residues 144 - 149 (chain Y) in PDB entry 3HI6
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 144 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y ALA* 1.3 73.6 - - - +
145Y VAL* 1.3 65.8 + - - +
146Y GLN* 3.1 44.8 - - + +
160Y GLU* 5.4 0.2 - - - -
194Y GLU 3.5 1.4 - - - +
195Y VAL* 3.5 4.9 - - - +
196Y THR* 2.9 56.0 + - + +
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Residues in contact with VAL 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133Y CYS* 4.5 7.0 - - - -
135Y LEU* 3.7 34.3 - - + -
143Y ALA 4.2 0.8 + - - +
144Y LYS* 1.3 83.3 + - - +
146Y GLN* 1.3 65.4 + - - +
147Y TRP* 4.3 7.7 + - - +
158Y SER* 5.6 1.6 + - - -
160Y GLU* 3.9 22.5 + - - +
174Y LEU* 4.2 11.4 - - + -
176Y SER* 3.8 23.8 + - - +
193Y CYS* 4.3 21.1 - - + -
194Y GLU 3.5 4.5 - - - +
195Y VAL* 4.4 3.8 - - + -
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Residues in contact with GLN 146 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y LYS* 3.1 40.9 + - + +
145Y VAL* 1.3 75.3 - - - +
147Y TRP* 1.3 62.8 + - - +
148Y LYS* 4.0 13.1 + - + +
153Y LEU* 3.6 39.4 - - + +
192Y ALA 3.8 0.3 - - - +
193Y CYS* 3.2 5.1 - - - -
194Y GLU* 2.8 64.7 + - + +
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Residues in contact with TRP 147 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y ILE* 4.0 17.0 - - + -
131Y VAL* 3.4 46.7 - - + -
132Y VAL 4.0 0.9 - - - -
133Y CYS* 3.6 21.5 - - + -
145Y VAL* 4.6 6.3 - - + +
146Y GLN* 1.3 75.4 - - - +
148Y LYS* 1.3 61.5 + - - +
153Y LEU* 3.6 8.3 - - - +
154Y GLN* 2.9 50.2 + - + +
158Y SER* 3.6 24.9 - - - -
176Y SER* 3.0 44.0 + - - -
178Y LEU* 3.6 27.3 - - + +
191Y TYR* 5.2 2.7 - - + -
192Y ALA 3.5 20.4 - - - -
193Y CYS* 4.0 8.7 - - + -
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Residues in contact with LYS 148 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Y GLN* 4.0 11.8 + - + +
147Y TRP* 1.3 77.4 - - - +
149Y VAL* 1.3 63.3 + - - +
150Y ASP 4.0 0.4 - - - -
151Y ASN* 3.0 59.0 + - - +
152Y ALA 3.4 3.8 - - - +
153Y LEU* 4.3 14.1 - - + +
190Y VAL* 3.6 3.6 - - - +
191Y TYR* 3.8 1.6 - - - -
192Y ALA* 2.9 46.0 + - + +
194Y GLU* 5.5 15.7 - - + -
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Residues in contact with VAL 149 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y TRP* 6.0 0.2 - - + -
148Y LYS* 1.3 75.7 - - - +
150Y ASP* 1.3 70.2 + - - +
152Y ALA* 3.0 25.3 + - + +
154Y GLN* 3.6 32.8 - - + +
178Y LEU* 4.3 8.1 - - + -
180Y LEU* 4.8 4.0 - - + -
188Y HIS* 3.3 47.9 + - + +
190Y VAL 3.4 4.0 - - - +
191Y TYR* 3.9 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