Contacts of the strand formed by residues 147 - 151 (chain Q) in PDB entry 3SDI
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 147 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41Q LYS* 4.4 5.2 - - - +
46Q VAL* 3.5 9.4 - - - +
109Q VAL* 3.9 27.4 - - + -
110Q GLU* 5.9 1.6 - - + +
138Q ILE 4.6 0.7 - - - -
139Q ALA* 3.5 4.5 - - - -
140Q GLY 3.2 37.2 + - - +
142Q ASP* 3.5 29.8 + - - +
144Q ASP* 4.5 5.0 + - - -
145Q GLU* 3.4 43.3 + - - +
146Q PRO* 1.3 79.5 - - - +
148Q LEU* 1.3 62.1 + - - +
149Q TYR* 4.5 17.0 + - + +
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Residues in contact with LEU 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q GLY* 3.4 28.9 - - - +
40Q VAL* 4.4 3.6 - - - +
41Q LYS* 4.2 11.0 - - + +
46Q VAL* 4.1 6.5 - - + -
48Q LEU* 3.9 17.0 - - + -
137Q LEU* 4.3 20.2 - - + -
138Q ILE 3.6 6.3 - - - +
139Q ALA* 3.8 22.4 - - + -
147Q LYS* 1.3 75.4 - - - +
149Q TYR* 1.3 65.5 + - - +
159Q SER* 3.1 10.9 - - - -
160Q TRP* 3.0 51.9 + - + +
161Q SER 4.3 2.9 - - - +
162Q ALA* 4.0 9.2 - - - -
163Q GLN 4.2 2.0 - - - +
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Residues in contact with TYR 149 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Q VAL* 4.3 11.0 - - + -
110Q GLU* 3.3 44.6 - - + +
113Q THR* 3.4 39.7 - - + +
136Q THR 3.7 0.3 - - - +
137Q LEU* 3.3 9.6 - - - +
138Q ILE* 2.9 36.0 + - + +
147Q LYS* 4.5 21.8 - - + +
148Q LEU* 1.3 80.8 - - - +
150Q GLN* 1.3 59.9 + - - +
157Q TYR* 4.2 9.0 - + - -
158Q SER* 3.2 25.8 - - - -
159Q SER* 3.5 25.1 + - - +
160Q TRP* 4.7 1.6 - - - -
63R SER* 4.9 7.1 - - - -
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Residues in contact with GLN 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Q SER* 4.6 1.6 + - - -
136Q THR 3.2 9.2 - - - +
137Q LEU* 4.4 6.3 - - + -
149Q TYR* 1.3 75.5 - - - +
151Q THR* 1.3 71.6 + - - +
152Q GLU* 3.3 25.5 + - - +
156Q ILE 3.9 0.2 - - - +
157Q TYR* 3.1 25.6 - - - +
158Q SER* 2.9 13.0 + - - -
160Q TRP* 2.9 37.4 - - + +
163Q GLN* 3.1 23.2 + - + +
165Q ILE* 3.8 26.1 - - + +
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Residues in contact with THR 151 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q THR* 3.8 28.7 - - + +
116Q VAL* 4.1 1.4 - - + +
117Q ALA* 4.1 15.0 - - + +
120Q GLN* 2.8 24.2 + - - -
135Q SER* 3.2 8.7 + - - -
136Q THR* 2.5 55.0 + - - +
138Q ILE* 4.2 7.0 - - + -
150Q GLN* 1.3 82.9 - - - +
152Q GLU* 1.3 62.5 + - - +
156Q ILE 3.4 8.5 - - - -
157Q TYR* 3.9 5.6 - - + -
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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