Contacts of the strand formed by residues 152 - 159 (chain D) in PDB entry 3H3B
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 VAL 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D GLU* 3.6 45.1 - - + +
146D VAL* 4.4 9.9 - - + -
151D SER* 1.3 75.8 - - - +
153D LYS* 1.3 65.7 + - - +
154D ILE* 4.8 4.7 - - + -
215D MET 3.7 0.7 - - - +
216D GLN* 3.3 5.9 - - - +
217D LEU* 2.8 65.2 + - + -
220D LEU* 3.6 12.8 - - + +
250D VAL* 4.3 14.4 - - + -
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 6.2 1.8 - - - -
160A THR* 5.7 2.8 + - - -
141D SER* 4.4 3.1 + - - -
144D GLU* 4.4 12.1 - - - +
152D VAL* 1.3 76.2 - - - +
154D ILE* 1.3 64.7 + - - +
155D SER* 4.1 1.3 + - - -
205D THR* 5.0 4.9 + - - -
214D PHE* 3.8 48.9 - - + -
215D MET 3.6 6.1 - - - +
216D GLN* 4.4 23.3 - - + +
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Residues in contact with ILE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLN* 4.2 2.9 - - - +
141D SER* 3.7 7.4 - - - +
144D GLU* 5.4 2.0 - - + -
152D VAL* 4.8 8.1 - - + -
153D LYS* 1.3 77.0 - - - +
155D SER* 1.3 68.7 + - - +
170D TRP* 4.0 19.3 - - + -
214D PHE* 3.2 8.0 - - - +
215D MET* 2.9 60.7 + - + +
217D LEU* 4.2 6.5 - - + -
228D TYR* 3.8 18.8 - - + -
248D THR* 3.4 34.1 - - + +
250D VAL* 3.9 21.5 - - + -
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D GLN 5.0 1.7 + - - -
140D GLN* 3.3 8.4 - - - +
141D SER* 3.2 42.5 + - - -
153D LYS* 4.1 1.2 + - - -
154D ILE* 1.3 77.4 - - - +
156D CYS* 1.3 61.6 + - - +
157D LYS* 4.1 1.7 + - - +
170D TRP* 4.6 0.4 - - - -
212D THR* 4.1 7.0 - - - -
213D ALA 3.4 4.5 - - - -
214D PHE* 3.6 24.9 - - - -
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Residues in contact with CYS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 3.8 25.6 - - - -
139D GLN 3.7 3.6 - - - -
155D SER* 1.3 75.2 - - - +
157D LYS* 1.3 59.9 + - - +
158D ALA* 3.7 1.9 + - - +
163D PHE* 5.1 0.7 - - - -
168D ILE* 4.7 7.0 - - - -
170D TRP* 3.8 8.1 - - + -
211D SER 3.9 0.3 - - - +
212D THR* 3.3 4.7 - - - +
213D ALA* 2.6 42.3 + - + +
230D CYS* 2.0 54.3 - - + -
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Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN 3.5 1.7 - - - +
138D LEU* 3.4 4.8 - - - -
139D GLN* 2.7 55.2 + - + +
155D SER* 4.1 1.5 + - - +
156D CYS* 1.3 70.9 - - - +
158D ALA* 1.3 70.9 + - - +
159D SER* 5.2 4.8 + - - -
210D SER* 2.8 29.4 + - - +
211D SER* 3.9 2.0 - - - -
212D THR* 3.4 19.9 + - + +
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN 3.6 4.5 - - - -
138D LEU* 3.8 7.0 - - + -
156D CYS 3.7 1.3 + - - +
157D LYS* 1.3 81.5 - - - +
159D SER* 1.3 62.7 + - - +
161D TYR* 3.3 33.7 - - + +
163D PHE* 3.5 17.9 - - + -
168D ILE* 5.4 0.2 - - + -
211D SER* 2.9 35.8 + - - +
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Residues in contact with SER 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLU 3.7 3.3 + - - -
137D GLN* 3.0 45.1 + - - +
157D LYS* 5.2 6.4 + - - +
158D ALA* 1.3 76.2 - - - +
160D GLY* 1.3 60.3 + - - +
161D TYR* 3.3 15.8 - - - +
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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