Contacts of the helix formed by residues 152 - 159 (chain D) in PDB entry 3T79
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 SER 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D VAL* 1.3 81.3 - - - +
153D PHE* 1.3 60.9 + - - +
154D GLU* 3.3 17.0 + - - +
155D ASP* 3.5 24.0 + - - -
156D ARG* 2.8 24.6 + - - +
269D PHE 4.3 7.7 + - - -
270D GLN* 4.6 1.1 - - - +
271D VAL* 4.4 28.0 - - - +
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Residues in contact with PHE 153 (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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152D SER* 1.3 70.3 + - - +
154D GLU* 1.3 67.3 + - + +
156D ARG* 2.7 67.0 + - - +
157D THR* 2.9 31.0 + - + +
242D TYR* 4.1 11.4 - + - -
243D PRO 3.7 14.8 - - - -
244D ARG* 4.2 0.4 - - - -
245D GLU* 3.6 42.4 - - + -
248D LEU* 3.6 25.4 - - + -
269D PHE* 3.3 39.1 + + + +
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Residues in contact with GLU 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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152D SER* 3.3 8.2 + - - +
153D PHE* 1.3 85.7 - - + +
155D ASP* 1.3 73.5 + - - +
157D THR* 2.9 36.2 + - - +
158D THR* 3.0 12.4 + - - -
269D PHE 4.9 0.4 + - - -
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Residues in contact with ASP 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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151D VAL* 3.6 21.9 - - + +
152D SER* 3.4 19.5 + - - +
153D PHE 3.2 0.4 - - - -
154D GLU* 1.3 90.1 + - - +
156D ARG* 1.3 62.9 + - - +
158D THR* 2.8 30.7 - - - +
159D VAL* 3.4 6.8 + - - +
182D LYS* 5.6 2.5 - - - +
183D PRO* 3.6 21.5 - - + +
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Residues in contact with ARG 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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142D ASP* 2.6 51.9 + - - -
145D TRP* 3.2 47.0 - - + -
146D LYS* 4.3 16.6 - - - +
151D VAL* 3.4 25.7 + - + +
152D SER 2.8 7.8 + - - +
153D PHE* 2.7 60.7 + - + +
155D ASP* 1.3 72.0 - - - +
157D THR* 1.3 55.8 + - - +
159D VAL* 3.1 20.6 + - - +
242D TYR* 3.6 17.7 - - + +
248D LEU* 4.9 0.2 - - - +
252D TYR* 4.8 2.0 + - - -
268D TRP 2.1 36.2 + - - -
269D PHE* 3.6 1.2 - - - +
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Residues in contact with THR 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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153D PHE* 3.1 42.8 - - + +
154D GLU* 2.9 19.4 + - - +
156D ARG* 1.3 74.6 - - - +
158D THR* 1.3 63.5 + - - +
159D VAL 3.4 0.8 - - - +
230D HIS* 3.8 19.4 + - - -
242D TYR* 3.5 41.6 - - + +
243D PRO 5.0 0.7 - - - +
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Residues in contact with THR 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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154D GLU* 3.0 17.0 + - - -
155D ASP* 2.8 29.8 + - - +
157D THR* 1.3 78.2 - - - +
159D VAL* 1.3 63.6 + - - +
160D SER* 3.4 3.6 + - - -
163D ASP* 4.8 1.4 - - - +
182D LYS* 3.9 23.2 - - + +
183D PRO* 3.5 30.3 - - + -
230D HIS* 4.0 7.5 + - - -
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Residues in contact with VAL 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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145D TRP* 3.5 21.8 - - + -
155D ASP 3.5 9.9 - - - +
156D ARG* 3.1 23.8 - - - +
157D THR 3.4 1.3 - - - +
158D THR* 1.3 76.8 - - + +
160D SER* 1.3 69.2 + - - +
161D LEU 3.8 1.7 + - - -
163D ASP* 4.6 0.4 - - - -
164D LEU* 4.4 9.4 - - + -
179D HIS* 3.7 35.4 - - + +
183D PRO* 4.9 3.8 - - + -
185D PHE* 4.9 4.0 - - + -
230D HIS* 3.5 8.2 + - - -
232D PRO* 4.4 0.5 - - - +
233D ILE* 3.9 31.5 + - + +
242D TYR* 5.8 0.3 - - - -
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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