Contacts of the helix formed by residues 158 - 164 (chain D) in PDB entry 3P9I
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 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D PHE* 3.7 1.3 - - - -
152D ASN* 3.5 20.9 - - - +
157D MET* 1.3 76.3 - - - +
159D ALA* 1.3 59.6 + - - +
160D PHE* 3.6 7.1 + - - +
161D GLU* 2.9 43.2 + - - +
162D TYR* 2.9 28.1 + - - +
268D TRP* 6.5 0.4 - - - -
322D PRO* 4.8 17.3 - - - -
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Residues in contact with ALA 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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133D LEU* 6.2 1.6 - - + -
151D PHE* 3.5 25.4 - - + -
152D ASN* 4.3 2.0 + - - -
158D SER* 1.3 72.7 - - - +
160D PHE* 1.3 67.0 + - + +
162D TYR* 3.2 3.1 + - - +
163D HIS* 2.9 40.1 + - + +
320D HIS* 3.7 26.1 + - + +
321D ASN* 3.7 15.5 - - - +
322D PRO* 5.8 1.5 - - + +
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Residues in contact with PHE 160 (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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158D SER* 3.3 6.3 + - - +
159D ALA* 1.3 74.3 - - + +
161D GLU* 1.3 67.1 + - + +
163D HIS* 3.4 39.6 + + - +
164D GLY* 3.6 3.6 + - - -
173D PHE* 4.2 6.7 - + - -
229D LEU* 4.4 18.7 - - + +
231D HIS* 3.9 10.4 + - - -
267D ASP* 3.5 30.1 - - + -
268D TRP* 3.9 25.4 - + - -
321D ASN* 4.0 19.1 - - - -
322D PRO* 5.1 4.5 - - + -
404D SAH 3.6 55.9 - + + +
604D SNY 4.1 4.3 - - - -
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Residues in contact with GLU 161 (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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157D MET* 3.6 16.8 - - + +
158D SER* 2.9 47.5 + - - +
160D PHE* 1.3 77.0 - - + +
162D TYR* 1.3 62.6 + - - +
164D GLY* 3.2 11.8 + - - -
165D THR* 3.4 14.4 - - - +
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Residues in contact with TYR 162 (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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132D VAL* 3.8 27.1 - - + +
151D PHE* 3.5 24.2 - + + -
155D TYR* 3.6 36.2 - + + -
157D MET* 3.5 21.4 - - + -
158D SER 2.9 9.4 + - - +
159D ALA 3.2 8.5 + - - +
161D GLU* 1.3 74.9 - - - +
163D HIS* 1.3 64.2 + + - +
165D THR* 2.8 40.1 + - - -
166D ASP* 2.6 44.9 + - + +
169D PHE* 4.4 7.9 - + - -
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Residues in contact with HIS 163 (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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133D LEU* 5.8 1.4 - - - +
151D PHE* 5.7 1.3 - + - -
159D ALA* 2.9 36.4 + - + +
160D PHE* 3.5 30.9 - + - +
161D GLU 3.3 0.2 - - - -
162D TYR* 1.3 80.4 - + - +
164D GLY* 1.3 57.8 + - - +
165D THR 3.2 4.3 + - - -
166D ASP 3.5 7.4 + - - +
167D PRO* 5.1 0.2 - - - +
169D PHE* 3.7 31.1 - + - -
170D ASN* 3.2 46.0 + - + +
173D PHE* 3.3 50.6 - + + +
174D ASN* 5.5 0.2 + - - -
231D HIS* 4.3 5.6 - - + +
404D SAH 5.6 1.4 + - - -
604D SNY 6.1 0.6 - - - -
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Residues in contact with GLY 164 (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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160D PHE 3.6 3.8 + - - -
161D GLU 3.2 8.5 + - - -
162D TYR 3.0 1.6 - - - -
163D HIS* 1.3 79.3 - - - +
165D THR* 1.3 61.8 + - - +
166D ASP 3.6 0.7 - - - -
167D PRO* 5.9 0.4 - - - -
231D HIS* 4.0 27.9 - - - +
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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