Contacts of the helix formed by residues 157 - 162 (chain D) in PDB entry 4P9O
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 PHE 157 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 4.5 8.5 - - - -
153D TYR* 2.9 16.9 + - + +
154D GLY 3.4 3.7 - - - +
156D THR* 1.4 91.2 - - - +
158D PRO* 1.4 61.1 - - - +
159D GLU 3.4 2.7 - - - -
160D TRP* 3.6 33.2 + + + +
161D PHE* 2.9 31.5 + - + -
187D PRO* 3.3 35.4 - - + -
188D VAL* 3.5 25.8 - - + -
191D VAL* 3.6 30.3 - - + -
192D HIS* 3.9 9.9 - + - -
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Residues in contact with PRO 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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155A ALA 3.1 27.1 - - - +
156A THR* 3.5 21.1 - - + +
158A PRO* 3.6 19.3 - - + -
154D GLY 3.3 12.3 - - - +
155D ALA* 4.1 5.6 - - - +
156D THR 3.7 1.8 - - - +
157D PHE* 1.4 88.0 - - - +
159D GLU* 1.3 59.8 + - + +
162D GLY* 2.9 23.2 + - - +
166D LYS* 3.1 21.1 + - - +
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Residues in contact with GLU 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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156A THR 5.1 8.0 + - - +
157A PHE* 4.6 18.3 - - + -
187A PRO* 4.8 4.9 - - - +
190A ASN* 5.4 4.5 - - - +
191A VAL* 4.7 14.1 - - + +
186C ARG* 4.0 12.0 + - - -
190C ASN* 5.4 5.2 - - - +
300C 2CV 5.5 0.9 + - - -
157D PHE 3.4 1.0 - - - -
158D PRO* 1.3 80.8 - - - +
160D TRP* 1.3 77.6 + - + +
166D LYS* 3.9 22.1 - - - +
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Residues in contact with TRP 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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182C MET* 4.4 10.8 - - + +
186C ARG* 3.6 28.0 - - - +
157D PHE* 3.6 35.7 + + + +
159D GLU* 1.3 96.4 + - + +
161D PHE* 1.4 77.0 + + + +
162D GLY 3.9 0.2 - - - -
166D LYS* 3.3 12.7 - - - +
170D THR* 2.7 29.8 + - + +
183D GLY 3.2 25.6 - - - -
184D ILE* 3.6 43.4 - - + +
187D PRO* 3.8 15.3 - - + -
188D VAL* 3.9 6.5 - - + -
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Residues in contact with PHE 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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149D ALA* 3.6 35.2 - - + +
150D THR* 3.3 13.2 - - - +
153D TYR* 3.8 20.2 - - + +
154D GLY* 3.0 15.6 - - - -
157D PHE* 2.9 17.1 + - + +
160D TRP* 1.4 89.1 - - + +
162D GLY* 1.3 63.3 + - - +
163D ASP 3.2 4.8 + - - -
167D SER* 3.3 27.6 - - - +
170D THR* 3.6 24.9 - - + -
171D LEU* 4.6 4.7 - - + -
174D VAL* 5.8 0.2 - - + -
184D ILE* 3.7 20.9 - - + -
188D VAL* 4.4 8.1 - - + -
199D PHE* 3.7 31.0 - + - -
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Residues in contact with GLY 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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150D THR* 4.0 5.6 - - - +
154D GLY* 3.7 16.4 - - - -
157D PHE 3.6 1.2 + - - -
158D PRO* 2.9 25.2 + - - -
160D TRP 3.9 0.6 - - - -
161D PHE* 1.3 74.6 - - - +
163D ASP* 1.3 62.8 + - - +
166D LYS* 4.1 5.2 - - - +
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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