Contacts of the helix formed by residues 150 - 155 (chain D) in PDB entry 2NPP
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 LEU 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D VAL* 3.3 30.7 - - + -
112D LEU* 3.8 22.2 - - + -
113D ARG* 4.0 11.7 - - + +
128D PHE* 4.0 8.6 - - + -
131D LEU* 3.6 29.6 - - + -
132D VAL* 3.7 18.1 - - + +
135D LEU* 3.8 16.4 - - + -
146D SER 4.0 6.1 - - - +
147D ALA* 2.9 15.9 + - - +
149D GLY* 1.3 78.2 - - - +
151D PHE* 1.3 65.2 + - - +
152D SER 3.7 0.4 - - - -
153D VAL* 3.5 17.6 - - - +
154D CYS* 3.7 12.1 - - - -
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Residues in contact with PHE 151 (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* 4.0 15.7 - - + -
136D ALA* 4.5 4.0 - - + -
147D ALA* 3.2 30.5 - - + -
148D CYS 3.4 12.5 + - - +
149D GLY 3.3 2.0 - - - -
150D LEU* 1.3 76.7 - - - +
152D SER* 1.3 68.7 + - - +
153D VAL 3.1 1.2 + - - -
154D CYS* 3.2 6.6 + - - -
155D TYR* 3.1 26.2 + + - +
166D LEU* 3.6 48.0 - - + -
169D TYR* 3.9 11.9 - + + -
170D PHE* 3.7 33.0 - + + -
173D LEU* 3.3 31.9 - - + -
192D PHE* 4.5 15.0 - + + -
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Residues in contact with SER 152 (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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113D ARG* 3.6 11.1 + - - -
148D CYS 5.0 0.2 + - - -
149D GLY 4.7 0.3 + - - -
150D LEU 3.7 0.4 - - - -
151D PHE* 1.3 78.6 - - - +
153D VAL* 1.3 62.3 + - - +
156D PRO* 3.2 26.2 - - - +
191D GLU* 3.1 56.2 + - - +
192D PHE* 4.6 3.2 - - - +
195D VAL* 4.0 19.1 - - - +
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Residues in contact with VAL 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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113D ARG* 3.9 33.0 - - + +
116D SER* 3.5 32.7 + - - +
117D HIS* 4.0 25.3 + - + +
124D LEU* 4.7 1.0 - - - +
128D PHE* 4.3 8.3 - - + -
150D LEU* 3.5 22.9 - - - +
152D SER* 1.3 89.3 + - - +
154D CYS* 1.3 61.3 + - - +
156D PRO* 4.3 3.7 - - - +
157D ARG* 4.7 13.2 + - - +
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Residues in contact with CYS 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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124D LEU* 3.8 18.9 - - + +
128D PHE* 3.5 30.5 - - + -
129D VAL* 3.6 24.2 - - + -
132D VAL* 4.3 7.2 - - - -
150D LEU 3.7 15.3 - - - -
151D PHE* 3.2 7.4 + - - -
153D VAL* 1.3 78.3 - - - +
155D TYR* 1.3 68.0 + - - +
156D PRO* 3.5 2.8 - - - -
157D ARG 3.6 5.9 + - - -
158D VAL* 3.3 21.0 - - - +
166D LEU* 4.3 12.3 - - - -
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Residues in contact with TYR 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 PHE* 3.1 15.6 + - + +
154D CYS* 1.3 79.9 - - - +
156D PRO* 1.3 70.7 - - + +
158D VAL* 3.2 16.8 - - - +
163D LYS* 3.2 53.8 - - + +
166D LEU* 3.5 30.7 - - + -
167D ARG* 2.8 24.1 + - + -
192D PHE* 4.0 15.5 - + + -
195D VAL* 3.5 30.3 - - + -
196D LEU* 2.8 24.3 - - + +
197D GLU* 2.7 23.9 + - - -
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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