Contacts of the helix formed by residues 157 - 162 (chain D) in PDB entry 2E9X
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 ASP 157 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D LYS 4.2 1.2 + - - -
156D VAL* 1.3 71.6 - - - +
158D LEU* 1.3 62.2 + - - +
159D PHE* 3.1 17.8 + - - +
160D ARG* 2.9 48.8 + - + +
161D ALA* 3.0 23.9 + - - +
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Residues in contact with LEU 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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77A VAL* 5.6 2.5 - - + -
81A TYR* 6.0 2.9 - - + -
1020C LEU* 5.9 2.0 - - + -
104D PHE* 3.9 22.2 - - + -
105D PRO* 3.6 15.0 - - + +
134D MET* 4.4 4.9 - - - -
137D THR* 4.7 4.5 - - + -
138D GLU* 3.6 43.7 - - + +
141D LEU* 4.1 20.0 - - + -
156D VAL* 3.2 23.4 + - + +
157D ASP* 1.3 73.7 + - - +
159D PHE* 1.3 61.0 + - - +
161D ALA* 3.6 9.9 - - + -
162D VAL* 3.0 35.8 + - + +
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Residues in contact with PHE 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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105D PRO* 3.8 23.6 - - + +
106D HIS* 2.9 53.8 + + + -
109D GLU* 3.7 34.5 - - + -
157D ASP* 3.1 19.3 + - - +
158D LEU* 1.3 77.8 - - - +
160D ARG* 1.3 66.0 + - + +
162D VAL 3.6 1.2 - - - +
164D LYS* 4.0 27.1 - - - -
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Residues in contact with ARG 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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73A ARG* 6.2 0.4 - - - +
1019C PHE* 4.8 4.7 - - - +
157D ASP* 2.9 38.1 + - + +
159D PHE* 1.3 88.3 - - + +
161D ALA* 1.3 61.8 + - - +
162D VAL 3.5 3.1 - - - +
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Residues in contact with ALA 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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77A VAL* 5.8 0.2 - - + -
1019C PHE* 3.8 36.3 + - + +
1020C LEU* 3.4 26.2 + - + +
156D VAL* 4.1 14.4 - - + -
157D ASP 3.0 15.2 + - - +
158D LEU* 4.1 14.6 - - + -
160D ARG* 1.3 79.2 - - - +
162D VAL* 1.3 60.6 + - - +
163D PRO* 3.8 4.7 - - - +
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Residues in contact with VAL 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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81A TYR* 4.6 10.1 - - + +
1008C VAL* 6.4 0.2 - - + -
1020C LEU* 4.2 13.5 - - + -
102D LYS 3.2 27.1 - - - +
103D PHE* 4.5 0.9 - - - -
104D PHE* 4.2 15.3 - - + -
105D PRO* 3.9 26.0 - - + -
106D HIS* 2.6 30.7 + - - +
158D LEU* 3.0 25.5 + - + +
159D PHE 3.6 2.8 - - - +
160D ARG 4.4 2.9 - - - +
161D ALA* 1.3 77.3 - - - +
163D PRO* 1.3 70.1 - - + +
164D LYS* 4.7 0.5 - - - +
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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