Contacts of the helix formed by residues 2174 - 2183 (chain E) in PDB entry 1PDW
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 GLY2174 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2169E VAL 4.3 0.3 - - - +
2170E GLU* 2.9 24.8 + - - -
2171E ALA 4.7 0.2 - - - -
2172E LEU 3.6 1.2 - - - -
2173E ASN* 1.3 79.6 - - - +
2175E LYS* 1.3 66.4 + - - -
2176E GLU* 3.0 5.9 + - - -
2177E VAL* 3.2 10.7 + - - +
2178E ALA 3.2 8.5 + - - -
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Residues in contact with LYS2175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2170E GLU* 3.0 44.0 + - + +
2174E GLY* 1.3 71.4 - - - -
2176E GLU* 1.3 62.1 + - - +
2178E ALA* 3.5 6.6 - - - +
2179E ALA* 3.3 19.8 + - - +
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Residues in contact with GLU2176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2173E ASN 5.7 0.4 - - - +
2174E GLY* 3.0 2.3 + - - -
2175E LYS* 1.3 76.7 - - - +
2177E VAL* 1.3 66.7 + - + +
2179E ALA* 3.1 15.6 + - + +
2180E GLN* 3.0 29.2 + - + +
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Residues in contact with VAL2177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2029E ALA* 4.1 21.1 - - + +
2169E VAL* 4.1 11.2 - - + -
2173E ASN* 3.4 41.5 - - + +
2174E GLY 3.2 3.8 + - - +
2176E GLU* 1.3 75.4 - - + +
2178E ALA* 1.3 67.1 + - - +
2180E GLN* 2.8 38.3 + - - +
2181E VAL* 2.9 15.5 + - + +
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Residues in contact with ALA2178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2166E LEU* 3.5 23.9 - - + +
2169E VAL* 3.9 11.1 - - - +
2170E GLU* 3.9 26.5 - - + +
2174E GLY 3.2 9.5 + - - +
2175E LYS* 3.5 11.9 - - - +
2176E GLU 3.2 0.2 - - - -
2177E VAL* 1.3 79.7 - - - +
2179E ALA* 1.3 54.7 + - - +
2181E VAL* 3.7 1.2 + - - +
2182E LYS* 3.1 27.7 + - - +
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Residues in contact with ALA2179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2175E LYS 3.3 8.2 + - - +
2176E GLU* 3.1 12.2 + - + +
2177E VAL 3.0 0.8 - - - -
2178E ALA* 1.3 78.0 - - - +
2180E GLN* 1.3 63.6 + - - +
2181E VAL 3.2 1.3 - - - -
2182E LYS* 4.3 7.0 - - - +
2183E ALA* 3.1 26.2 + - - +
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Residues in contact with GLN2180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2176E GLU* 3.0 27.6 + - + +
2177E VAL* 2.8 36.8 + - - +
2179E ALA* 1.3 77.0 - - - +
2181E VAL* 1.3 63.8 + - + +
2183E ALA* 4.1 3.3 - - - +
2184E PRO* 3.2 19.8 - - - +
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Residues in contact with VAL2181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025E VAL* 3.9 32.8 - - + +
2028E ARG* 3.8 22.7 + - + +
2029E ALA* 3.5 37.9 - - + +
2166E LEU* 4.1 7.6 - - + -
2169E VAL* 4.8 1.8 - - + -
2177E VAL* 2.9 20.2 + - + +
2178E ALA* 3.9 4.7 - - - +
2180E GLN* 1.3 77.8 - - + +
2182E LYS* 1.3 65.2 + - - +
2184E PRO* 3.1 12.1 - - - +
2185E LEU* 3.6 14.1 - - + +
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Residues in contact with LYS2182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2166E LEU* 3.9 24.6 - - + +
2178E ALA 3.1 19.4 + - - +
2179E ALA* 3.5 6.7 + - - +
2181E VAL* 1.3 75.8 - - - +
2183E ALA* 1.3 67.5 + - - +
2185E LEU* 2.9 27.7 + - - +
2186E VAL 4.2 1.7 + - - -
2187E LEU* 4.0 16.5 + - + +
2188E LYS* 3.3 44.3 + - - +
2189E ASP* 4.5 5.5 + - - +
2190E LEU* 3.9 13.9 - - - +
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Residues in contact with ALA2183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2179E ALA 3.1 15.8 + - - +
2180E GLN* 4.1 3.1 - - - +
2182E LYS* 1.3 81.3 - - - +
2184E PRO* 1.3 67.9 - - + +
2185E LEU 3.4 0.5 + - - -
2186E VAL* 3.9 8.7 + - - +
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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