Contacts of the helix formed by residues 2109 - 2115 (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 PRO2109 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2104E ALA* 3.6 28.0 - - + +
2105E ILE* 3.7 11.9 - - - +
2106E CYS 3.6 12.3 - - - +
2107E ALA 3.2 5.6 - - - -
2108E GLY* 1.3 89.6 - - - +
2110E THR* 1.3 54.8 + - - +
2111E ALA 3.0 0.7 - - - -
2112E LEU* 2.8 31.5 + - + +
2124E THR 3.7 16.8 - - - +
2125E THR* 3.6 20.0 - - + -
2133E MSE 3.2 21.0 - - + +
2154E THR* 3.9 8.7 - - + -
2155E SER 4.6 0.7 - - - +
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Residues in contact with THR2110 (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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2079E ALA* 4.2 6.9 - - - +
2083E SER* 3.5 11.7 + - - -
2107E ALA* 2.7 22.7 + - + +
2109E PRO* 1.3 76.9 - - - +
2111E ALA* 1.3 56.5 + - - +
2112E LEU 3.1 0.2 - - - -
2113E LEU* 3.3 7.8 + - - +
2114E ALA* 3.1 23.7 + - - +
2125E THR* 5.3 1.6 - - + -
2129E ALA* 4.2 30.7 - - + +
2132E LYS* 3.4 38.1 + - + +
2133E MSE 3.8 15.9 - - - +
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Residues in contact with ALA2111 (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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2072E LEU* 4.0 16.6 - - + -
2079E ALA 4.5 1.1 - - - +
2082E LEU* 4.1 23.6 - - + +
2083E SER* 3.2 22.0 - - - +
2088E VAL* 5.4 0.4 - - + -
2092E LEU* 4.3 2.0 - - + +
2108E GLY* 2.8 16.8 + - - +
2110E THR* 1.3 79.9 + - - +
2112E LEU* 1.3 62.2 + - - +
2114E ALA* 3.9 0.4 - - - +
2115E HIS* 3.3 33.2 + - - +
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Residues in contact with LEU2112 (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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2072E LEU* 4.2 12.3 - - + -
2092E LEU* 4.3 5.2 - - + -
2102E ILE* 3.9 27.4 - - + +
2104E ALA* 4.3 6.5 - - + -
2109E PRO* 2.8 27.3 + - + +
2111E ALA* 1.3 77.8 - - - +
2113E LEU* 1.3 62.0 + - - +
2115E HIS 3.4 1.0 + - - -
2116E GLU 3.0 3.6 + - - -
2117E ILE* 2.8 54.6 + - + +
2123E VAL* 5.0 1.1 - - + -
2133E MSE 4.4 7.6 - - + -
2139E TYR* 3.2 11.4 + - + +
2152E ILE* 4.4 17.9 - - + -
2153E LEU 5.8 0.2 - - - +
2154E THR* 4.1 20.0 - - + -
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Residues in contact with LEU2113 (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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2109E PRO 3.4 1.8 + - - -
2110E THR* 3.3 10.6 + - - +
2112E LEU* 1.3 79.9 - - - +
2114E ALA* 1.3 65.1 + - - +
2116E GLU* 2.9 16.8 + - - +
2119E PHE* 4.0 9.8 - - + -
2132E LYS* 3.2 32.5 - - + +
2133E MSE 3.7 20.9 - - - +
2135E ASN* 4.5 9.4 - - + +
2138E HIS* 3.9 28.0 - - + -
2139E TYR* 3.2 21.9 + - + -
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Residues in contact with ALA2114 (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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2083E SER* 3.8 35.0 - - - +
2089E LYS* 3.7 10.0 + - - -
2110E THR 3.1 13.0 + - - +
2111E ALA 4.0 3.8 - - - +
2113E LEU* 1.3 82.6 - - - +
2115E HIS* 1.3 62.9 + - + +
2116E GLU* 3.3 5.1 + - - +
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Residues in contact with HIS2115 (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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2082E LEU 3.1 27.5 + - - -
2083E SER* 3.7 13.8 + - - -
2084E GLU 4.9 0.4 - - - -
2085E SER 3.4 12.7 + - - -
2088E VAL* 3.6 6.7 - - + -
2089E LYS* 3.3 65.1 + - + +
2092E LEU* 3.7 9.5 - - - +
2093E LYS* 3.7 11.8 - - - -
2111E ALA* 3.3 20.2 + - + +
2113E LEU 3.2 0.8 - - - -
2114E ALA* 1.3 83.1 - - + +
2116E GLU* 1.3 73.7 + - - +
2117E ILE* 3.4 21.2 + - + +
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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