Contacts of the strand formed by residues 2101 - 2105 (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 LEU2101 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2068E ASP 3.5 16.6 + - - +
2069E VAL* 3.4 15.3 - - + -
2070E VAL 3.3 10.9 + - - -
2095E GLN* 2.8 23.4 + - - -
2100E GLY* 1.3 70.9 - - - -
2102E ILE* 1.3 66.4 + - - +
2148E LYS* 4.7 6.3 - - - -
2150E GLY 4.4 4.5 - - - +
2151E LEU* 3.3 49.0 - - + +
2153E LEU* 4.2 19.7 - - + -
2168E ILE* 4.7 6.1 - - + +
2171E ALA* 3.9 15.5 - - + -
2172E LEU* 3.4 30.3 - - + -
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Residues in contact with ILE2102 (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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2070E VAL* 3.7 10.3 - - + +
2072E LEU* 4.8 3.4 - - + -
2092E LEU* 3.7 41.5 - - + +
2095E GLN* 3.5 25.8 - - + -
2096E GLU* 4.3 8.1 - - + +
2100E GLY 3.6 3.6 - - - +
2101E LEU* 1.3 74.2 - - - +
2103E ALA* 1.3 66.7 + - - +
2104E ALA 5.1 0.2 - - - +
2112E LEU* 3.9 24.4 - - + +
2117E ILE* 3.9 22.2 - - + -
2151E LEU 2.8 13.4 + - - +
2152E ILE* 3.7 11.3 - - + +
2153E LEU* 2.8 27.9 + - - +
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Residues in contact with ALA2103 (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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2069E VAL* 4.2 8.0 - - + +
2070E VAL 2.9 13.1 + - - +
2071E VAL* 3.3 2.3 - - - -
2072E LEU* 2.7 32.7 + - - +
2101E LEU* 4.3 1.1 - - + -
2102E ILE* 1.3 75.0 - - - +
2104E ALA* 1.3 55.7 + - - +
2153E LEU* 3.1 10.8 - - + +
2164E PHE* 3.5 24.9 - - + -
2168E ILE* 3.5 23.8 - - + -
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Residues in contact with ALA2104 (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* 3.3 17.9 - - + -
2102E ILE 4.2 0.2 - - - -
2103E ALA* 1.3 74.6 - - - +
2105E ILE* 1.3 61.4 + - - +
2108E GLY 3.8 5.2 - - - +
2109E PRO* 3.6 33.4 - - + +
2112E LEU* 4.3 15.7 - - + +
2153E LEU 2.8 6.5 + - - -
2154E THR* 3.0 29.5 - - + -
2155E SER 3.1 2.3 + - - -
2164E PHE* 3.7 2.7 - - - -
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Residues in contact with ILE2105 (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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2018E GLU* 4.0 14.6 - - + +
2072E LEU 3.0 13.4 + - - +
2073E PRO* 3.9 5.6 - - + -
2074E GLY* 3.0 27.2 + - - +
2104E ALA* 1.3 76.3 - - - +
2106E CYS* 1.3 74.7 + - + +
2107E ALA 3.0 6.4 + - - -
2108E GLY 3.1 2.9 + - - -
2109E PRO* 3.7 3.8 - - - +
2155E SER* 3.5 28.7 - - - +
2157E GLY 3.4 26.0 - - - +
2160E THR* 4.0 0.2 - - - +
2161E SER* 3.6 26.7 - - - +
2164E PHE* 4.0 25.8 - - + -
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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