Contacts of the strand formed by residues 113 - 116 (chain E) in PDB entry 2PWZ
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 CYS 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71E ASP 2.9 11.0 + - - +
72E VAL* 3.3 6.7 - - + +
73E VAL 2.8 32.4 + - - +
111E LYS 3.9 0.4 + - - -
112E ALA* 1.3 71.9 - - - +
114E ILE* 1.3 55.9 + - - +
142E LYS* 3.4 27.1 - - - -
144E PHE* 4.0 10.8 - - + -
238E LEU* 3.9 28.5 - - + -
242E LEU* 4.1 17.5 - - - -
274E GLY* 3.8 21.5 - - - -
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Residues in contact with ILE 114 (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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73E VAL* 3.4 9.6 - - + +
75E ILE* 4.0 17.3 - - + -
102E VAL* 5.1 5.6 - - + -
105E VAL* 3.8 29.8 - - + -
110E PRO 5.4 3.1 - - - +
112E ALA 3.7 13.5 - - - +
113E CYS* 1.3 77.4 - - - +
115E GLY* 1.3 61.1 + - - +
116E ILE* 3.7 24.9 - - + -
132E LEU* 3.9 35.0 - - + -
142E LYS* 2.7 15.6 + - + +
143E LEU* 4.1 7.4 - - + +
144E PHE* 2.8 33.5 + - - +
238E LEU* 5.5 0.7 - - - -
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Residues in contact with GLY 115 (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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73E VAL 2.7 13.4 + - - -
74E LEU* 3.5 17.5 - - - +
75E ILE* 2.9 28.6 + - - +
113E CYS 4.1 0.4 - - - -
114E ILE* 1.3 73.5 - - - +
116E ILE* 1.3 65.2 + - - -
117E ILE* 3.5 2.6 + - - +
144E PHE* 3.4 9.0 - - - -
146E VAL* 4.0 10.8 - - - -
234E PHE* 4.9 2.7 - - - -
238E LEU* 5.5 1.0 - - - +
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Residues in contact with ILE 116 (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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75E ILE* 3.9 21.3 - - + +
98E VAL* 4.6 6.3 - - + -
102E VAL* 4.4 3.6 - - + -
114E ILE* 3.7 22.4 - - + -
115E GLY* 1.3 69.8 - - - -
117E ILE* 1.3 61.5 + - - +
118E THR* 3.8 13.9 - - - +
121E VAL* 3.6 7.9 - - + +
124E THR* 3.3 33.2 - - - +
125E VAL* 3.8 17.7 - - + -
128E ALA* 4.1 16.8 - - + -
143E LEU* 3.8 20.0 - - + -
144E PHE 2.7 14.4 + - - +
145E GLY* 3.6 0.3 - - - -
146E VAL* 2.9 25.9 + - - +
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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