Contacts of the strand formed by residues 29 - 35 (chain E) in PDB entry 1WOH
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 ALA 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E TRP* 3.9 4.0 - - + -
28E GLN* 1.3 76.9 - - - +
30E ASP* 1.3 62.5 + - - +
31E VAL 3.8 10.1 - - - +
79E THR* 3.6 11.4 - - - +
80E PHE 4.0 9.0 - - - +
81E ALA* 3.7 29.6 - - + -
110E ARG 3.1 6.3 + - - -
111E CYS* 2.9 28.2 - - - +
112E ARG 3.5 0.3 + - - -
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Residues in contact with ASP 30 (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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29E ALA* 1.3 70.8 - - - +
31E VAL* 1.3 62.9 + - - +
77E GLY 3.7 4.5 - - - +
78E VAL* 3.3 24.5 - - + -
79E THR* 2.8 40.1 + - - +
112E ARG* 2.9 53.9 + - - +
113E VAL 3.0 10.2 + - - -
301E PHE* 4.0 8.7 - - + -
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Residues in contact with VAL 31 (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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15E PHE* 5.8 2.7 - - + -
29E ALA* 3.8 3.0 - - - +
30E ASP* 1.3 82.2 - - - +
32E ALA* 1.3 66.1 + - - +
78E VAL* 4.1 11.0 - - + -
79E THR 2.9 5.6 + - - +
80E PHE* 3.2 38.0 - - + +
81E ALA 2.9 24.1 + - - -
111E CYS* 4.3 1.6 - - - -
113E VAL 3.4 13.5 - - - +
115E VAL* 3.9 13.5 - - + -
297E LEU* 3.9 18.2 - - + -
301E PHE* 3.5 30.5 - - + -
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Residues in contact with ALA 32 (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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27E TRP* 3.4 35.4 - - + -
31E VAL* 1.3 80.5 - - - +
33E ALA* 1.3 62.8 + - - +
81E ALA* 3.2 8.5 - - + +
83E ALA* 5.5 1.1 - - + -
107E VAL* 3.7 16.8 - - + +
111E CYS* 3.7 9.3 - - + +
113E VAL 3.3 4.6 + - - -
114E PRO* 3.4 5.0 - - - +
115E VAL 2.8 25.0 + - - +
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Residues in contact with ALA 33 (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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15E PHE* 3.7 41.1 - - + -
31E VAL* 6.1 0.2 - - + -
32E ALA* 1.3 73.7 - - - +
34E LEU* 1.3 60.8 + - - +
35E GLY 4.4 0.2 - - - -
56E ARG* 5.0 0.7 - - - +
81E ALA 2.9 12.5 + - - +
82E ASP* 3.7 7.9 - - - +
83E ALA* 2.8 34.0 + - - +
107E VAL* 5.2 0.4 - - - -
115E VAL* 3.3 13.2 - - + +
117E LEU* 4.7 8.7 - - + -
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Residues in contact with LEU 34 (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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23E PRO* 4.6 3.8 - - + -
32E ALA 5.5 0.2 - - - +
33E ALA* 1.3 75.6 - - - +
35E GLY* 1.3 65.2 + - - +
36E VAL* 4.4 1.9 - - + +
56E ARG* 4.5 0.7 - - - -
83E ALA* 4.2 11.2 - - + +
84E GLY 3.5 16.2 - - - +
85E ASP 4.4 0.9 - - - -
86E VAL* 4.0 27.8 - - + +
100E ILE 4.9 0.4 - - - +
103E ALA* 3.9 9.6 - - + +
104E ALA* 3.8 34.8 - - + +
107E VAL* 4.1 20.4 - - + -
115E VAL 2.9 7.1 + - - -
116E PHE* 3.3 27.4 - - + +
117E LEU* 2.9 24.0 + - - +
127E LEU* 5.1 3.1 - - + -
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Residues in contact with GLY 35 (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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34E LEU* 1.3 73.7 - - - +
36E VAL* 1.3 64.7 + - - +
37E PRO* 3.6 1.6 - - - -
52E PRO* 4.3 3.4 - - - -
56E ARG* 3.6 6.4 - - - +
84E GLY 2.9 12.1 + - - -
85E ASP* 3.1 19.3 + - - +
86E VAL* 2.9 28.4 + - - +
117E LEU* 3.5 13.2 - - - -
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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