Contacts of the strand formed by residues 84 - 90 (chain E) in PDB entry 43C9
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 84 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E GLN* 3.8 24.5 - - - +
38E GLN 3.1 20.6 - - - +
39E LYS* 3.9 9.2 - - + +
40E PRO* 5.6 1.6 - - - -
82E ASP 2.9 5.6 + - - +
83E GLN* 1.3 77.8 - - - +
85E ASP* 1.3 66.2 + - - +
86E TYR* 4.1 2.4 - - - +
102E THR 3.8 0.5 - - - +
103E LYS* 3.7 0.9 - - - -
104E LEU* 2.8 36.5 + - - +
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Residues in contact with ASP 85 (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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36E TYR 3.7 0.2 - - - +
37E GLN* 3.6 3.8 - - - -
38E GLN* 2.9 42.0 + - + +
84E ALA* 1.3 77.6 - - - +
86E TYR* 1.3 63.5 - - - +
87E PHE* 3.8 30.7 + - + -
102E THR 3.3 4.7 + - - +
103E LYS* 2.9 50.8 + - - +
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Residues in contact with TYR 86 (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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6E GLN* 3.1 8.9 + - - +
21E MET* 3.6 35.2 - - + -
35E TRP* 5.0 2.2 - - + -
36E TYR 3.4 14.1 - - - +
37E GLN* 2.7 32.9 + - + -
47E LEU* 3.5 28.3 - - + -
62E PHE* 3.9 10.0 - + - -
73E LEU* 4.1 11.9 - - + -
75E ILE* 4.1 10.0 - - + +
82E ASP* 2.9 20.4 + - - +
84E ALA* 4.1 10.1 - - + -
85E ASP* 1.3 75.0 - - - +
87E PHE* 1.3 61.7 + - - +
101E GLY* 3.1 2.4 - - - -
102E THR* 2.9 35.8 + - - +
104E LEU* 3.7 26.5 - - + -
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Residues in contact with PHE 87 (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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6E GLN* 3.3 5.2 - - - +
35E TRP* 3.3 6.8 - - - -
36E TYR* 2.8 43.5 + - + +
38E GLN* 3.2 35.0 - - + -
44E PRO* 5.0 6.1 - - + -
85E ASP* 3.8 29.6 - - + -
86E TYR* 1.3 76.1 - - - +
88E CYS* 1.3 61.5 + - - +
98E PHE* 5.0 2.0 - - + -
99E GLY 3.6 11.7 - - - +
100E GLY 3.5 10.5 - - - -
101E GLY* 3.2 34.5 - - - -
39F GLN* 4.4 5.8 - - - -
44F GLY* 6.4 1.6 - - - -
45F LEU* 3.5 33.0 - - + -
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Residues in contact with CYS 88 (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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4E MET* 3.9 8.5 - - - +
6E GLN* 3.2 21.6 + - - -
23E CYS* 2.0 52.7 - - + -
33E LEU* 4.3 4.0 - - + -
34E ALA 3.1 12.6 - - - +
35E TRP* 4.0 12.1 - - + -
87E PHE* 1.3 74.7 - - - +
89E GLN* 1.3 58.1 + - - +
98E PHE* 3.4 4.6 - - - +
99E GLY* 2.7 35.7 + - - -
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Residues in contact with GLN 89 (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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4E MET* 5.1 0.4 - - - -
33E LEU* 3.5 5.8 - - - +
34E ALA 3.0 29.2 + - - -
36E TYR* 3.0 30.0 + - + -
88E CYS* 1.3 75.2 - - - +
90E GLN* 1.3 62.5 + - - +
91E HIS* 3.1 21.3 - - - +
96E ARG* 2.9 43.1 + - - +
97E THR 3.4 8.1 - - - +
98E PHE* 3.2 41.0 - - + -
35F HIS* 4.6 2.5 + - - -
37F VAL* 5.2 0.6 - - - +
47F TRP* 3.5 13.3 - - - -
95F TYR* 3.8 3.3 + - - -
103F TRP* 5.4 0.7 - - - -
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Residues in contact with GLN 90 (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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2E VAL* 3.9 22.0 - - + +
4E MET* 3.6 29.5 - - - +
27E LEU* 3.8 20.4 - - - +
32E TYR 3.4 3.8 - - - -
33E LEU* 4.7 0.2 - - + -
89E GLN* 1.3 74.4 - - - +
91E HIS* 1.3 62.0 + - - +
92E TYR* 2.8 29.7 + - - +
93E ARG 2.8 30.0 + - - +
95E PRO 3.1 17.6 + - - -
96E ARG* 3.1 25.7 - - - +
97E THR* 3.2 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