Contacts of the strand formed by residues 61 - 67 (chain E) in PDB entry 3EI4
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 ILE 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E ASN* 5.0 13.9 + - - +
34E ALA* 4.0 19.1 - - + -
36E ASN* 2.8 22.3 + - - +
37E THR 4.2 6.1 - - - +
38E ARG 3.7 29.8 - - - +
39E LEU* 4.3 12.6 - - + +
57E MET* 4.3 23.6 - - + -
59E GLY 4.6 4.3 - - - +
60E LYS* 1.3 70.0 - - - +
62E ALA* 1.3 64.5 + - - +
63E VAL 4.2 3.4 - - - +
64E MET* 4.0 15.7 - - + -
79E ILE* 3.8 27.8 - - + -
80E LEU 3.9 3.8 - - - +
81E THR* 4.7 0.7 - - - +
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Residues in contact with ALA 62 (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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16E ASN 5.6 1.6 - - - +
60E LYS 3.2 0.8 + - - +
61E ILE* 1.3 75.8 - - - +
63E VAL* 1.3 68.2 + - + +
64E MET 4.4 0.3 + - - -
80E LEU* 2.6 19.0 + - + +
81E THR 3.9 1.1 - - - -
82E ALA* 3.7 20.9 - - + +
120E ILE* 3.8 27.8 - - + +
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Residues in contact with VAL 63 (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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61E ILE* 4.4 0.9 - - - -
62E ALA* 1.3 82.0 - - - +
64E MET* 1.3 63.9 + - - +
65E GLU* 4.0 17.7 - - + +
78E PHE* 3.3 13.6 - - + +
79E ILE* 3.2 11.0 - - - +
80E LEU* 2.9 41.7 + - + +
120E ILE* 3.9 24.0 - - + +
122E GLY* 3.7 45.1 - - - +
133E LEU* 5.0 0.7 - - + -
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Residues in contact with MET 64 (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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17E GLY* 3.3 30.5 - - - +
18E CYS 4.1 0.4 - - - -
19E VAL* 3.7 30.6 - - + +
32E LEU* 3.5 22.4 - - - +
34E ALA* 3.8 16.2 - - + -
39E LEU* 3.6 27.8 - - + -
61E ILE* 4.0 7.2 - - + -
62E ALA 4.3 0.6 + - - -
63E VAL* 1.3 75.8 - - - +
65E GLU* 1.3 72.1 + - - +
77E LEU* 3.9 13.5 - - + -
78E PHE 3.4 3.8 - - - -
79E ILE* 3.6 19.3 - - + -
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Residues in contact with GLU 65 (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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19E VAL* 3.7 16.2 - - - +
63E VAL* 4.0 18.8 - - + +
64E MET* 1.3 83.8 + - - +
66E LEU* 1.3 64.0 + - - +
67E PHE* 3.9 0.9 - - - -
76E LEU 3.9 0.3 - - - +
77E LEU* 3.6 6.1 - - - +
78E PHE* 2.8 43.9 + - + +
122E GLY 4.6 10.1 - - - +
123E ILE* 5.5 0.2 - - - -
124E ILE* 3.5 30.7 - - + +
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Residues in contact with LEU 66 (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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19E VAL* 4.1 17.6 - - + +
20E THR 3.5 29.8 - - - +
21E GLY* 3.6 19.5 - - - +
22E HIS 4.3 1.1 - - - +
23E PHE* 3.8 31.2 - - + -
32E LEU* 3.9 19.7 - - + -
65E GLU* 1.3 79.6 + - - +
67E PHE* 1.3 61.9 + - - +
75E ASP* 4.3 14.4 - - + +
76E LEU 3.3 15.0 - - - +
77E LEU* 3.8 13.0 - - + -
124E ILE* 4.5 3.6 - - - +
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Residues in contact with PHE 67 (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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65E GLU 3.9 2.5 - - - -
66E LEU* 1.3 77.8 - - - +
68E ARG* 1.3 59.7 + - - +
69E PRO* 3.6 20.9 - - + +
75E ASP* 4.3 5.7 - - - +
76E LEU* 2.8 55.5 + - + +
77E LEU 3.7 15.0 - - - -
78E PHE* 3.7 7.9 - - + -
88E ILE* 3.5 33.4 - - + -
124E ILE* 3.9 26.5 - - + -
128E CYS* 3.4 24.2 - - - -
145E LEU* 3.7 30.3 - - + -
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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