Contacts of the strand formed by residues 42 - 47 (chain E) in PDB entry 3SR2
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 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E THR* 5.0 1.1 - - + -
36E LEU 3.7 5.2 - - - -
37E THR* 3.9 15.0 - - + +
41E SER* 1.3 78.0 - - - +
43E TRP* 1.3 66.9 + - - +
115E LYS* 3.4 9.2 - - - +
116E VAL* 3.2 40.4 + - + -
119E PRO* 3.9 18.6 - - + +
122E VAL* 4.2 15.7 - - + -
123E ILE* 5.8 0.4 - - + -
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Residues in contact with TRP 43 (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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18E HIS* 5.0 2.2 - - - -
35E THR* 3.2 9.0 - - - +
36E LEU* 2.9 61.5 + - + +
37E THR 4.8 0.2 - - - -
38E ASP* 3.8 31.6 - - + -
41E SER* 4.2 17.5 - - - -
42E ALA* 1.3 77.3 - - - +
44E THR* 1.3 63.6 + - - +
88E PHE* 3.3 30.1 - + - -
90E LYS* 3.4 56.2 + - + +
93E CYS* 5.4 2.1 - - - -
113E LEU* 3.8 23.1 - - + +
114E GLU* 3.4 7.4 - - - -
115E LYS* 3.5 36.3 - - + +
116E VAL* 4.7 0.2 - - - -
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Residues in contact with THR 44 (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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33E VAL* 4.8 10.1 - - + -
34E ILE 3.6 8.3 - - - +
35E THR* 3.7 16.9 + - - +
43E TRP* 1.3 76.9 + - - +
45E GLY* 1.3 65.7 + - - +
46E THR* 5.9 0.9 - - - +
113E LEU* 3.7 5.3 - - - -
114E GLU* 3.2 34.0 + - - +
116E VAL* 3.7 26.1 - - + +
122E VAL* 5.5 2.8 - - - +
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Residues in contact with GLY 45 (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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33E VAL* 3.9 4.7 - - - +
34E ILE* 3.0 39.6 + - - +
44E THR* 1.3 77.8 - - - +
46E THR* 1.3 63.9 + - - -
47E VAL* 5.4 0.2 - - - -
111E PHE* 5.6 1.3 - - - -
112E ASN 4.0 10.1 - - - -
113E LEU* 3.3 17.6 - - - +
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Residues in contact with THR 46 (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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32E PHE 3.8 11.7 - - - +
33E VAL* 4.8 12.4 - - + +
44E THR* 5.9 1.0 - - - +
45E GLY* 1.3 74.7 + - - -
47E VAL* 1.3 80.3 + - - +
48E SER* 4.2 6.3 - - - +
51E GLU* 4.4 5.4 - - - +
111E PHE* 5.0 5.9 - - - +
112E ASN 4.9 3.5 + - - +
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Residues in contact with VAL 47 (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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31E GLY* 3.5 1.0 - - - -
32E PHE* 2.9 80.0 + - + -
34E ILE* 5.2 2.5 - - + -
46E THR* 1.3 82.4 - - - +
48E SER* 1.3 69.1 + - - +
51E GLU* 4.2 12.8 - - + +
52E ILE* 4.0 8.5 - - + +
111E PHE* 4.0 35.4 - - + -
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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