Contacts of the strand formed by residues 42 - 48 (chain E) in PDB entry 5BOU
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 HIS 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ARG* 3.4 3.6 - - - +
39E SER* 2.9 30.6 + - - +
41E THR* 1.3 107.6 + - - +
43E ALA* 1.3 61.3 + - - +
141E ALA* 3.6 5.0 - - - +
181E ILE 5.4 0.4 + - - -
183E GLY* 4.4 10.5 + - - -
184E ASN 4.8 1.0 + - - -
185E PRO* 4.2 30.3 - - + +
188E LEU* 3.6 20.0 - - + -
214E ILE* 3.9 27.6 - - + -
215E VAL 3.4 5.6 - - - +
216E GLY* 3.8 16.4 - - - -
217E LYS* 4.6 5.1 + - + -
218E ASP 5.5 0.8 + - - -
219E THR* 3.5 19.0 + - + -
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Residues in contact with ALA 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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37E LEU 3.7 5.2 - - - -
38E ARG* 3.9 13.0 - - + -
42E HIS* 1.3 75.4 - - - +
44E VAL* 1.3 63.7 + - - +
134E ILE* 3.4 28.9 - - + +
135E GLY 4.5 1.6 - - - +
141E ALA* 4.3 7.0 - - + -
142E HIS 3.9 10.8 - - - +
214E ILE* 3.5 2.6 - - - +
215E VAL* 2.8 42.5 + - + +
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Residues in contact with VAL 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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36E GLY* 3.5 3.5 - - - -
37E LEU* 2.8 52.0 + - + +
43E ALA* 1.3 80.1 - - - +
45E LEU* 1.3 73.3 + - - +
46E VAL* 3.9 17.7 - - + -
134E ILE* 4.0 4.6 - - - +
188E LEU* 4.0 22.9 - - + -
189E ILE* 4.0 24.9 - - + -
212E ILE* 4.6 1.6 - - + -
213E ALA 3.4 8.3 - - - +
214E ILE* 3.9 24.7 - - + -
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Residues in contact with LEU 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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35E VAL 3.4 9.2 - - - +
36E GLY* 4.2 2.7 - - - -
44E VAL* 1.3 72.3 - - - +
46E VAL* 1.3 65.4 + - - +
62E ILE* 4.4 9.2 - - + -
70E GLY 4.2 0.7 - - - +
71E LEU* 3.6 33.7 - - - +
72E SER* 3.6 23.8 - - - +
132E LEU* 3.6 21.8 - - + +
134E ILE* 3.7 40.6 - - + +
211E SER 4.7 0.2 - - - -
212E ILE* 3.4 5.6 - - - +
213E ALA* 2.8 40.4 + - + +
221E PHE* 4.3 9.6 - - + -
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Residues in contact with VAL 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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34E THR* 3.0 3.4 + - - -
35E VAL* 2.6 46.8 + - + +
37E LEU* 4.9 1.3 - - + -
44E VAL* 3.9 17.0 - - + -
45E LEU* 1.3 79.7 - - - +
47E ALA* 1.3 60.9 + - - +
189E ILE 4.7 2.2 - - - +
192E GLY* 3.8 29.2 - - - +
193E VAL* 4.1 5.4 - - + +
196E ILE* 3.7 29.4 - - + +
210E LEU* 3.9 19.5 - - + -
211E SER 3.5 4.5 - - - +
212E ILE* 4.3 11.2 - - + -
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Residues in contact with ALA 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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33E VAL 4.0 1.6 - - - -
34E THR* 3.6 15.7 - - - +
46E VAL* 1.3 77.3 - - - +
48E LEU* 1.3 61.0 + - - +
49E LYS 3.5 1.9 + - - -
61E LYS* 3.7 30.5 - - + -
62E ILE* 4.3 13.7 - - + -
72E SER* 4.8 0.2 - - - -
196E ILE* 3.9 5.2 - - - -
209E ASN 3.9 0.7 - - - +
210E LEU* 3.9 2.9 - - - +
211E SER* 2.8 40.4 + - - +
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Residues in contact with LEU 48 (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 SER* 2.6 41.5 + - - +
33E VAL* 3.0 35.9 + - + +
47E ALA* 1.3 70.3 - - - +
49E LYS* 1.3 60.1 + - - +
61E LYS* 3.6 7.5 - - - -
196E ILE* 3.6 8.2 - - + +
199E SER 5.9 0.7 - - - +
200E LEU* 3.9 18.8 - - + -
203E GLU* 4.9 11.2 - - + +
205E LEU* 4.0 21.1 - - + -
209E ASN* 3.2 39.5 - - - +
210E LEU* 5.4 0.4 - - - +
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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