Contacts of the strand formed by residues 44 - 47 (chain P) in PDB entry 5A0Q
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 VAL 44 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35P VAL* 6.2 0.2 - - + -
36P GLY* 3.2 3.6 - - - -
37P ILE* 3.0 53.4 + - + +
42P GLY 3.7 0.6 + - - +
43P VAL* 1.3 81.3 - - - +
45P LEU* 1.4 69.2 + - - +
46P ALA* 5.1 2.2 - - + -
136P CYS* 5.1 0.2 - - - -
183P LEU* 5.1 1.3 - - + +
186P ALA* 4.3 2.7 - - + +
187P ILE* 3.8 30.3 - - + -
190P ALA* 4.1 6.7 - - + -
209P VAL* 3.8 14.8 - - + -
210P GLY 3.5 6.7 - - - +
211P ILE* 3.2 26.0 - - + -
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Residues in contact with LEU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P VAL 3.3 4.7 - - - +
36P GLY* 3.6 17.0 - - - -
44P VAL* 1.4 80.3 - - - +
46P ALA* 1.3 63.4 + - - +
64P VAL* 5.2 2.0 - - + +
72P GLY 4.7 0.4 - - - -
73P LEU* 4.0 8.3 - - - +
74P VAL* 3.5 42.6 - - + +
134P LEU* 3.9 18.8 - - + +
136P CYS* 3.5 43.9 - - + +
145P LEU* 3.7 10.3 - - + -
209P VAL* 3.5 3.1 - - - +
210P GLY 2.9 34.5 + - - +
217P PHE* 5.3 3.6 - - + -
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Residues in contact with ALA 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P SER* 3.5 2.3 - - - -
35P VAL* 3.1 44.9 + - + +
44P VAL* 5.1 0.7 - - + -
45P LEU* 1.3 76.2 - - - +
47P THR* 1.3 65.1 + - - +
64P VAL* 5.6 0.7 - - - -
74P VAL* 4.3 4.0 - - - +
190P ALA* 5.0 9.2 - - + -
191P ILE* 6.0 2.2 - - + -
194P LEU* 4.5 6.7 - - + +
207P ILE* 4.6 7.9 - - + -
208P GLU 3.5 13.0 - - - +
209P VAL* 4.0 14.6 - - + +
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Residues in contact with THR 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA 4.3 0.3 + - - -
33P PRO 3.0 17.6 + - - -
34P SER* 3.8 4.3 + - - -
46P ALA* 1.3 77.1 - - - +
48P GLU* 1.4 70.5 + - - +
49P LYS* 5.4 0.2 - - + -
63P LYS* 3.6 40.1 + - + +
64P VAL* 4.5 3.8 - - + -
74P VAL* 4.1 13.5 - - + -
194P LEU* 4.3 5.6 - - - +
207P ILE* 3.3 6.5 - - - +
208P GLU* 3.0 46.4 + - + +
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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