Contacts of the strand formed by residues 44 - 49 (chain L) in PDB entry 5T0G
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 44 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L LEU 3.7 5.8 - - - +
39L LYS* 3.6 22.2 - - + +
43L HIS* 1.3 75.3 - - - +
45L VAL* 1.3 68.2 + - - +
46L LEU* 4.3 0.6 - - - +
135L ALA* 4.8 7.0 - - + -
137L TYR* 2.5 28.0 + - + +
142L PRO* 4.0 7.6 - - + -
144L ILE* 4.3 11.4 - - + -
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Residues in contact with VAL 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L VAL 4.6 0.3 - - - +
37L GLY* 3.8 0.3 - - - -
38L LEU* 2.7 57.8 + - + +
39L LYS* 4.5 0.2 - - - +
43L HIS* 5.3 4.5 - - + +
44L ALA* 1.3 80.0 - - - +
46L LEU* 1.3 64.4 + - - +
47L VAL* 4.2 18.8 - - + +
144L ILE* 6.0 0.9 - - - -
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Residues in contact with LEU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L THR* 6.0 0.2 - - - +
37L GLY* 4.1 12.1 - - - -
44L ALA 5.9 0.7 - - - +
45L VAL* 1.3 76.5 - - - +
47L VAL* 1.3 66.7 + - - +
63L ILE* 3.4 37.8 - - + +
71L GLY* 3.9 32.8 - - - +
72L ILE* 4.0 10.5 - - - +
73L SER* 4.8 4.7 - - - +
133L LEU* 4.5 7.6 - - + +
135L ALA* 4.2 19.1 - - + -
144L ILE* 6.0 2.0 - - + -
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Residues in contact with VAL 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L THR* 2.4 26.5 + - - -
36L VAL* 2.9 34.7 + - + +
38L LEU* 5.8 3.8 - - + -
45L VAL* 4.2 17.7 - - + +
46L LEU* 1.3 80.5 - - - +
48L ALA* 1.3 65.7 + - - +
63L ILE* 4.3 2.2 - - - -
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Residues in contact with ALA 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ALA 4.2 2.0 - - - -
35L THR* 3.5 16.8 - - - +
47L VAL* 1.3 84.5 - - - +
49L LEU* 1.3 64.1 + - - +
50L LYS* 4.3 1.7 + - + +
62L LYS* 3.8 21.3 - - + -
63L ILE* 3.7 29.5 - - + +
73L SER* 3.9 4.0 - - - +
74L ILE 5.6 0.2 - - - +
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Residues in contact with LEU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L SER* 2.9 38.8 + - - -
34L ALA* 3.4 29.9 + - + +
48L ALA* 1.3 78.2 - - - +
50L LYS* 1.3 74.0 + - - +
51L ARG* 4.5 11.2 - - + -
62L LYS* 3.6 11.9 - - - +
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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