Contacts of the strand formed by residues 47 - 50 (chain L) in PDB entry 1S5E
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 THR 47 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3K GLN* 3.8 35.5 + - + +
39L ILE* 3.8 20.9 - - + -
40L ILE 3.3 10.8 - - - +
41L THR* 3.5 12.8 - - + +
45L GLY 3.2 14.1 + - - -
46L ALA* 1.3 72.4 - - - +
48L PHE* 1.3 76.7 + - - +
93L PRO* 3.5 19.5 - - + +
94L HIS* 4.0 4.2 + - - +
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Residues in contact with PHE 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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18L HIS* 3.2 46.9 - + + -
20L LEU* 4.7 4.5 - - + -
39L ILE* 3.3 6.1 - - - +
40L ILE* 2.8 38.7 + - + +
42L PHE* 3.7 25.8 - + - -
46L ALA* 3.7 31.2 - - + -
47L THR* 1.3 81.3 - - - +
49L GLN* 1.3 60.4 + - - +
85L LEU* 3.6 18.4 - - + -
87L VAL* 3.7 20.4 - - + -
93L PRO* 4.2 5.4 - - - -
94L HIS* 3.4 15.3 - + + +
96L ILE* 3.8 19.5 - - + -
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Residues in contact with GLN 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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1K THR* 4.1 12.7 + - - +
37L MET* 3.4 28.5 - - + +
38L ALA 3.3 9.9 - - - +
39L ILE* 4.5 1.8 - - + +
48L PHE* 1.3 75.8 - - - +
50L VAL* 1.3 61.3 + - - +
51L GLU* 3.6 30.9 + - + +
52L VAL* 4.7 1.0 - - - +
72L LEU* 5.8 0.2 - - - -
91L LYS* 4.1 8.8 - - - +
92L THR 3.8 12.3 - - - +
93L PRO* 3.0 37.8 - - + +
94L HIS 3.0 9.2 + - - +
95L ALA* 3.4 7.7 - - + -
96L ILE* 2.9 31.3 + - - +
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Residues in contact with VAL 50 (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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37L MET* 3.4 22.7 - - - +
38L ALA* 2.9 14.9 + - + +
49L GLN* 1.3 75.6 + - - +
51L GLU* 1.3 65.8 + - - +
65L ILE* 3.8 32.5 - - + +
68L MET* 3.8 18.2 - - + -
69L LYS* 3.8 25.8 - - + -
72L LEU* 3.5 32.1 - - + -
96L ILE* 4.4 7.6 - - + +
31M LEU* 4.7 7.9 - - + -
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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