Contacts of the strand formed by residues 47 - 50 (chain C) in PDB entry 5XVO
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 ILE 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.5 33.7 - - + +
10C LYS 4.1 1.3 - - - +
12C SER* 3.5 20.4 - - - +
14C LEU* 3.9 24.2 - - + -
42C LEU* 4.1 12.6 - - + -
44C THR* 3.6 33.2 - - - +
45C THR 3.4 0.8 + - - -
46C ASP* 1.3 84.0 - - - +
48C SER* 1.3 75.4 + - - +
49C LEU* 4.7 3.6 - - + -
50D THR* 3.3 3.5 - - - -
51D THR* 2.9 41.2 + - + +
-20R C 4.4 1.8 - - - -
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER 3.0 11.0 + - - -
13C LYS* 4.1 23.8 - - - -
14C LEU 2.8 25.4 + - - -
46C ASP 4.2 0.4 + - - -
47C ILE* 1.3 80.3 - - - +
49C LEU* 1.3 64.0 + - - +
48D SER* 5.2 6.1 - - - -
49D LEU 3.4 9.6 - - - -
50D THR* 4.2 6.7 - - - +
-21R T 3.2 29.3 + - - +
-20R C 4.2 4.0 - - - -
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS* 5.5 0.2 - - - -
14C LEU* 3.2 28.0 - - + +
40C LEU* 6.1 1.3 - - + -
42C LEU* 3.6 31.4 - - + -
47C ILE* 4.7 1.3 - - + +
48C SER* 1.3 77.9 - - - +
50C THR* 1.3 62.2 + - - +
53C LEU* 4.6 5.6 - - + -
54C LEU* 3.6 41.7 - - + -
66C PHE* 5.0 4.0 - - + -
47D ILE 3.9 0.2 - - - +
48D SER* 3.3 2.1 - - - +
49D LEU* 2.9 50.6 + - + +
51D THR* 4.3 14.6 - - + -
54D LEU* 5.0 2.5 - - + -
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Residues in contact with THR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS* 4.5 8.5 - - - -
14C LEU 3.4 13.1 + - - +
15C SER* 4.0 17.0 - - - -
16C TYR 4.3 2.1 + - - -
49C LEU* 1.3 81.5 - - - +
51C THR* 1.3 63.2 + - - +
52C MET* 3.7 8.6 + - - +
53C LEU* 3.2 25.5 + - - +
54C LEU* 3.2 22.0 + - - +
45D THR 5.0 2.7 - - - -
46D ASP 6.0 0.7 - - - -
47D ILE 3.2 9.0 - - - +
48D SER* 4.1 15.7 - - - +
49D LEU* 5.8 0.7 - - - -
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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