Contacts of the strand formed by residues 58 - 62 (chain K) in PDB entry 5OA3
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 58 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15K LEU* 4.6 0.9 - - + -
49K MET* 3.8 22.7 - - + +
52K LEU* 3.6 24.5 - - + -
53K LYS* 3.5 44.7 - - + +
56K GLY* 3.4 5.5 - - - +
57K TYR* 1.3 85.7 - - - +
59K LYS* 1.3 68.7 + - - +
60K GLU 4.2 0.7 + - - -
69K TRP* 4.4 12.3 - - + -
70K TYR 3.1 9.2 - - - +
71K LEU* 3.6 22.4 - - + -
72K THR* 4.2 1.8 - - - -
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Residues in contact with LYS 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K GLY 5.9 0.9 - - - -
58K VAL* 1.3 77.7 - - - +
60K GLU* 1.3 62.5 + - - +
68K TYR 3.5 1.0 - - - +
69K TRP* 3.2 9.6 - - - -
70K TYR* 2.9 52.0 + - + +
71K LEU 5.7 0.4 - - - -
72K THR* 4.1 23.6 - - - +
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Residues in contact with GLU 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14972 G 4.4 11.3 + - - -
49K MET 5.0 1.9 - - - +
50K GLN* 5.2 5.0 - - - +
53K LYS* 3.1 54.0 + - + +
58K VAL 4.2 0.8 + - - +
59K LYS* 1.3 75.1 - - - +
61K GLN* 1.3 69.2 + - - +
62K PHE* 4.3 2.8 - - + +
67K PHE* 4.3 18.7 - - - -
68K TYR 3.6 2.5 - - - +
69K TRP* 2.8 38.8 + - + +
70K TYR* 5.6 0.2 - - - -
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Residues in contact with GLN 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 3.5 30.7 - - + -
27D ARG* 3.1 40.0 + - + +
28D GLU* 3.4 26.2 - - + +
59K LYS 4.1 0.2 + - - -
60K GLU* 1.3 82.0 - - - +
62K PHE* 1.3 62.9 + - - +
63K ALA 4.1 0.4 - - - -
67K PHE* 4.1 1.2 - - - -
68K TYR* 2.9 45.2 + - + +
70K TYR* 4.3 11.3 - - + -
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Residues in contact with PHE 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14972 G 3.2 76.3 - + + +
27D ARG* 3.3 26.0 + - - -
25K LYS* 3.9 7.6 - - + -
60K GLU* 4.3 3.3 + - + +
61K GLN* 1.3 76.0 - - - +
63K ALA* 1.3 62.6 + - - +
65K ARG* 3.6 34.1 - - - -
66K HIS 3.4 14.8 - - - -
67K PHE* 3.6 48.9 - + + -
23d VAL 5.5 0.2 - - - -
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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