Contacts of the helix formed by residues 48 - 55 (chain T) in PDB entry 1KYO
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 LEU 48 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O THR* 3.7 18.2 - - + +
87O HIS* 4.5 5.6 - - + +
264O ASP* 5.5 1.8 - - - +
40T TYR* 6.1 0.7 - - + -
41T GLU* 3.7 52.9 - - + +
44T ASN* 3.3 31.6 - - + +
46T GLY 3.5 0.4 - - - -
47T LYS* 1.3 78.1 - - - +
49T TRP* 1.3 64.9 + - - +
50T LYS* 3.3 18.8 - - + +
51T ASP* 3.3 18.0 + - - +
52T VAL* 3.1 24.0 + - - +
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Residues in contact with TRP 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O HIS* 3.9 18.9 + - + +
91O ARG* 3.9 9.4 - - + -
117O GLY* 3.6 35.6 - - - +
118O VAL 3.5 15.5 - - - -
119O SER* 3.0 33.7 - - - -
120O HIS* 3.3 24.4 + - - -
121O THR* 3.7 18.1 - - + +
48T LEU* 1.3 70.3 - - - +
50T LYS* 1.3 65.7 + - + +
52T VAL* 3.1 28.6 + - + -
53T LYS* 2.8 56.4 + - + +
56T ILE* 5.5 2.7 - - + -
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Residues in contact with LYS 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41T GLU* 3.1 39.3 + - - +
45T LYS* 5.6 5.5 - - - +
48T LEU* 3.9 22.2 - - + +
49T TRP* 1.3 79.2 - - + +
51T ASP* 1.3 74.1 + - - +
53T LYS* 3.2 10.6 + - - +
54T ALA* 3.2 21.3 + - - +
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Residues in contact with ASP 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T LYS* 3.4 21.9 + - - +
46T GLY* 2.6 41.8 + - - +
48T LEU* 3.5 27.7 - - - +
49T TRP 3.2 0.4 - - - -
50T LYS* 1.3 90.8 + - - +
52T VAL* 1.3 60.0 + - - +
54T ALA* 3.6 12.1 + - - +
55T LYS* 3.4 25.8 - - - +
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Residues in contact with VAL 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O HIS* 4.0 9.0 - - + +
88O ALA* 3.6 44.0 - - + +
91O ARG* 4.8 9.2 - - - -
46T GLY 4.2 6.1 - - - +
47T LYS 4.1 2.5 - - - +
48T LEU 3.1 16.4 + - - +
49T TRP* 3.1 29.3 + - + +
51T ASP* 1.3 76.4 - - - +
53T LYS* 1.3 62.0 + - - +
55T LYS* 3.3 18.1 + - + +
56T ILE* 3.1 31.3 - - + +
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Residues in contact with LYS 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O THR* 4.6 18.0 - - + +
49T TRP* 2.8 45.9 + - + +
50T LYS* 3.2 9.2 + - - +
52T VAL* 1.3 75.0 - - - +
54T ALA* 1.3 64.8 + - - +
56T ILE* 3.2 25.2 + - + +
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Residues in contact with ALA 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50T LYS 3.2 11.4 + - - +
51T ASP* 3.7 12.3 - - - +
53T LYS* 1.3 74.2 - - - +
55T LYS* 1.3 59.5 + - + +
56T ILE 2.9 14.1 + - - -
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Residues in contact with LYS 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ALA* 5.5 8.2 - - + +
147Q LYS* 5.5 6.7 - - - +
46T GLY* 3.7 28.1 + - - -
51T ASP* 3.4 21.5 - - - +
52T VAL* 3.3 12.4 + - + +
54T ALA* 1.3 75.0 - - + +
56T ILE* 1.3 68.6 + - + +
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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