Contacts of the helix formed by residues 102 - 107 (chain K) in PDB entry 5K0Y
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 102 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31K LEU* 4.3 22.4 - - + -
43K VAL* 4.6 11.2 - - + +
46K VAL* 3.8 24.0 - - + +
47K LYS* 3.9 35.9 - - + +
50K LEU* 4.2 17.0 - - + -
101K LYS* 1.4 73.1 - - + +
103K GLU* 1.4 64.1 + - + +
105K PHE* 3.3 17.3 + - - +
106K LEU* 3.5 27.0 + - + +
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Residues in contact with GLU 103 (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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31K LEU* 4.1 25.3 - - + +
34K GLU* 4.8 7.7 - - - +
35K TYR* 3.7 22.7 + - - +
101K LYS* 3.6 39.3 + - + +
102K ILE* 1.4 76.1 - - + +
104K ASP* 1.4 62.0 + - - +
105K PHE 3.1 0.9 + - - -
106K LEU* 3.2 11.9 + - - +
107K GLU* 3.1 35.4 + - - +
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Residues in contact with ASP 104 (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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86K VAL* 3.7 25.2 - - + +
100K LEU* 4.5 13.8 - - + +
101K LYS* 3.1 43.6 + - - +
103K GLU* 1.4 74.1 - - - +
105K PHE* 1.4 57.9 + - + +
107K GLU* 3.7 13.6 - - - +
108K ARG* 3.2 40.3 + - - +
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Residues in contact with PHE 105 (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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46K VAL* 3.9 24.0 - - + -
49K THR* 5.3 5.8 - - - -
50K LEU* 3.7 34.3 - - + -
53K ILE* 4.0 26.5 - - + -
81K LEU* 4.5 7.4 - - + -
84K ILE* 5.2 3.4 - - + -
86K VAL* 4.0 32.5 - - + +
100K LEU* 4.3 14.8 - - + -
101K LYS 3.5 20.2 - - - -
102K ILE* 3.5 9.6 - - - +
103K GLU 3.1 0.6 - - - -
104K ASP* 1.4 72.6 - - - +
106K LEU* 1.4 57.8 - - - +
107K GLU 3.2 1.8 - - - -
108K ARG* 3.0 26.9 + - - +
109K ARG* 3.8 7.3 + - - +
148K ILE* 4.5 20.9 - - + +
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Residues in contact with LEU 106 (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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31K LEU* 4.7 7.6 - - + -
35K TYR* 3.5 42.2 - - + -
37K LEU* 4.2 28.9 - - + -
42K GLU 5.2 0.7 - - - +
43K VAL* 6.1 0.9 - - + -
46K VAL* 3.9 21.8 - - + -
102K ILE* 3.6 31.4 - - + +
103K GLU* 3.4 8.7 - - - +
105K PHE* 1.4 77.2 - - - +
107K GLU* 1.4 59.5 + - - +
108K ARG 3.4 0.5 + - - -
109K ARG* 3.4 35.6 + - - +
112K THR* 3.3 17.3 + - - +
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Residues in contact with GLU 107 (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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35K TYR* 3.7 23.4 + - + +
103K GLU* 3.1 38.8 + - - +
104K ASP* 3.6 11.0 + - - +
105K PHE 3.1 0.4 + - - -
106K LEU* 1.4 74.6 - - - +
108K ARG* 1.4 89.4 + - - +
112K THR* 2.9 19.6 + - - -
113K GLN* 3.4 14.2 + - - -
116K LYS* 4.2 13.5 + - - +
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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