Contacts of the helix formed by residues 106 - 111 (chain K) in PDB entry 5DST
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 ASN 106 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303I TYR* 3.0 13.7 + - - -
102K SER* 2.9 26.7 - - - +
103K MET 3.0 7.3 + - - -
105K HIS* 1.3 96.9 + - - +
107K LYS* 1.3 59.2 + - - +
108K HIS* 3.1 21.0 - - + -
109K VAL* 2.9 32.9 + - + +
110K PHE* 3.5 7.3 - - + -
215K PHE* 5.6 0.7 - - + -
318K CYS* 3.2 23.8 - - - +
319K HIS* 3.3 28.2 - - - +
322K MET* 4.9 0.9 - - - +
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Residues in contact with LYS 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I TYR* 3.9 16.7 + - + +
103K MET 3.3 2.6 + - - -
104K TYR* 3.3 38.5 + - - +
105K HIS 3.8 1.2 - - - -
106K ASN* 1.3 76.1 - - - +
108K HIS* 1.3 56.0 + - - +
110K PHE 3.0 2.4 + - - +
111K LYS* 2.9 32.2 + - + +
131K LYS 4.0 17.0 - - - -
132K ALA* 3.4 31.2 - - + +
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Residues in contact with HIS 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347I THR* 4.2 25.6 + - + +
382I LEU* 3.1 56.1 + - + +
383I CYS* 5.4 1.3 - - + -
105K HIS 4.9 0.2 + - - -
106K ASN* 3.7 38.1 - - + -
107K LYS* 1.3 78.5 + - - +
109K VAL* 1.3 76.2 + - + +
110K PHE 3.3 0.2 - - - -
111K LYS* 4.3 10.0 + - - +
113K LYS* 5.5 0.9 - - - +
317K LYS 5.3 3.2 + - - -
319K HIS* 4.6 3.3 - - + +
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Residues in contact with VAL 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K ASN* 2.9 20.3 + - + +
108K HIS* 1.3 103.8 - - + +
110K PHE* 1.3 63.3 + - + +
113K LYS* 3.0 25.7 - - - +
181K ILE* 3.4 14.3 - - + +
213K LEU* 3.3 34.3 - - + -
215K PHE* 4.3 15.0 - - + -
317K LYS* 4.7 12.3 - - + +
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Residues in contact with PHE 110 (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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102K SER 4.2 0.7 - - - -
103K MET* 3.6 45.5 - - + -
106K ASN 3.5 15.5 - - - -
107K LYS 3.0 2.2 + - - +
109K VAL* 1.3 82.5 - - + +
111K LYS* 1.3 67.6 + - - +
112K ASP 3.1 0.7 + - - -
113K LYS* 2.8 18.6 + - - +
115K VAL* 3.9 18.4 - - + -
129K ALA* 4.4 10.5 - - + -
132K ALA* 3.6 33.0 - - + +
133K GLY 4.1 1.1 - - - -
134K ALA* 3.5 12.1 - - + +
181K ILE* 3.7 28.7 - - + -
183K ILE* 4.4 4.5 - - + -
215K PHE* 3.9 36.8 - + - -
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Residues in contact with LYS 111 (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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107K LYS* 2.9 17.3 + - + +
108K HIS* 4.3 8.5 + - - +
109K VAL 3.7 1.6 - - - -
110K PHE* 1.3 75.5 - - - +
112K ASP* 1.3 93.2 + - - +
113K LYS* 3.1 12.3 + - - +
132K ALA 4.5 1.3 - - - +
133K GLY* 3.3 15.9 - - - +
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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