Contacts of the helix formed by residues 106 - 111 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303M TYR* 3.1 12.8 + - - -
102O SER* 2.9 25.2 - - - +
103O MET 2.9 7.7 + - - -
105O HIS* 1.3 97.9 + - - +
107O LYS* 1.3 63.0 + - - +
108O HIS* 3.1 23.0 - - + -
109O VAL* 3.0 27.7 + - + +
110O PHE* 3.5 8.2 - - + -
215O PHE* 5.5 0.9 - - + -
318O CYS* 3.4 21.9 - - - +
319O HIS* 3.2 28.6 - - - +
322O MET* 5.0 0.9 - - - +
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Residues in contact with LYS 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345M TYR* 3.7 18.7 + - + +
103O MET 3.3 2.4 + - - -
104O TYR* 3.3 37.4 + - - +
105O HIS 3.8 1.2 - - - -
106O ASN* 1.3 75.5 - - - +
108O HIS* 1.3 57.8 + - - +
110O PHE* 3.0 2.4 + - - +
111O LYS* 2.9 33.8 + - + +
131O LYS 4.2 15.5 - - - -
132O ALA* 3.4 30.3 - - + +
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Residues in contact with HIS 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M THR* 4.1 25.0 + - + +
382M LEU* 2.9 57.9 + - + +
383M CYS* 5.3 1.3 - - + -
105O HIS 4.8 0.2 + - - -
106O ASN* 3.6 37.5 - - + -
107O LYS* 1.3 78.7 + - - +
109O VAL* 1.3 75.7 + - + +
111O LYS* 4.2 10.0 + - - +
113O LYS* 5.5 1.2 - - - +
317O LYS 5.2 3.6 + - - -
319O HIS* 4.5 2.9 - - + +
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Residues in contact with VAL 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O ASN* 3.0 18.9 + - + +
108O HIS* 1.3 102.9 - - + +
110O PHE* 1.3 63.1 + - + +
113O LYS* 3.0 26.1 - - - +
181O ILE* 3.4 14.4 - - + +
213O LEU* 3.3 33.4 - - + -
215O PHE* 4.2 17.0 - - + -
317O LYS* 4.8 11.2 - - + +
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Residues in contact with PHE 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O SER 4.3 0.2 - - - -
103O MET* 3.6 45.8 - - + -
106O ASN 3.5 15.0 - - - -
107O LYS 3.0 1.8 + - - +
109O VAL* 1.3 84.0 - - + +
111O LYS* 1.3 65.9 + - - +
112O ASP 3.2 0.7 + - - -
113O LYS* 3.0 18.8 + - - +
115O VAL* 4.0 17.3 - - + -
129O ALA* 4.5 9.6 - - + -
132O ALA* 3.7 32.8 - - + +
133O GLY 4.1 1.3 - - - -
134O ALA* 3.6 11.8 - - - +
181O ILE* 3.6 28.7 - - + -
183O ILE* 4.4 4.9 - - + -
215O PHE* 3.8 36.8 - + - -
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Residues in contact with LYS 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O LYS* 2.9 16.4 + - + +
108O HIS* 4.2 9.0 + - - +
109O VAL 3.7 1.4 - - - -
110O PHE* 1.3 74.0 - - - +
112O ASP* 1.3 94.4 + - - +
113O LYS* 3.3 11.3 + - - +
132O ALA 4.5 1.3 - - - +
133O GLY* 3.4 17.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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