Contacts of the helix formed by residues 107 - 111 (chain I) in PDB entry 1DZG
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 LYS 107 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54I ALA* 3.6 19.6 - - - +
57I ARG* 3.6 31.2 + - + +
58I PHE* 3.8 10.3 - - - +
61I THR* 4.1 25.5 + - - -
103I MET 3.3 3.9 + - - -
104I GLU 3.4 13.8 + - - +
105I VAL 3.3 8.5 - - - +
106I PHE* 1.3 75.3 - - - +
108I PHE* 1.3 58.4 + - - +
109I ASP* 3.3 4.0 - - - +
110I THR* 2.6 49.7 + - + +
338I MET* 6.4 0.4 - - - -
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Residues in contact with PHE 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 5.0 0.5 + - - -
51I LEU* 3.9 11.0 - - + -
54I ALA* 4.5 7.6 - - + -
55I ASN* 3.4 23.3 - - - -
84I SER* 3.8 16.2 - - - -
87I PHE 5.5 0.7 - - - -
88I ALA* 4.4 13.2 - - + -
91I LYS* 5.0 7.0 - - + -
102I LEU 4.8 1.6 - - - -
103I MET* 3.2 32.6 + - + +
106I PHE* 2.9 37.6 + + + -
107I LYS* 1.3 72.1 - - - +
109I ASP* 1.3 59.4 + - - +
111I ILE* 3.3 23.0 + - + +
114I LYS* 5.5 0.5 - - - +
119I ILE* 3.7 37.2 - - + +
123I PHE* 3.6 31.9 - + - -
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Residues in contact with ASP 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I TYR* 3.9 29.1 + - + +
25I SER* 3.8 20.8 - - - -
26I PRO* 4.0 22.7 - - + +
103I MET* 3.9 5.0 + - - +
104I GLU* 3.7 41.5 - - - +
107I LYS* 4.0 2.1 - - - +
108I PHE* 1.3 76.3 - - - +
110I THR* 1.3 78.0 + - - +
111I ILE 3.3 4.3 + - - +
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Residues in contact with THR 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ALA* 4.0 1.4 - - - +
57I ARG* 2.6 45.9 + - - -
107I LYS* 2.6 41.3 + - + +
109I ASP* 1.3 84.0 - - - +
111I ILE* 1.3 59.3 + - - +
112I SER* 3.0 10.7 + - - -
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Residues in contact with ILE 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 3.3 14.9 + - - -
50I GLU* 3.6 46.9 - - + +
51I LEU* 3.7 23.1 - - + +
54I ALA* 3.8 16.2 - - + -
57I ARG* 5.3 1.1 - - - +
108I PHE* 3.3 12.4 + - - +
109I ASP 3.3 2.6 - - - +
110I THR* 1.3 72.4 + - - +
112I SER* 1.3 68.4 + - - +
114I LYS* 3.3 22.0 - - + +
119I ILE* 4.5 8.3 - - + -
122I PHE* 3.9 24.2 - - + -
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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