Contacts of the helix formed by residues 107 - 112 (chain B) in PDB entry 5D3E
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 TYR 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR* 3.6 29.2 - - + +
32B GLU* 3.6 34.5 + - + +
34B ASN* 3.9 16.6 - - + -
103B LEU* 2.9 29.1 + - + +
106B ASN* 1.3 85.6 - - + +
108B LEU* 1.3 65.8 + - - +
109B ILE 3.6 1.1 - - - -
110B LYS 4.1 1.3 - - - -
111B ASN* 3.2 33.8 + - - +
102F SER* 3.6 20.4 + - - -
106F ASN* 3.3 40.6 + - + +
107F TYR* 4.0 25.1 - + - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 3.6 27.6 - - + -
35B GLU 6.0 1.1 - - - +
36B PRO* 6.3 0.4 - - + -
37B LEU* 3.9 18.6 - - + +
45B LEU* 3.7 23.1 - - + -
103B LEU* 3.0 17.4 + - + +
104B LEU* 3.6 28.3 - - + +
107B TYR* 1.3 75.0 - - - +
109B ILE* 1.3 66.0 + - - +
110B LYS 3.5 0.2 + - - -
111B ASN* 3.7 5.0 + - - +
112B CYS* 3.6 18.7 + - - +
123B TYR* 3.6 44.4 - - + +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 2.8 36.7 + - + +
105B ASP* 4.1 16.8 - - - +
108B LEU* 1.3 72.3 - - - +
110B LYS* 1.3 70.2 + - - +
111B ASN 3.4 0.2 + - - -
112B CYS* 3.7 19.8 + - - +
120B LYS* 4.3 26.3 + - + +
123B TYR* 3.7 31.6 - - + +
124B LEU* 4.3 24.9 - - + -
127B LYS* 4.3 7.2 - - + +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP 3.6 19.7 + - - +
106B ASN* 3.8 31.0 + - - +
107B TYR 4.0 5.6 - - - +
108B LEU 3.2 0.4 - - - -
109B ILE* 1.3 83.4 - - - +
111B ASN* 1.3 74.2 + - - +
112B CYS 3.9 4.5 - - - +
34F ASN* 6.0 0.2 - - - +
106F ASN 5.4 2.2 + - - -
110F LYS* 3.9 37.2 - - + +
111F ASN* 5.9 1.4 + - - -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASN* 2.3 51.6 + - - +
35B GLU 4.6 3.6 + - - -
36B PRO* 5.4 14.6 - - + +
106B ASN 5.1 0.5 - - - +
107B TYR* 3.2 22.1 + - - +
108B LEU* 4.3 2.7 - - - +
109B ILE 3.3 0.4 - - - -
110B LYS* 1.3 91.4 - - - +
112B CYS* 1.3 63.0 + - - +
113B SER 3.8 0.7 + - - -
106F ASN* 5.6 0.2 - - - +
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 5.9 7.9 - - + -
108B LEU 3.6 17.6 + - - +
109B ILE* 3.8 12.9 - - - +
110B LYS 3.4 6.1 - - - +
111B ASN* 1.3 81.3 - - - +
113B SER* 1.3 66.8 + - - +
116B GLN* 4.3 13.9 - - + -
119B SER* 4.1 12.3 - - - -
120B LYS* 4.0 43.9 + - - -
123B TYR* 4.4 4.9 - - + -
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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