Contacts of the helix formed by residues 445 - 449 (chain J) in PDB entry 4DVQ
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 PHE 445 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97J VAL* 3.3 35.2 - - + -
100J LEU* 4.1 19.7 - - + -
101J GLN* 4.1 18.8 - - + +
104J ASP* 3.5 19.7 - - - -
382J LEU* 3.8 24.7 - - + -
383J GLU 5.8 0.2 - - - -
384J ARG* 3.2 59.6 + - + -
405J VAL* 5.2 3.1 - - + -
438J PHE* 5.1 4.9 - - + -
441J VAL* 4.7 5.2 - - + -
444J GLY* 1.3 79.1 - - - +
446J GLY* 1.3 64.0 + - - +
449J GLN* 2.9 23.5 + - - +
601J HEM 3.4 4.2 + - - -
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Residues in contact with GLY 446 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J GLN* 3.8 31.3 - - - -
104J ASP* 4.2 7.4 - - - -
445J PHE* 1.3 80.6 - - - +
447J MET* 1.3 63.0 + - - -
448J ARG 4.1 0.2 - - - -
449J GLN* 3.5 16.9 + - - +
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Residues in contact with MET 447 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J ASP* 5.2 1.2 + - - +
108J PRO* 5.4 5.9 - - + +
137J TRP* 3.6 23.8 - - + -
138J ARG* 4.1 26.0 - - - +
141J ARG* 3.3 30.0 + - + +
142J LEU* 3.7 29.6 - - + -
145J ASN* 3.9 18.3 + - - +
446J GLY* 1.3 74.3 - - - -
448J ARG* 1.3 58.8 + - - +
449J GLN 3.4 1.3 - - - -
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Residues in contact with ARG 448 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J PRO* 3.4 37.1 + - + +
109J CYS* 5.1 0.6 - - - +
110J ARG* 3.0 32.1 - - - +
129J VAL 2.7 29.5 + - - -
130J PHE 4.2 0.6 + - - -
132J LEU 2.4 26.4 + - - -
133J ASN* 2.5 24.0 + - - +
137J TRP* 3.4 28.2 - - + +
141J ARG* 3.5 5.9 + - - +
384J ARG* 3.3 23.3 - - - +
445J PHE 3.5 1.8 - - - -
446J GLY 3.2 0.6 - - - -
447J MET* 1.3 78.0 - - - +
449J GLN* 1.3 66.6 + - - +
601J HEM 3.0 44.2 + - - +
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Residues in contact with GLN 449 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J ARG* 2.6 41.9 + - - +
149J LEU* 3.5 16.3 - - + +
443J PHE* 3.6 16.7 - - - +
444J GLY 4.6 4.4 + - - -
445J PHE* 2.9 32.0 + - - +
446J GLY 3.6 11.4 - - - +
447J MET 3.4 1.0 - - - -
448J ARG* 1.3 76.5 - - - +
450J CYS* 1.3 72.6 - - - +
453J ARG* 3.5 43.9 + - - +
601J HEM 3.7 1.6 - - - -
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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