Contacts of the helix formed by residues 48 - 53 (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 ARG 48 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47I ASN* 5.2 2.4 + - - -
46J GLY 3.8 3.0 + - - -
47J ASN* 1.3 76.5 + - - +
49J TRP* 1.3 105.7 + - + +
51J ARG* 3.9 5.0 + - - +
52J LEU* 3.1 38.5 + - - +
81J TYR* 3.9 20.2 + - + -
82J ASN* 3.7 22.0 + - - +
83J LEU* 3.4 35.0 + - + +
84J GLY* 4.7 12.3 + - - -
241J PRO* 6.0 4.0 - - - +
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Residues in contact with TRP 49 (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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47I ASN* 3.9 11.7 - - - -
49I TRP* 3.6 77.1 - + + -
50I LEU* 4.2 17.9 - - + -
53I LEU* 4.6 9.0 - - + -
47J ASN* 3.2 14.4 + - - +
48J ARG* 1.3 120.6 - - + +
50J LEU* 1.3 60.3 + - - +
51J ARG 3.2 1.8 - - - -
52J LEU* 3.6 24.5 - - + +
53J LEU* 3.3 34.6 + - + +
244J LEU* 3.9 24.9 - - + -
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Residues in contact with LEU 50 (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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49I TRP* 4.5 6.3 - - + -
244I LEU* 4.3 30.3 - - + -
247I TRP* 5.2 12.3 - - + -
47J ASN* 3.2 34.8 + - + +
49J TRP* 1.3 77.4 - - - +
51J ARG* 1.3 57.6 + - - +
53J LEU* 4.9 5.2 - - + +
54J GLN* 2.9 30.5 - - - +
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Residues in contact with ARG 51 (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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44J HIS* 5.6 2.4 + - - -
47J ASN 3.0 13.1 + - - +
48J ARG* 4.0 6.7 + - - +
49J TRP 3.2 0.4 - - - -
50J LEU* 1.3 78.2 - - - +
52J LEU* 1.3 61.8 + - - +
53J LEU 3.1 1.8 - - - -
54J GLN* 2.9 25.2 + - + +
55J ILE* 3.2 13.0 + - + +
61J TYR* 3.3 37.8 + - + +
64J LEU* 5.2 6.5 - - - +
67J GLU* 5.2 3.4 - - - -
68J MET* 5.4 5.9 - - - -
81J TYR* 3.0 53.4 + - - +
83J LEU* 4.4 13.3 - - - +
88J MET* 4.9 7.5 - - - +
239J PHE* 3.3 40.2 - - - +
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Residues in contact with LEU 52 (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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53I LEU* 6.1 2.0 - - + -
48J ARG* 3.1 29.5 + - - +
49J TRP* 3.6 35.2 - - + +
51J ARG* 1.3 79.5 - - - +
53J LEU* 1.3 76.3 + - + +
55J ILE* 3.5 19.4 - - - +
56J TRP 3.7 1.2 + - - -
239J PHE* 3.1 31.4 - - + +
240J MET* 3.1 42.2 - - + +
241J PRO* 5.8 2.7 - - + -
244J LEU* 5.1 9.6 - - + -
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Residues in contact with LEU 53 (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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49I TRP* 4.7 16.4 - - + -
52I LEU* 6.1 1.1 - - + -
53I LEU* 5.2 12.3 - - + -
244I LEU* 4.5 24.5 - - + -
247I TRP* 3.8 26.2 - - + -
248I ILE* 4.6 18.6 - - + -
49J TRP* 3.3 19.5 + - + +
50J LEU* 5.0 4.9 - - + -
51J ARG 3.1 0.8 - - - -
52J LEU* 1.3 87.3 - - + +
54J GLN* 1.3 57.0 + - - +
55J ILE 2.9 4.9 - - - -
56J TRP* 3.1 26.7 + - + +
57J ARG* 3.3 9.4 + - - +
248J ILE* 3.8 28.5 - - + -
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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
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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