Contacts of the helix formed by residues 47 - 59 (chain I) 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 ASN 47 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45I PRO 3.8 0.6 + - - +
46I GLY* 1.3 72.9 - - - -
48I ARG* 1.3 74.5 + - - +
49I TRP* 3.2 13.0 + - - +
50I LEU* 3.1 32.4 + - + +
51I ARG* 2.8 31.0 + - - +
81I TYR* 3.7 1.8 - - - -
82I ASN* 6.3 0.8 - - - +
48J ARG* 5.2 2.1 + - - -
49J TRP* 3.9 23.4 - - - -
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Residues in contact with ARG 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I GLY 4.0 1.0 + - - -
47I ASN* 1.3 81.7 - - - +
49I TRP* 1.3 99.2 + - + +
51I ARG* 4.1 6.0 + - - +
52I LEU* 3.3 23.3 + - - +
81I TYR* 3.5 20.9 + - + -
82I ASN* 3.4 22.5 + - - +
83I LEU* 2.7 44.3 + - + +
84I GLY* 4.4 8.1 - - - +
85I GLY 4.9 2.8 - - - +
241I PRO* 6.3 0.8 - - - +
47J ASN* 5.7 0.6 - - - +
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Residues in contact with TRP 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ASN* 3.2 8.4 - - - +
48I ARG* 1.3 119.2 - - + +
50I LEU* 1.3 59.5 + - - +
51I ARG 3.2 4.7 - - - -
52I LEU* 3.7 21.8 - - + +
53I LEU* 3.1 36.8 + - + +
241I PRO* 6.3 0.7 - - + -
244I LEU* 3.7 31.0 - - + -
47J ASN* 3.7 23.1 - - - -
49J TRP* 3.6 76.0 - + + -
50J LEU* 4.5 9.2 - - + -
53J LEU* 4.7 11.4 - - + -
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Residues in contact with LEU 50 (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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47I ASN* 3.1 34.8 + - + +
49I TRP* 1.3 75.5 - - - +
51I ARG* 1.3 59.3 + - - +
53I LEU* 4.4 6.1 - - + +
54I GLN* 3.1 24.7 + - - +
49J TRP* 4.2 18.4 - - + -
244J LEU* 4.6 17.5 - - + -
247J TRP* 6.2 3.4 - - + -
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Residues in contact with ARG 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I HIS* 5.8 0.7 - - - -
47I ASN 2.8 14.4 + - - +
48I ARG* 4.6 4.4 + - - +
50I LEU* 1.3 78.6 - - - +
52I LEU* 1.3 65.2 + - - +
53I LEU 3.3 0.4 - - - -
54I GLN* 3.1 22.6 + - + +
55I ILE* 3.4 11.2 + - + +
61I TYR* 3.4 36.1 + - + +
64I LEU* 5.0 0.8 - - - +
67I GLU* 4.7 4.0 - - - +
68I MET* 3.9 24.7 - - - +
81I TYR* 3.4 42.2 + - - +
83I LEU* 4.5 14.6 - - - +
88I MET* 5.2 7.5 - - - +
239I PHE* 3.3 43.6 - - - +
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Residues in contact with LEU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ARG* 3.3 21.2 + - - +
49I TRP* 3.4 23.9 + - + +
51I ARG* 1.3 81.2 - - - +
53I LEU* 1.3 76.8 + - + +
55I ILE* 3.6 13.0 + - - +
56I TRP* 3.6 13.3 + - - +
239I PHE* 3.3 28.6 - - - +
240I MET* 3.3 42.6 - - + +
241I PRO* 4.6 2.9 - - + -
244I LEU* 4.6 14.4 - - + -
248I ILE* 5.2 1.3 - - + -
53J LEU* 6.1 1.1 - - + -
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Residues in contact with LEU 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I TRP* 3.1 21.7 + - + +
50I LEU* 5.2 4.9 - - + -
51I ARG 3.3 0.2 - - - -
52I LEU* 1.3 83.6 - - + +
54I GLN* 1.3 60.3 + - - +
55I ILE 3.1 1.3 - - - -
56I TRP* 3.1 14.7 + - + +
57I ARG* 2.8 30.8 + - - +
248I ILE* 4.0 27.6 - - + -
49J TRP* 4.6 11.9 - - + -
52J LEU* 6.1 1.6 - - + -
53J LEU* 5.2 12.3 - - + -
244J LEU* 4.2 30.3 - - + -
247J TRP* 3.8 24.1 - - + -
248J ILE* 5.0 14.6 - - + -
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Residues in contact with GLN 54 (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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50I LEU 3.1 21.9 + - - +
51I ARG* 3.1 12.9 + - + +
53I LEU* 1.3 76.8 - - - +
55I ILE* 1.3 58.1 + - + +
57I ARG* 3.9 29.9 + - - +
58I GLU* 2.9 55.7 + - - +
60I GLY 4.2 0.6 - - - +
61I TYR* 6.6 0.4 - - + -
247J TRP* 4.4 12.9 - - - -
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Residues in contact with ILE 55 (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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51I ARG* 3.4 13.0 + - + +
52I LEU* 3.7 10.8 - - - +
53I LEU 3.1 0.2 - - - -
54I GLN* 1.3 77.2 - - + +
56I TRP* 1.3 58.9 + - - +
59I GLN* 2.9 26.2 + - - -
60I GLY 3.6 23.1 - - - +
61I TYR* 3.5 25.6 - - + -
235I VAL 3.8 2.9 - - - +
236I GLN* 3.6 39.8 + - - +
239I PHE* 3.3 45.8 - - + -
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Residues in contact with TRP 56 (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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52I LEU 3.6 4.4 + - - +
53I LEU* 3.1 26.3 + - + +
55I ILE* 1.3 79.5 - - - +
57I ARG* 1.3 74.8 + - + +
59I GLN* 3.7 11.4 + - - +
236I GLN* 5.7 0.7 + - - -
240I MET* 5.3 4.7 - - + +
248I ILE* 3.0 47.9 + - + +
249I SER* 3.2 22.6 + - - -
56J TRP* 4.2 22.9 - + - -
247J TRP* 4.4 27.4 - + - -
248J ILE* 4.4 23.1 - - + -
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Residues in contact with ARG 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I LEU 2.8 16.2 + - - +
54I GLN* 3.9 28.6 + - - +
56I TRP* 1.3 88.7 - - + +
58I GLU* 1.3 68.1 + - - +
59I GLN* 3.9 6.6 + - - +
246J ARG* 3.6 18.0 - - - +
247J TRP* 3.2 62.6 - - + +
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Residues in contact with GLU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I GLN* 2.9 54.0 + - - +
57I ARG* 1.3 87.6 + - + +
59I GLN* 1.3 81.4 + - - +
60I GLY* 3.2 15.1 + - - +
61I TYR* 5.6 0.3 - - - -
63I HIS* 4.3 18.9 + - - -
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Residues in contact with GLN 59 (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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55I ILE 2.9 13.3 + - - -
56I TRP 3.7 9.8 + - - +
57I ARG 3.5 5.7 + - - +
58I GLU* 1.3 82.1 + - - +
60I GLY* 1.3 56.1 + - - +
232I LYS* 3.2 31.2 + - - +
236I GLN* 3.2 40.0 - - - +
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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