Contacts of the helix formed by residues 47 - 59 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PRO 5.3 0.7 - - - +
46D GLY* 1.3 74.9 - - - +
48D ARG* 1.3 64.1 + - - +
49D TRP* 3.1 36.9 + - + +
50D LEU* 3.0 38.4 + - - +
51D ARG* 3.2 17.0 + - - +
81D TYR* 3.7 6.7 + - - -
82D ASN* 5.1 10.5 - - + +
48E ARG* 6.0 0.2 - - - -
49E TRP* 3.6 14.4 - - - -
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASN* 1.3 73.0 - - - +
49D TRP* 1.3 107.5 + - + +
51D ARG* 3.4 26.5 + - - +
52D LEU* 3.0 33.5 + - + +
81D TYR* 3.8 15.5 + - + -
82D ASN* 4.0 6.7 + - - +
83D LEU* 3.1 47.0 + - - +
84D GLY* 3.8 16.0 + - - +
239D PHE 5.0 2.2 - - - +
241D PRO* 6.0 4.6 - - - +
47E ASN* 4.5 8.1 - - - +
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Residues in contact with TRP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASN* 3.2 17.8 - - + +
48D ARG* 1.3 122.3 - - + +
50D LEU* 1.3 66.7 + - - +
52D LEU* 3.3 15.5 + - + +
53D LEU* 3.1 32.8 + - + +
241D PRO* 6.5 0.4 - - + -
244D LEU* 3.8 18.4 - - + -
47E ASN* 3.8 21.2 - - - +
49E TRP* 3.4 54.2 - + + +
50E LEU* 3.7 22.9 - - + -
53E LEU* 3.5 31.9 - - + -
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLY* 6.1 1.3 - - - -
47D ASN* 3.0 30.7 + - - +
49D TRP* 1.3 77.7 - - - +
51D ARG* 1.3 54.3 + - - +
53D LEU* 3.6 5.4 - - - +
54D GLN* 2.7 50.0 + - - +
49E TRP* 4.2 16.8 - - + -
244E LEU* 4.5 20.6 - - + -
247E TRP* 4.7 4.5 - - + -
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASN 3.2 10.6 + - - +
48D ARG* 3.4 22.9 + - - +
50D LEU* 1.3 78.9 - - - +
52D LEU* 1.3 58.5 + - - +
54D GLN* 3.1 6.9 + - - +
55D ILE* 2.9 44.1 + - + +
61D TYR* 4.1 30.3 + - + +
64D LEU* 6.4 0.2 - - - +
81D TYR* 3.3 43.3 + - - +
83D LEU* 4.0 12.3 - - - +
88D MET* 5.1 10.7 - - - +
239D PHE* 3.6 41.7 + - + +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ARG* 3.0 25.9 + - + +
49D TRP* 3.3 20.8 + - + +
51D ARG* 1.3 74.8 - - - +
53D LEU* 1.3 64.1 + - + +
55D ILE* 3.2 12.1 + - - +
56D TRP* 2.7 35.2 + - + +
239D PHE* 4.1 16.4 - - + +
240D MET* 3.8 36.3 - - + +
241D PRO* 4.9 1.8 - - + -
244D LEU* 4.0 17.3 - - + -
248D ILE* 3.8 30.3 - - + -
53E LEU* 5.2 4.0 - - + -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D TRP* 3.1 21.1 + - + +
50D LEU* 3.7 3.4 - - - +
52D LEU* 1.3 84.5 - - + +
54D GLN* 1.3 62.5 + - - +
56D TRP* 3.1 8.1 + - + +
57D ARG 2.9 19.2 + - - -
49E TRP* 4.1 20.4 - - + -
52E LEU* 5.4 1.1 - - + -
53E LEU* 4.4 13.2 - - + -
56E TRP* 3.5 36.3 - - + -
244E LEU* 4.1 14.1 - - + -
247E TRP* 3.4 23.3 - - + -
248E ILE* 3.5 30.1 - - + -
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Residues in contact with GLN 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 2.7 26.7 + - - +
51D ARG* 3.2 12.3 - - - +
53D LEU* 1.3 72.5 - - - +
55D ILE* 1.3 53.3 + - + +
57D ARG* 3.1 26.1 + - - +
58D GLU* 2.7 71.0 + - - +
60D GLY 4.8 0.4 - - - -
61D TYR* 6.3 2.9 - - + -
63D HIS* 5.3 7.2 - - + +
247E TRP* 3.9 18.9 - - - -
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ARG* 2.9 25.5 + - + +
52D LEU* 3.5 8.3 - - - +
54D GLN* 1.3 73.6 - - + +
56D TRP* 1.3 59.5 + - - +
59D GLN* 2.7 30.8 + - - -
60D GLY 3.3 27.8 - - - +
61D TYR* 4.0 22.2 - - + -
235D VAL 4.1 2.2 - - - +
236D GLN* 3.9 34.1 + - + +
239D PHE* 3.7 42.2 - - + -
240D MET* 6.3 1.3 - - - -
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Residues in contact with TRP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 2.7 20.3 + - + +
53D LEU* 3.1 13.0 + - + +
55D ILE* 1.3 75.6 - - - +
57D ARG* 1.3 86.9 + - + +
59D GLN* 3.9 11.5 + - - +
236D GLN* 5.8 1.1 + - - +
240D MET* 6.0 2.0 - - - -
248D ILE* 3.6 42.7 + - + -
249D SER* 4.0 9.2 - - - +
56E TRP* 3.7 27.5 - + + -
247E TRP* 3.7 35.2 - + - -
248E ILE* 3.9 21.1 - - - -
250E PRO* 5.7 1.1 - - + -
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU 2.9 12.0 + - - +
54D GLN* 3.5 31.7 + - - +
56D TRP* 1.3 87.3 - - + +
58D GLU* 1.3 70.3 + - - +
59D GLN* 3.2 10.5 + - - +
246E ARG* 6.2 1.0 - - - +
247E TRP* 3.5 68.4 - - + +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLN* 2.7 57.1 + - - +
57D ARG* 1.3 77.5 - - - +
59D GLN* 1.3 71.8 + - - +
60D GLY* 3.4 17.7 + - - +
61D TYR* 5.2 0.9 - - - -
62D GLU 5.2 1.4 + - - -
63D HIS* 3.8 24.7 + - - -
232D LYS* 5.0 1.2 + - - -
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Residues in contact with GLN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ILE 2.7 17.6 + - - -
56D TRP 4.0 9.4 - - - +
57D ARG 3.2 10.0 - - - +
58D GLU* 1.3 77.2 - - - +
60D GLY* 1.3 56.6 + - - +
232D LYS* 2.9 34.3 + - - +
236D GLN* 3.8 33.8 - - - +
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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