Contacts of the helix formed by residues 56 - 70 (chain D) in PDB entry 1VI9
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 PRO 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C CSD 4.1 11.7 - - - +
53D CSD 5.3 1.8 - - - +
54D VAL 3.6 6.1 - - - +
55D MSE 1.3 90.1 - - + +
57D PRO* 1.3 75.2 - - + +
58D SER* 4.0 9.2 - - - +
59D HIS* 2.9 34.3 + - + +
60D LEU* 3.6 4.7 + - - +
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Residues in contact with PRO 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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54D VAL* 5.9 1.3 - - + -
55D MSE 3.3 2.9 - - - +
56D PRO* 1.3 82.6 - - + +
58D SER* 1.3 63.1 + - - +
60D LEU* 3.1 22.7 + - + +
86D SER* 4.3 3.6 - - - +
88D GLU* 3.8 21.5 - - + +
89D GLN* 3.8 31.6 - - + +
92D HIS* 3.2 38.1 - - + +
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Residues in contact with SER 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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56D PRO* 4.0 10.6 - - - +
57D PRO* 1.3 73.9 - - - +
59D HIS* 1.3 65.6 + - - +
61D THR* 3.3 4.5 + - - -
62D GLU* 3.0 25.5 + - - +
92D HIS* 3.6 19.3 + - - -
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Residues in contact with HIS 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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40C GLN* 3.0 59.6 + - + +
52C GLY* 3.7 12.0 - - - -
53C CSD 3.4 25.6 + - - +
55D MSE 3.4 20.8 - - + +
56D PRO* 2.9 25.5 + - + +
58D SER* 1.3 76.6 + - - +
60D LEU* 1.3 73.0 + - + +
62D GLU* 3.2 14.2 + - - +
63D ILE* 2.9 38.9 + - + +
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Residues in contact with LEU 60 (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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8D ILE* 4.4 2.9 - - + -
36D LEU* 3.8 32.0 - - + +
37D ASN 4.0 14.4 - - - +
38D THR* 4.4 11.7 - - + -
55D MSE 4.7 2.9 - - + -
56D PRO 4.0 7.0 - - - +
57D PRO 3.3 11.9 - - - +
59D HIS* 1.3 85.0 - - + +
61D THR* 1.3 63.3 + - - +
63D ILE* 3.3 10.6 + - - +
64D VAL* 3.3 17.0 + - - +
89D GLN* 3.9 45.5 - - + +
92D HIS* 4.8 2.0 - - + -
93D ILE* 4.4 15.3 - - + -
96D ILE* 3.8 15.3 - - + -
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Residues in contact with THR 61 (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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57D PRO 3.5 0.4 + - - -
58D SER* 3.3 10.0 + - - -
59D HIS 3.3 0.2 - - - -
60D LEU* 1.3 79.8 - - - +
62D GLU* 1.3 56.3 + - - +
64D VAL* 3.2 5.5 + - - +
65D GLN* 3.0 54.9 + - + +
92D HIS* 2.8 41.9 + - + +
95D GLY 6.5 0.2 - - - -
96D ILE* 4.0 10.6 + - + +
99D GLN* 3.9 8.6 + - - +
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Residues in contact with GLU 62 (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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51C THR* 2.7 41.0 + - + +
52C GLY* 2.8 35.6 + - - +
58D SER* 3.0 13.6 + - - +
59D HIS* 3.3 17.6 + - - +
61D THR* 1.3 73.4 - - - +
63D ILE* 1.3 61.7 + - - +
65D GLN* 3.1 15.0 + - - +
66D GLY 2.9 13.2 + - - -
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Residues in contact with ILE 63 (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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13C VAL* 4.0 13.7 - - + -
40C GLN* 3.6 17.9 - - + +
41C PHE 3.5 8.3 - - - +
42C SER* 3.2 32.9 - - - +
51C THR* 3.3 2.4 + - - +
52C GLY* 3.6 13.2 - - - -
36D LEU* 3.9 27.6 - - + -
59D HIS* 2.9 30.8 + - + +
60D LEU 3.3 7.6 + - - +
62D GLU* 1.3 75.7 - - - +
64D VAL* 1.3 63.0 + - - +
66D GLY 3.1 2.3 + - - -
67D ILE* 3.1 38.5 + - + +
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Residues in contact with VAL 64 (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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6D LEU* 4.0 9.4 - - + -
36D LEU* 3.9 13.2 - - + -
60D LEU 3.3 12.8 + - - +
61D THR 3.2 4.2 + - - +
62D GLU 3.2 0.4 - - - -
63D ILE* 1.3 76.4 - - + +
65D GLN* 1.3 60.7 + - - +
67D ILE* 3.1 10.9 + - + +
68D ALA* 3.0 19.1 + - - +
73D LEU* 4.0 23.5 - - + +
96D ILE* 3.6 35.2 - - + +
99D GLN* 3.3 33.2 - - + +
100D VAL* 4.8 1.1 - - + -
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C THR* 4.7 3.9 - - + +
61D THR* 3.0 41.6 + - - +
62D GLU* 3.1 14.1 + - - +
64D VAL* 1.3 74.8 - - - +
66D GLY* 1.3 58.2 + - - +
68D ALA* 3.3 6.0 + - - +
69D ALA* 3.0 27.7 + - - +
99D GLN* 3.5 18.8 - - - +
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Residues in contact with GLY 66 (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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42C SER* 3.9 10.8 - - - -
43C ASN* 3.8 2.6 - - - +
50C TRP* 5.3 2.0 - - - -
51C THR* 3.6 27.7 - - - +
62D GLU 2.9 11.3 + - - -
63D ILE 3.1 1.1 + - - -
65D GLN* 1.3 73.6 - - - +
67D ILE* 1.3 66.2 + - - +
69D ALA* 3.1 16.7 + - - +
70D ILE* 3.2 16.6 + - - +
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Residues in contact with ILE 67 (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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13C VAL* 3.9 17.5 - - + -
14C TYR* 3.9 29.6 - - + -
42C SER* 3.8 19.5 - - - +
6D LEU* 5.0 2.9 - - + -
34D TRP* 4.1 23.1 - - + -
63D ILE* 3.1 34.1 + - + +
64D VAL* 3.1 12.1 + - + +
66D GLY* 1.3 76.1 - - - +
68D ALA* 1.4 63.3 + - - +
70D ILE* 3.2 22.0 + - + +
72D LYS* 3.4 19.1 + - + -
73D LEU* 4.2 12.3 - - + +
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Residues in contact with ALA 68 (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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64D VAL 3.0 11.7 + - - +
65D GLN* 3.5 12.1 - - - +
67D ILE* 1.4 76.4 - - - +
69D ALA* 1.3 54.9 + - - +
71D ASP* 2.7 32.2 + - - +
73D LEU* 3.8 29.7 - - + +
99D GLN* 4.6 3.1 - - - +
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Residues in contact with ALA 69 (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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49C LYS* 2.9 38.6 + - + +
65D GLN 3.0 13.9 + - - +
66D GLY* 3.1 13.6 + - - +
68D ALA* 1.3 76.3 - - - +
70D ILE* 1.3 55.6 + - + +
71D ASP* 3.2 10.2 + - - +
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Residues in contact with ILE 70 (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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14C TYR* 3.9 20.6 - - + -
43C ASN* 3.7 35.9 - - + +
47C TYR* 3.6 46.3 - - + -
49C LYS* 4.0 22.7 - - + +
66D GLY 3.2 11.3 + - - +
67D ILE* 3.2 20.9 - - - +
69D ALA* 1.3 73.7 - - + +
71D ASP* 1.3 71.2 + - - +
72D LYS* 3.4 22.9 + - + +
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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