Contacts of the helix formed by residues 13 - 27 (chain D) in PDB entry 1VLP
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 ASP 13 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 1.3 83.1 + - - +
14D MSE 1.3 66.7 + - - +
15D TYR* 3.4 26.8 - - + -
16D LYS* 3.0 19.6 + - - +
17D ILE 4.0 0.5 + - - -
133D ILE* 2.8 36.4 - - + +
177D PHE* 4.2 8.8 - - - +
179D THR* 3.5 14.4 + - - -
180D ARG* 3.6 13.1 + - - +
214D SER* 2.5 32.2 + - - +
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Residues in contact with MSE 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR 3.8 0.2 + - - -
13D ASP* 1.3 72.7 - - - +
15D TYR* 1.3 63.1 + - - +
16D LYS 3.0 1.0 + - - -
17D ILE* 3.0 13.2 + - - +
18D THR* 3.3 17.9 + - + -
76D GLU 5.4 2.0 - - - +
77D ILE* 4.0 35.0 - - + -
79D TYR* 3.1 28.7 - - - +
214D SER 2.8 14.3 + - - +
216D ILE* 3.8 19.5 - - + -
226D PRO* 3.3 36.3 - - - +
227D ILE 3.6 15.5 + - - +
228D GLY* 3.7 23.3 - - - +
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Residues in contact with TYR 15 (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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13D ASP* 3.1 39.3 + - + -
14D MSE 1.3 78.0 - - - +
16D LYS* 1.3 78.7 + - + +
18D THR* 3.2 9.8 + - - -
19D MSE 2.9 39.0 + - + +
132D GLU* 3.1 20.4 + - - -
133D ILE* 3.3 6.4 - - - +
177D PHE* 4.4 13.9 - + - -
180D ARG* 3.1 28.8 + - - -
214D SER* 5.8 0.7 - - - -
228D GLY* 4.2 6.1 - - - -
229D THR 3.0 31.6 - - - +
230D VAL 5.5 0.2 - - - -
231D ALA* 3.7 30.7 - - + -
233D GLU* 4.2 1.6 - - - -
294D ARG* 6.4 0.4 - - - -
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Residues in contact with LYS 16 (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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12D THR* 3.8 9.9 - - + +
13D ASP 3.0 13.0 + - - +
15D TYR* 1.3 92.1 - - + +
17D ILE* 1.3 56.6 + - - +
19D MSE 3.6 3.1 - - - +
20D HIS* 3.0 27.4 + - - +
34D TYR* 4.5 2.2 + - - -
129D ILE* 2.7 36.0 + - - +
130D LEU* 3.6 19.1 - - + +
132D GLU* 2.9 25.4 + - + +
133D ILE* 3.3 38.4 - - + +
233D GLU* 2.5 35.0 + - - -
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Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU 4.6 9.9 - - - +
10D LEU* 5.4 0.7 - - + -
12D THR* 4.4 6.7 - - + -
14D MSE 3.0 7.6 + - - +
16D LYS* 1.3 74.3 - - - +
18D THR* 1.3 61.2 + - - +
20D HIS* 3.2 4.7 + - - +
21D ALA* 2.9 27.2 + - - +
65D PHE* 4.1 24.9 - - + -
73D LEU* 4.5 14.4 - - + -
77D ILE* 4.7 4.5 - - + -
80D LEU* 4.3 17.0 - - + -
84D TYR* 3.6 28.3 + - + +
130D LEU* 4.2 15.0 - - + -
216D ILE* 3.6 28.0 - - + -
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Residues in contact with THR 18 (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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14D MSE 3.3 24.5 + - + +
15D TYR* 3.2 22.0 + - - +
17D ILE* 1.3 72.8 - - - +
19D MSE 1.3 58.2 + - - +
21D ALA* 3.2 3.6 + - - -
22D ALA* 2.9 25.3 + - - +
77D ILE* 4.1 26.7 - - + -
79D TYR* 4.7 7.9 - - + +
80D LEU* 4.2 6.7 - - + -
228D GLY 5.6 1.9 - - - -
229D THR 4.5 2.4 + - - -
256D TRP* 4.0 18.0 - - - -
260D PHE* 3.3 22.0 - - + -
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Residues in contact with MSE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TYR* 2.9 33.0 + - + +
16D LYS* 3.6 4.7 - - - +
18D THR* 1.3 77.0 + - - +
20D HIS* 1.3 56.1 + - - +
22D ALA* 3.2 4.1 + - - +
23D VAL* 2.8 35.8 + - - +
125D TRP* 5.8 0.2 - - - -
129D ILE* 3.4 22.7 - - + -
230D VAL* 4.0 1.6 - - + -
231D ALA* 3.1 54.1 - - + +
233D GLU* 3.5 18.8 - - + +
234D TRP* 3.5 35.4 - - + +
256D TRP* 4.1 10.3 - - + -
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Residues in contact with HIS 20 (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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16D LYS 3.0 19.3 + - - +
17D ILE 3.3 7.2 - - - +
19D MSE 1.3 74.6 - - - +
21D ALA* 1.3 57.0 + - - +
23D VAL* 3.8 1.0 - - - -
24D PHE* 2.8 32.1 + - - +
84D TYR* 2.8 22.8 + + - +
87D TYR* 3.0 39.1 + + - -
88D ILE* 3.8 6.3 - - + +
93D TYR* 3.4 24.0 + - - -
126D LYS* 3.0 25.5 + - + -
129D ILE* 3.4 22.6 - - + +
130D LEU* 3.9 15.5 - - + +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE 2.9 13.5 + - - +
18D THR 3.2 8.3 + - - +
20D HIS* 1.3 75.8 - - - +
22D ALA* 1.3 57.1 + - - +
24D PHE* 3.7 1.4 - - - +
25D THR* 2.8 35.9 + - - -
80D LEU* 3.9 15.5 - - + -
81D PRO* 4.1 6.5 - - + -
84D TYR* 3.5 33.6 - - + -
259D THR* 4.7 0.4 - - - -
260D PHE* 4.1 9.6 - - + -
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Residues in contact with ALA 22 (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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18D THR 2.9 17.0 + - - +
19D MSE 3.6 3.8 - - - +
21D ALA* 1.3 76.5 - - - +
23D VAL* 1.3 57.4 + - - +
25D THR 3.3 0.7 + - - -
26D ASN* 3.0 38.2 + - - +
234D TRP* 3.7 20.0 - - + -
256D TRP* 3.6 26.7 - - + -
259D THR* 4.2 12.6 - - + +
260D PHE* 4.0 6.4 - - + -
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Residues in contact with VAL 23 (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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19D MSE 2.8 23.3 + - + +
20D HIS* 3.9 4.7 - - - +
22D ALA* 1.3 69.5 - - - +
24D PHE* 1.3 61.0 + - - +
27D PHE* 2.8 43.0 + - - +
125D TRP* 3.5 68.0 - - + +
126D LYS* 3.5 16.8 - - + +
129D ILE* 4.0 10.8 - - + -
234D TRP* 4.0 14.8 - - + -
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Residues in contact with PHE 24 (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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20D HIS 2.8 21.2 + - - +
21D ALA 3.7 1.8 - - - +
23D VAL* 1.3 74.9 - - - +
25D THR* 1.3 72.1 + - - +
28D PRO* 3.4 24.8 - - + +
83D ALA* 3.6 35.2 - - + -
84D TYR* 3.7 23.3 - - + -
87D TYR* 3.5 52.9 - + + -
126D LYS* 4.0 23.1 - - + +
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Residues in contact with THR 25 (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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21D ALA 2.8 23.3 + - - -
22D ALA 3.7 3.1 - - - -
23D VAL 3.2 0.2 - - - -
24D PHE* 1.3 89.5 - - - +
26D ASN* 1.3 65.3 + - - +
28D PRO* 4.2 4.0 - - - +
81D PRO* 3.8 23.0 - - + +
83D ALA* 6.1 0.3 - - - +
84D TYR* 5.0 0.3 - - - +
259D THR* 4.0 23.3 - - + +
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Residues in contact with ASN 26 (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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22D ALA 3.0 24.3 + - - +
25D THR* 1.3 80.9 - - - +
27D PHE* 1.3 95.7 + - + +
28D PRO* 3.3 8.6 - - - +
234D TRP* 4.0 7.1 - - - -
255D CYS* 3.9 24.1 + - - +
258D ASN* 5.5 3.1 - - - +
259D THR* 2.7 29.0 + - - -
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Residues in contact with PHE 27 (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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23D VAL* 2.8 28.3 + - + +
26D ASN* 1.3 99.0 - - + +
28D PRO* 1.3 63.8 - - - +
29D ASP 3.2 3.8 + - - -
30D VAL* 3.5 32.7 + - + +
125D TRP* 3.7 31.5 - + + +
126D LYS 5.0 0.5 + - - -
234D TRP* 3.7 29.2 - + - -
238D VAL* 3.9 25.1 - - + -
241D ILE* 4.4 18.2 - - + -
255D CYS* 4.4 13.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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