Contacts of the helix formed by residues 16 - 24 (chain D) in PDB entry 6VVT
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 THR 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.0 8.7 - - + +
15D ALA* 1.3 78.1 - - - +
17D ALA* 1.3 65.3 + - - +
18D ASP* 3.6 8.0 + - - +
19D ASP* 2.8 36.9 + - - +
20D ILE* 2.9 23.0 + - - +
308D SER* 5.4 15.3 - - - +
310D MET* 6.5 0.4 - - + -
311D GLY* 5.0 15.7 - - - +
314D LEU* 6.0 0.2 - - - -
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Residues in contact with ALA 17 (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 THR* 1.3 74.4 - - - +
18D ASP* 1.3 57.4 + - - +
20D ILE* 3.4 10.8 + - - +
21D ARG* 2.9 60.4 + - - +
311D GLY* 6.0 0.2 - - - -
313D VAL 5.9 1.1 + - - +
314D LEU* 5.7 3.5 - - - +
315D ASP* 3.9 26.2 - - + +
316D ALA* 4.3 7.7 - - - +
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Residues in contact with ASP 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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16D THR* 3.1 9.0 + - - +
17D ALA* 1.3 75.3 - - - +
19D ASP* 1.3 55.9 + - - +
21D ARG* 3.0 26.3 + - - +
22D ASN* 2.7 50.2 + - - +
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Residues in contact with ASP 19 (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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1125C ASN* 3.8 20.9 + - - -
14D LEU 4.1 1.2 - - - +
15D ALA* 3.9 6.3 - - + -
16D THR* 2.8 44.6 + - - +
18D ASP* 1.3 75.8 - - - +
20D ILE* 1.3 58.2 + - - +
22D ASN* 3.2 13.1 + - - +
23D TRP* 2.9 51.5 + - + +
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Residues in contact with ILE 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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1123C CYS* 3.6 17.7 - - + -
15D ALA* 4.3 18.8 - - + +
16D THR 2.9 19.8 + - - +
17D ALA* 3.6 7.9 - - - +
19D ASP* 1.3 74.4 - - - +
21D ARG* 1.3 64.2 + - - +
23D TRP* 3.2 13.1 + - + +
24D SER* 3.1 22.2 + - - -
93D GLY 4.9 0.2 - - - +
94D HIS* 4.0 9.4 - - + -
314D LEU* 4.6 3.8 - - + -
316D ALA* 3.2 27.1 - - + +
317D VAL 3.8 4.5 - - - -
318D PRO* 3.3 48.9 - - + +
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Residues in contact with ARG 21 (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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17D ALA* 2.9 42.7 + - - +
18D ASP* 3.0 31.4 + - - +
20D ILE* 1.3 77.1 - - - +
22D ASN* 1.3 66.8 + - - +
24D SER* 3.5 18.7 + - - +
94D HIS* 4.5 14.5 + - + +
96D GLU* 2.2 42.9 + - - +
315D ASP* 3.8 24.7 + - - +
316D ALA* 4.2 8.3 - - + +
38J GLU* 5.9 2.9 - - - -
57J ARG* 4.0 8.9 + - - +
58J ASN* 5.7 5.4 - - - +
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Residues in contact with ASN 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 ASP* 2.7 40.6 + - - +
19D ASP* 3.6 13.3 + - - +
21D ARG* 1.3 73.7 - - - +
23D TRP* 1.3 70.3 + - + +
2007D SO4 3.5 8.8 + - - -
57J ARG* 3.0 26.6 + - - +
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Residues in contact with TRP 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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1120C GLN* 3.5 43.7 + - + -
1124C LEU 4.0 2.0 - - - -
1125C ASN* 3.5 47.8 + - + -
1126C VAL 4.9 0.9 - - - -
15D ALA* 3.6 20.0 - - + -
19D ASP* 2.9 26.9 + - + +
20D ILE* 3.2 20.4 + - + +
22D ASN* 1.3 82.4 - - + +
24D SER* 1.3 64.2 + - - +
25D TYR* 3.5 19.9 - - - -
92D MET* 3.5 36.1 + - + +
93D GLY 5.9 0.2 - - - +
318D PRO* 4.5 7.6 - - + -
2007D SO4 4.0 3.8 + - - -
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Residues in contact with SER 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 ILE 3.1 7.0 + - - -
21D ARG 3.7 5.9 - - - +
22D ASN 3.3 1.0 - - - -
23D TRP* 1.3 79.7 - - - +
25D TYR* 1.3 55.8 + - - +
26D GLY 3.0 11.4 + - - -
92D MET 3.3 10.8 - - - -
93D GLY 2.9 25.1 - - - -
94D HIS* 2.8 38.2 + - - -
57J ARG* 2.4 37.5 + - - +
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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