Contacts of the helix formed by residues 21 - 28 (chain D) in PDB entry 1V15
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 LYS 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D GLY* 3.3 1.4 - - - -
20D ASP* 1.3 81.9 - - - +
22D TRP* 1.3 63.6 + - - +
23D LEU 3.3 1.8 - - - -
24D ASP* 2.9 71.2 + - - +
25D ASP* 4.2 8.2 + - - +
70D ASN* 4.4 5.2 - - - +
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Residues in contact with TRP 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 VAL* 3.5 24.2 - - + -
19D GLY 3.3 18.7 + - - +
20D ASP 3.1 8.8 + - - -
21D LYS* 1.3 76.6 - - - +
23D LEU* 1.3 96.6 + - + +
24D ASP 3.3 0.9 + - - -
25D ASP* 3.4 13.2 + - - +
32D ALA* 3.7 33.6 - - + +
33D PRO 3.5 23.1 - - - -
35D PRO* 3.8 21.3 - - + -
57D VAL* 6.3 1.6 - - + -
58D TRP* 4.3 10.3 - + - -
61D VAL* 4.2 23.5 - - + +
67D LEU* 3.5 46.0 + - + +
70D ASN* 5.9 0.7 - - + -
121D VAL* 3.7 23.3 - - + -
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Residues in contact with LEU 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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20D ASP 4.9 0.6 + - - -
21D LYS 3.3 0.6 - - - -
22D TRP* 1.3 112.4 - - + +
24D ASP* 1.3 66.9 + - - +
25D ASP 3.1 2.2 - - - -
26D ALA* 3.0 24.3 + - + +
27D GLY 4.1 1.0 + - - -
58D TRP* 4.3 9.4 - - + -
61D VAL* 6.0 0.4 - - + -
67D LEU 5.4 0.7 - - - +
70D ASN* 5.9 1.5 - - + +
71D LEU* 3.7 22.7 - - + -
99D TYR* 3.7 46.6 + - + +
121D VAL* 3.9 19.3 - - + -
123D THR* 5.3 0.3 - - - +
16J C 3.4 29.8 + - + +
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Residues in contact with ASP 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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21D LYS* 2.9 68.3 + - - +
23D LEU* 1.3 78.0 - - - +
25D ASP* 1.3 62.7 + - - +
26D ALA 3.2 0.5 + - - -
27D GLY* 3.5 10.6 + - - -
28D LYS* 4.4 6.1 + - - +
70D ASN* 3.8 14.0 + - - -
16J C 3.1 39.1 + - - +
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Residues in contact with ASP 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 LYS* 4.2 5.9 + - - -
22D TRP 3.4 11.2 + - - +
23D LEU 3.1 1.0 - - - -
24D ASP* 1.3 82.4 - - - +
26D ALA* 1.3 58.9 + - - +
27D GLY 3.2 0.9 - - - -
28D LYS* 2.9 52.3 + - + +
29D ASP* 6.1 0.2 - - - -
31D GLY* 3.6 8.1 + - - -
32D ALA* 4.0 10.3 - - + +
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Residues in contact with ALA 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 TRP 4.1 1.2 + - - -
23D LEU* 3.0 27.8 + - + +
25D ASP* 1.3 78.1 - - - +
27D GLY* 1.3 55.5 + - - +
28D LYS 3.3 3.2 + - - +
31D GLY* 3.8 5.4 - - - -
32D ALA* 3.7 8.4 - - + +
99D TYR* 3.8 26.5 - - + -
121D VAL 3.3 22.1 - - - +
122D THR* 3.3 22.7 - - - +
123D THR* 3.3 3.7 + - - -
126D ARG* 4.4 2.1 - - - +
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Residues in contact with GLY 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 LEU 4.1 0.4 + - - -
24D ASP 3.5 9.2 + - - -
25D ASP 3.2 0.8 - - - -
26D ALA* 1.3 76.4 - - - +
28D LYS* 1.3 59.6 + - - +
91D GLN* 3.7 16.9 + - - +
123D THR* 3.3 30.3 - - - +
125D LYS* 5.8 0.9 + - - -
126D ARG* 3.5 20.8 + - - -
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Residues in contact with LYS 28 (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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24D ASP 4.6 3.8 - - - +
25D ASP* 2.9 39.6 + - + +
27D GLY* 1.3 80.0 - - - +
29D ASP* 1.3 73.9 + - - +
30D SER* 2.6 20.6 + - - -
31D GLY* 2.9 13.6 + - - -
126D ARG* 3.4 11.8 - - - +
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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