Contacts of the helix formed by residues 15 - 25 (chain D) in PDB entry 1XOK
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 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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868A C 4.9 5.3 + - + +
869A C 6.0 2.2 - - - +
877B G 6.1 0.7 - - - +
13D LYS* 3.3 16.8 - - + +
14D PRO* 1.3 72.4 - - - +
16D LYS* 1.3 65.2 + - - +
17D ARG* 3.1 16.7 + - + +
18D SER* 3.0 25.4 + - - +
19D GLN* 3.1 29.7 + - - +
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Residues in contact with LYS 16 (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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15D THR* 1.3 75.8 - - - +
17D ARG* 1.3 57.6 + - + +
19D GLN* 4.2 5.6 - - - +
20D ASN* 2.9 30.5 + - - +
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Residues in contact with ARG 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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868A C 4.0 3.4 - - - +
877B G 3.3 55.3 + - - +
878B A 2.7 70.3 + - - +
880B G 2.6 44.1 + - - -
15D THR* 3.2 16.6 - - - +
16D LYS* 1.3 75.9 - - + +
18D SER* 1.3 66.7 + - - +
20D ASN* 3.0 6.6 + - - +
21D TYR 2.7 22.0 + - - -
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Residues in contact with SER 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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866A U 2.9 50.6 + - - +
867A G 2.5 30.5 + - - -
868A C 4.2 15.0 - - - +
878B A 4.1 0.4 - - - +
14D PRO* 3.3 1.2 - - - +
15D THR* 3.0 30.6 + - - -
17D ARG* 1.3 80.3 - - - +
19D GLN* 1.3 67.7 + - - +
21D TYR* 3.2 0.5 + - - +
22D ALA* 3.0 5.5 + - - +
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Residues in contact with GLN 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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848A C 2.3 41.9 + - - +
849A A 2.6 41.5 + - - +
863A G 4.0 5.3 + - - +
864A A 5.1 4.4 - - - +
867A G 3.8 14.4 - - - +
14D PRO* 3.5 10.4 - - + +
15D THR 3.1 21.1 + - - +
16D LYS* 4.2 4.6 - - - +
18D SER* 1.3 79.8 + - - +
20D ASN* 1.3 52.8 + - - +
22D ALA* 3.1 7.5 + - - +
23D ALA* 2.7 36.2 + - - +
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Residues in contact with ASN 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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878B A 5.0 11.5 + - - -
16D LYS 2.9 21.8 + - - +
17D ARG* 3.0 6.6 + - - +
19D GLN* 1.3 74.1 - - - +
21D TYR* 1.3 71.8 + - - +
23D ALA* 3.2 14.2 + - - +
24D LEU* 3.2 33.4 + - - +
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Residues in contact with TYR 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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866A U 3.1 70.4 + + + +
878B A 3.5 21.1 - + - +
17D ARG 2.7 15.2 + - - +
18D SER 3.3 9.2 - - - +
20D ASN* 1.3 76.8 - - - +
22D ALA* 1.3 64.0 + - - +
24D LEU* 3.1 10.5 + - - +
25D ARG* 2.9 57.2 + - + -
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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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864A A 3.8 35.9 - - - +
865A A 5.7 0.4 - - - -
866A U 3.2 16.9 + - + +
867A G 4.3 1.6 - - - +
18D SER 3.0 8.7 + - - +
19D GLN* 3.5 9.6 - - - +
21D TYR* 1.3 77.6 - - - +
23D ALA* 1.3 63.2 + - - +
25D ARG* 3.1 28.1 + - + +
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Residues in contact with ALA 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 GLN 2.7 20.3 + - - +
20D ASN* 3.2 10.7 + - - +
22D ALA* 1.3 74.5 - - - +
24D LEU* 1.3 65.5 + - + +
25D ARG 4.0 4.3 - - - +
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Residues in contact with LEU 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 ASN* 3.2 31.2 + - - +
21D TYR* 3.1 9.5 + - - +
23D ALA* 1.3 77.3 - - + +
25D ARG* 1.3 64.7 + - - +
26D LYS* 3.2 6.6 + - - +
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Residues in contact with ARG 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 TYR* 2.9 48.6 + - + +
22D ALA* 3.1 25.0 + - - +
23D ALA 4.0 4.2 - - - +
24D LEU* 1.3 73.7 - - - +
26D LYS* 1.3 74.4 + - - +
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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