Contacts of the helix formed by residues 27 - 35 (chain A) in PDB entry 1KPI
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 SER 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASP* 3.3 3.0 - - - +
26A LYS* 1.3 84.2 - - - +
28A ASN* 1.3 65.1 + - - +
29A GLU* 3.4 9.0 + - - +
30A PHE* 3.1 27.6 + - - +
31A PHE* 3.1 26.2 + - - -
106A ASN* 4.0 6.0 - - - +
268A LEU* 4.4 4.2 - - - +
269A LYS* 3.8 14.2 - - - +
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Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR 4.7 0.3 - - - +
27A SER* 1.3 69.4 + - - +
29A GLU* 1.3 67.3 + - - +
31A PHE* 3.2 3.2 + - - +
32A LYS* 2.9 29.9 + - - +
39A MET* 3.7 8.3 - - + +
83A TRP* 2.8 30.1 + - - +
106A ASN* 3.0 48.2 + - - +
109A ALA* 5.4 1.2 - - - +
110A HIS* 3.7 5.5 - - - +
903A SO4 3.4 35.7 + - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.3 5.5 + - - +
28A ASN* 1.3 78.8 - - - +
30A PHE* 1.3 62.5 + - - +
32A LYS* 3.4 17.1 + - + +
33A LEU* 3.2 27.9 + - + +
264A GLU* 5.6 1.9 - - - +
268A LEU* 3.4 35.8 - - + +
903A SO4 5.7 0.2 + - - -
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 4.1 18.4 - - + -
27A SER* 3.1 24.7 + - - +
29A GLU* 1.3 77.2 - - - +
31A PHE* 1.3 74.7 + + - +
33A LEU* 3.0 23.8 + - + +
34A TRP* 3.3 31.7 - + - -
258A LEU* 4.7 4.0 - - + -
265A ALA* 4.4 25.6 - - + -
268A LEU* 3.6 8.9 - - + +
269A LYS* 3.7 23.3 - - + -
273A THR* 4.1 12.8 - - + -
274A CYS* 4.6 7.6 - - - -
277A TYR* 3.8 45.5 - + + -
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A HIS* 3.7 31.0 - + - -
24A TYR* 3.9 7.4 - - - -
26A LYS* 3.7 25.6 - - + -
27A SER 3.1 21.8 + - - -
28A ASN 3.2 5.4 + - - +
30A PHE* 1.3 82.7 - + - +
32A LYS* 1.3 57.4 + - - +
34A TRP* 3.4 35.1 + + - +
35A LEU* 3.0 41.5 + - + +
39A MET* 3.9 13.7 - - + -
41A TYR* 3.9 21.1 - + - -
83A TRP* 3.4 33.9 - + + -
277A TYR* 4.5 7.6 - + - -
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASN* 2.9 20.6 + - - +
29A GLU* 3.4 20.3 - - + +
30A PHE 3.1 0.4 - - - -
31A PHE* 1.3 76.5 - - - +
33A LEU* 1.3 65.5 + - + +
34A TRP 3.1 1.0 + - - -
35A LEU* 3.6 14.8 - - - +
36A ASP 5.1 0.4 - - - +
39A MET* 3.4 34.3 - - + -
110A HIS* 4.2 6.4 - - - -
903A SO4 2.9 43.7 + - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 3.2 15.0 + - + +
30A PHE* 3.0 13.1 + - + +
32A LYS* 1.3 79.4 - - + +
34A TRP* 1.3 61.5 + - + +
35A LEU 5.0 0.3 - - - +
257A ALA* 4.3 1.9 - - - +
258A LEU* 5.7 0.9 - - + -
261A HIS* 3.2 42.6 + - + +
264A GLU* 3.3 35.9 - - + +
265A ALA* 3.6 41.7 - - + +
268A LEU* 4.2 15.9 - - + -
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Residues in contact with TRP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.3 38.3 + + - -
31A PHE* 3.5 31.4 - + - +
33A LEU* 1.3 80.7 - - + +
35A LEU* 1.3 89.5 + - + +
41A TYR* 3.8 29.2 - + - -
53A LEU* 4.8 2.6 - - - +
253A ALA 4.7 0.2 - - - +
254A TRP* 3.5 48.8 - + + +
257A ALA* 3.5 17.6 - - - +
258A LEU* 3.7 34.4 - - + +
277A TYR* 3.9 22.2 - + - -
281A LEU* 4.0 27.4 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.0 33.2 + - + +
32A LYS 3.6 10.7 + - - +
33A LEU 4.9 0.5 - - - +
34A TRP* 1.3 103.3 - - + +
36A ASP* 1.3 71.4 + - - +
39A MET* 3.8 34.1 - - + +
40A THR 4.1 2.7 - - - +
41A TYR* 3.8 13.9 - - + -
53A LEU* 4.8 0.4 - - - -
83A TRP* 4.0 22.0 - - + -
254A TRP* 3.4 31.9 - - + +
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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