Contacts of the helix formed by residues 23 - 34 (chain A) in PDB entry 4KJI
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 PRO 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASP 4.0 4.3 - - - +
22A TYR* 1.4 92.6 - - + +
24A ALA* 1.3 66.6 + - - +
25A GLU* 3.6 1.1 - - + +
26A GLU* 3.3 45.6 - - + +
27A LEU* 3.5 8.7 + - - +
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Residues in contact with ALA 24 (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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22A TYR 3.6 3.1 + - - -
23A PRO* 1.3 73.3 - - - +
25A GLU* 1.3 66.8 + - - +
27A LEU* 3.4 13.6 + - - +
28A ILE* 3.7 13.1 - - - +
28B ILE* 4.7 23.8 - - + +
32B ARG* 5.2 9.3 - - - +
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Residues in contact with GLU 25 (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 PRO* 5.1 0.2 - - - +
24A ALA* 1.3 78.9 - - - +
26A GLU* 1.3 67.7 + - - +
27A LEU 3.0 1.0 + - - -
28A ILE* 3.1 29.7 + - + +
29A ARG* 3.5 33.9 + - + +
24B ALA* 5.8 6.3 - - + -
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Residues in contact with GLU 26 (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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22A TYR* 4.4 15.9 - - + -
23A PRO* 3.3 42.3 + - + +
25A GLU* 1.3 77.1 - - - +
27A LEU* 1.3 71.6 + - + +
29A ARG* 3.6 26.9 + - - +
30A GLN* 3.4 31.0 + - - +
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Residues in contact with LEU 27 (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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18A LEU* 4.1 27.4 - - + -
19A LYS 5.2 2.2 - - - +
22A TYR* 4.6 15.3 - - + +
23A PRO 4.1 9.9 - - - +
24A ALA* 3.4 10.2 + - - +
25A GLU 3.0 0.8 + - - -
26A GLU* 1.3 81.2 - - + +
28A ILE* 1.3 63.3 + - + +
30A GLN* 2.8 46.6 + - - +
31A LEU* 3.6 13.3 + - + +
55A PRO* 4.5 9.0 - - + -
57A GLY* 3.6 44.2 - - - +
58A VAL* 5.4 4.9 - - + -
28B ILE* 6.1 2.0 - - + -
32B ARG* 6.3 0.9 - - - +
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Residues in contact with ILE 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 ALA 3.7 8.5 - - - +
25A GLU* 3.3 20.4 - - + +
27A LEU* 1.3 76.7 - - + +
29A ARG* 1.3 61.1 + - + +
31A LEU* 3.6 11.7 + - + +
32A ARG* 3.1 42.7 + - + +
18B LEU* 4.0 7.4 - - + +
24B ALA* 4.1 29.6 - - + +
27B LEU* 5.0 4.7 - - + -
28B ILE* 2.6 40.8 - - + -
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Residues in contact with ARG 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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25A GLU* 3.5 39.9 + - + +
26A GLU* 3.6 30.2 + - - +
27A LEU 2.8 4.6 + - - -
28A ILE* 1.3 74.4 - - + +
30A GLN* 1.3 66.0 + - + +
31A LEU 2.8 6.7 + - - -
32A ARG* 2.9 9.0 + - - +
33A GLU* 2.8 32.5 + - - +
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Residues in contact with GLN 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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22A TYR* 6.1 0.2 - - - -
26A GLU* 3.4 23.7 + - - +
27A LEU* 2.8 46.9 + - - +
29A ARG* 1.3 72.5 - - + +
31A LEU* 1.3 55.3 + - - +
33A GLU* 3.1 18.1 - - - +
34A GLY* 2.4 34.3 + - - -
35A GLY 3.5 0.3 + - - -
55A PRO* 4.1 26.4 - - + +
56A ARG 5.1 3.6 - - - +
57A GLY 5.9 0.2 - - - +
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Residues in contact with LEU 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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27A LEU* 3.9 21.1 - - + +
28A ILE* 3.9 11.2 - - + +
29A ARG 2.8 4.4 + - - -
30A GLN* 1.3 72.9 - - - +
32A ARG* 1.3 64.9 + - - +
33A GLU 2.8 7.2 + - - +
35A GLY* 3.0 26.9 + - - +
36A ILE* 3.8 15.9 - - + -
55A PRO* 2.9 43.3 - - + -
58A VAL* 5.6 7.9 - - + -
17B SER* 5.7 0.9 + - - -
18B LEU* 3.9 23.3 - - + +
31B LEU* 6.4 1.6 - - + -
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Residues in contact with ARG 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 ILE* 3.1 23.7 + - + +
29A ARG* 2.9 9.0 + - - +
31A LEU* 1.3 76.6 - - - +
33A GLU* 1.3 58.1 + - - +
18B LEU* 3.5 31.6 + - + +
19B LYS 3.3 8.5 + - - -
20B ALA* 3.1 39.1 + - - +
22B TYR 3.0 24.7 + - - -
23B PRO 4.5 0.4 - - - -
24B ALA* 4.3 17.0 - - - +
27B LEU* 6.3 0.4 - - - +
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Residues in contact with GLU 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 ARG* 2.8 30.0 + - - +
30A GLN* 3.1 20.5 - - - +
31A LEU 2.8 3.5 - - - +
32A ARG* 1.3 78.0 - - - +
34A GLY* 1.3 79.3 + - - +
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Residues in contact with GLY 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 GLN 2.4 26.4 + - - -
31A LEU 3.6 0.2 - - - -
33A GLU* 1.3 77.4 - - - +
35A GLY* 1.3 64.5 + - - +
55A PRO* 6.1 0.4 - - - -
15B THR* 5.6 2.9 - - - +
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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