Contacts of the helix formed by residues 22 - 36 (chain A) in PDB entry 4IME
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 ASN 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 2.9 30.7 + - - +
15A PHE 4.5 0.9 - - - -
16A ASN* 2.7 30.0 + - - +
20A SER 3.5 2.2 + - - -
21A ILE* 1.3 71.2 - - - +
23A GLU* 1.3 61.0 + - - +
24A LYS* 3.4 14.1 - - - +
25A GLY* 2.8 31.7 + - - +
26A LEU* 2.9 28.1 + - - +
264A GLU* 5.1 5.9 + - - +
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Residues in contact with GLU 23 (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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21A ILE* 3.5 6.6 + - - +
22A ASN* 1.3 70.5 - - - +
24A LYS* 1.3 67.2 + - - +
26A LEU* 3.2 3.8 + - - +
27A ARG* 2.9 63.7 + - - +
61A GLU* 4.8 6.2 - - - +
64A ARG* 4.4 11.5 + - - -
65A ILE* 3.8 35.3 - - + +
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Residues in contact with LYS 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 ASN* 3.4 10.4 - - - +
23A GLU* 1.3 78.4 - - - +
25A GLY* 1.3 63.3 + - - +
27A ARG* 3.4 8.7 + - - +
28A GLN* 3.1 49.5 + - + +
264A GLU* 4.1 22.6 + - - +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.7 8.5 - - - -
22A ASN* 2.8 19.1 - - - +
24A LYS* 1.3 74.4 - - - +
26A LEU* 1.3 63.9 + - - +
28A GLN* 3.1 6.6 + - - +
29A ILE* 3.0 25.8 + - - +
264A GLU* 3.2 31.6 - - - +
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Residues in contact with LEU 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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11A LEU* 4.0 20.9 - - + -
12A LEU 3.6 23.8 - - - +
13A VAL* 4.2 11.9 - - + -
14A SER* 3.7 9.7 - - - +
21A ILE* 4.3 10.5 - - + -
22A ASN 2.9 17.3 + - - +
23A GLU* 3.2 4.9 + - - +
25A GLY* 1.3 74.6 - - - +
27A ARG* 1.3 64.8 + - - +
29A ILE* 3.2 4.3 + - + +
30A VAL* 2.9 24.4 + - + +
62A ILE* 4.3 23.8 - - + +
65A ILE* 3.7 39.0 - - + -
66A ALA 4.9 1.1 - - - +
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Residues in contact with ARG 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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23A GLU* 2.9 52.1 + - - +
24A LYS* 3.7 7.2 - - - +
26A LEU* 1.3 77.2 - - - +
28A GLN* 1.3 57.2 + - + +
30A VAL* 3.3 4.4 + - - +
31A ARG* 2.9 33.8 + - + +
64A ARG* 4.8 6.5 - - - +
65A ILE* 3.7 21.9 - - + +
68A ASP* 2.8 36.9 + - - +
69A GLU* 2.9 51.1 + - + +
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Residues in contact with GLN 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 LYS* 3.1 45.8 + - + +
25A GLY* 3.1 7.8 + - - +
27A ARG* 1.3 76.7 - - + +
29A ILE* 1.3 57.4 + - - +
31A ARG* 3.4 6.6 + - - +
32A TYR* 2.9 29.6 + - - +
262A GLY 3.7 6.4 + - - +
263A VAL* 3.5 17.1 - - + +
264A GLU* 2.7 41.7 + - - +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.6 22.9 - - + -
12A LEU* 3.6 26.7 - - + +
13A VAL* 4.2 1.1 - - - -
14A SER* 3.8 20.2 - - - +
25A GLY 3.0 18.4 + - - +
26A LEU* 3.2 7.6 + - - +
28A GLN* 1.3 73.3 - - - +
30A VAL* 1.3 65.0 + - - +
32A TYR* 3.3 4.1 + - - +
33A ASN* 3.0 35.8 + - - +
210A ASN* 3.9 8.7 - - - +
258A LEU* 4.4 11.0 - - + -
263A VAL* 3.7 20.9 - - + -
265A ALA* 4.0 22.2 - - + +
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Residues in contact with VAL 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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11A LEU* 3.9 31.6 - - + -
26A LEU* 2.9 21.4 + - + +
27A ARG* 3.6 7.0 - - - +
29A ILE* 1.3 74.4 - - - +
31A ARG* 1.3 63.3 + - - +
33A ASN* 3.2 5.3 + - - +
34A ILE* 3.0 40.9 + - + +
42A LEU* 4.0 16.6 - - + +
65A ILE* 6.1 0.2 - - + -
66A ALA* 4.3 15.9 - - - +
69A GLU* 3.8 24.5 - - + -
70A ALA* 4.1 7.6 - - + +
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Residues in contact with ARG 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 ARG 2.9 19.5 + - - +
28A GLN* 3.8 6.7 - - - +
29A ILE 3.3 0.2 - - - -
30A VAL* 1.3 75.5 - - - +
32A TYR* 1.3 55.3 + - - +
34A ILE* 3.3 18.1 + - - +
35A ASP* 2.7 80.7 + - - +
69A GLU* 3.1 57.3 + - - +
73A GLU* 3.0 29.3 + - - -
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Residues in contact with TYR 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 GLN 2.9 19.3 + - - +
29A ILE* 3.6 6.3 - - - +
30A VAL 3.3 0.2 - - - -
31A ARG* 1.3 76.6 - - - +
33A ASN* 1.3 59.4 + - - +
36A LYS* 2.9 51.5 + - + +
37A MET* 3.0 34.4 + - + +
210A ASN 3.2 27.6 - - - -
211A VAL* 4.6 7.5 + - - +
257A LEU 5.4 0.9 + - - -
258A LEU* 3.6 16.4 - - + -
261A ASP* 2.7 44.5 + - + +
263A VAL* 3.5 22.0 - - + -
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Residues in contact with ASN 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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9A SER* 2.7 32.7 + - - -
11A LEU* 4.2 0.9 - - - +
29A ILE* 3.0 24.4 + - - +
30A VAL 3.5 8.3 - - - +
32A TYR* 1.3 80.0 - - - +
34A ILE* 1.3 58.0 + - - +
37A MET* 3.5 6.6 - - - +
38A LYS 3.0 24.9 + - - -
39A VAL* 3.2 17.5 + - + +
42A LEU* 3.8 26.0 - - + +
209A PHE 3.9 1.8 + - - -
210A ASN* 2.9 37.3 - - - +
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Residues in contact with ILE 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 VAL* 3.0 25.9 + - + +
31A ARG* 3.6 23.1 - - - +
33A ASN* 1.3 80.9 - - + +
35A ASP* 1.3 72.2 + - - +
38A LYS* 3.5 16.5 - - - +
39A VAL* 4.4 5.1 + - + +
42A LEU* 5.1 0.2 - - + -
70A ALA* 3.9 24.9 - - + +
73A GLU* 3.7 21.5 - - + +
74A ILE* 3.7 37.7 - - + -
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Residues in contact with ASP 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 ARG* 2.7 64.4 + - - +
34A ILE* 1.3 78.3 - - - +
36A LYS* 1.3 75.1 + - + +
38A LYS* 3.6 24.2 + - - +
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Residues in contact with LYS 36 (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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32A TYR* 2.9 43.1 + - + +
35A ASP* 1.3 91.5 + - + +
37A MET* 1.3 76.9 + - + +
38A LYS* 3.3 11.6 + - - +
214A VAL* 4.1 11.1 - - - +
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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