Contacts of the helix formed by residues 27 - 42 (chain D) in PDB entry 2IYL
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 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D GLY* 1.3 73.9 - - - +
28D LEU* 1.3 59.1 + - - +
29D GLU* 3.1 6.7 + - + +
30D GLU* 2.7 64.7 + - - +
31D VAL* 3.1 9.9 + - - +
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Residues in contact with LEU 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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26D GLY 3.6 2.9 + - - -
27D ASN* 1.3 71.6 - - - +
29D GLU* 1.3 71.0 + - + +
31D VAL* 3.5 8.8 + - - +
32D LEU* 3.4 38.5 + - + +
56D VAL 5.4 1.1 - - - +
57D ARG* 4.7 22.9 - - + +
64D LEU* 4.3 23.6 - - + +
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Residues in contact with GLU 29 (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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27D ASN* 3.1 7.0 - - + +
28D LEU* 1.3 88.7 - - + +
30D GLU* 1.3 62.0 + - - +
32D LEU* 3.8 10.0 + - + +
33D GLU* 3.4 22.2 + - - +
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Residues in contact with GLU 30 (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 PRO* 3.9 21.7 - - + +
26D GLY* 4.3 6.5 - - - -
27D ASN* 2.7 55.5 + - - +
29D GLU* 1.3 72.3 - - - +
31D VAL* 1.3 62.9 + - - +
33D GLU* 3.6 4.6 + - - +
34D GLU* 3.3 25.7 + - + +
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Residues in contact with VAL 31 (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 ILE* 3.2 17.5 - - + +
23D PRO* 3.4 26.7 - - - +
24D TRP* 3.6 37.0 - - + -
25D GLY 4.6 0.9 - - - +
26D GLY 3.7 13.7 - - - +
27D ASN 3.1 13.6 + - - +
28D LEU* 3.9 6.7 - - - +
29D GLU 3.4 0.2 - - - -
30D GLU* 1.3 76.7 - - - +
32D LEU* 1.3 60.9 + - + +
34D GLU 3.5 0.2 + - - -
35D LEU* 2.9 25.9 + - + +
64D LEU* 4.2 28.7 - - + -
68D VAL* 5.9 0.7 - - + -
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Residues in contact with LEU 32 (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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28D LEU* 3.4 28.1 + - + +
29D GLU* 4.2 9.2 - - + +
30D GLU 3.3 0.2 - - - -
31D VAL* 1.3 80.6 - - + +
33D GLU* 1.3 59.2 + - - +
35D LEU* 4.1 9.2 - - + -
36D GLU* 2.9 27.4 + - - +
53D LEU* 3.5 31.3 - - + +
56D VAL* 3.9 31.9 - - + -
57D ARG* 3.4 41.5 - - + +
64D LEU* 5.8 1.1 - - + -
68D VAL* 6.0 0.2 - - + -
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Residues in contact with GLU 33 (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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29D GLU 3.4 16.5 + - - +
30D GLU* 4.1 5.8 - - - +
31D VAL 3.4 0.2 - - - -
32D LEU* 1.3 79.0 - - - +
34D GLU* 1.3 78.2 + - - +
36D GLU* 3.5 13.2 + - - +
37D MET* 3.3 47.7 + - - +
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Residues in contact with GLU 34 (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 ALA 3.6 20.3 + - - +
22D ILE* 4.2 8.0 - - + +
23D PRO* 3.8 30.5 - - + -
30D GLU* 3.3 12.5 + - + +
31D VAL 4.2 1.1 - - - +
33D GLU* 1.3 89.9 - - - +
35D LEU* 1.3 60.2 + - - +
37D MET* 3.5 16.1 + - - +
38D ALA* 3.1 27.5 + - - +
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Residues in contact with LEU 35 (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 ILE* 3.6 18.6 - - + +
24D TRP* 4.1 3.1 - - + -
31D VAL* 2.9 19.1 + - + +
32D LEU* 3.5 16.2 - - + +
33D GLU 3.3 0.2 - - - -
34D GLU* 1.3 74.7 - - - +
36D GLU* 1.3 65.2 + - - +
38D ALA* 3.4 4.9 + - + +
39D LEU* 2.9 40.6 + - + +
52D ILE* 3.8 21.8 - - + -
53D LEU* 4.1 10.8 - - + -
68D VAL* 3.5 43.1 - - + -
302D LEU* 3.9 18.2 - - + -
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Residues in contact with GLU 36 (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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32D LEU 2.9 15.8 + - - +
33D GLU* 3.7 13.8 - - - +
35D LEU* 1.3 75.7 - - - +
37D MET* 1.3 72.0 + - + +
39D LEU* 3.9 0.3 - - - +
40D LEU* 2.8 53.3 + - + +
46D LEU* 4.8 10.1 - - + +
49D THR* 3.8 20.2 - - + -
50D GLU* 5.7 1.4 - - - +
53D LEU* 3.9 20.3 - - + +
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Residues in contact with MET 37 (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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33D GLU* 3.3 32.9 + - + +
34D GLU* 3.7 22.4 - - - +
35D LEU 3.1 0.4 - - - -
36D GLU* 1.3 101.6 - - + +
38D ALA* 1.3 53.6 + - - +
40D LEU* 3.7 14.3 - - + +
41D ALA* 2.8 38.2 + - - +
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Residues in contact with ALA 38 (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 ILE* 5.5 9.4 - - + -
34D GLU* 3.1 15.9 + - - +
35D LEU* 3.6 11.0 - - + +
37D MET* 1.3 78.4 - - - +
39D LEU* 1.3 64.7 + - + +
41D ALA* 3.6 5.6 + - - +
42D ALA* 3.1 24.1 + - - +
301D LEU* 5.3 10.2 - - - +
302D LEU* 5.6 6.3 - - + -
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Residues in contact with LEU 39 (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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35D LEU* 2.9 37.4 + - + +
36D GLU 3.9 1.6 - - - +
38D ALA* 1.3 75.0 - - + +
40D LEU* 1.3 67.0 + - - +
42D ALA* 3.0 9.8 + - - -
44D VAL* 3.2 44.0 + - + +
49D THR* 3.5 30.5 - - + +
52D ILE* 4.1 28.7 - - + -
53D LEU* 5.3 0.4 - - + -
72D LEU* 4.1 25.4 - - + -
301D LEU* 4.3 9.0 - - + -
302D LEU* 4.4 13.0 - - + -
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Residues in contact with LEU 40 (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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36D GLU* 2.8 47.8 + - + +
37D MET* 3.7 16.6 - - + +
39D LEU* 1.3 76.9 - - - +
41D ALA* 1.3 60.0 + - - +
43D ASP* 3.1 18.2 + - - +
45D GLY* 4.0 6.1 + - - +
46D LEU* 3.9 37.0 - - + +
49D THR* 3.8 18.2 - - - +
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Residues in contact with ALA 41 (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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37D MET 2.8 22.9 + - - +
38D ALA* 3.8 7.2 - - - +
40D LEU* 1.3 72.5 - - - +
42D ALA* 1.3 59.6 + - - +
43D ASP* 3.2 3.4 + - - +
262D LYS* 3.4 27.2 + - - +
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Residues in contact with ALA 42 (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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38D ALA 3.1 17.7 + - - +
39D LEU* 3.0 6.7 + - - +
40D LEU 3.0 1.4 - - - -
41D ALA* 1.3 76.1 - - - +
43D ASP* 1.3 65.1 + - - +
44D VAL* 3.2 4.7 - - + -
262D LYS* 3.1 12.9 - - + +
264D GLY* 2.9 28.9 + - - +
301D LEU* 3.7 31.2 - - + +
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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