Contacts of the helix formed by residues 27 - 40 (chain A) in PDB entry 4IBR
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 GLU 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 HIS 3.9 1.0 + - - -
26A PRO* 1.3 82.2 - - - +
28A THR* 1.3 75.0 + - - +
29A LEU* 3.2 32.6 - - - +
30A VAL* 3.4 22.8 + - + +
31A LYS* 3.0 15.4 + - - +
57A GLU* 4.5 11.9 - - - +
282A SER* 3.2 1.3 + - - -
286A HIS* 3.9 22.8 + - + +
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Residues in contact with THR 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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27A GLU* 1.3 78.3 - - - +
29A LEU* 1.3 63.7 + - - +
31A LYS* 3.0 4.3 + - - +
32A VAL* 2.9 26.7 + - + +
45A TYR* 3.5 40.4 - - + +
47A GLU* 4.7 5.3 + - - +
57A GLU* 5.2 5.2 - - - -
279A ILE* 4.3 11.2 - - + +
282A SER* 3.3 11.7 + - - -
283A LEU* 3.7 30.7 + - - +
286A HIS* 4.5 7.9 - - - +
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Residues in contact with LEU 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 GLU* 3.2 17.0 + - - +
28A THR* 1.3 77.9 - - - +
30A VAL* 1.3 70.6 + - + +
32A VAL* 3.4 5.7 + - + +
33A LYS* 3.1 59.3 + - + +
45A TYR* 6.1 1.8 - - + -
57A GLU* 3.1 28.5 + - + +
58A SER 4.1 9.6 - - - +
59A PHE* 4.0 28.5 - - + -
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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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26A PRO* 3.7 21.5 - - + -
27A GLU* 3.6 29.1 + - + +
28A THR 3.2 0.4 - - - -
29A LEU* 1.3 85.6 - - + +
31A LYS* 1.3 57.4 + - - +
33A LYS* 3.5 6.8 + - + +
34A ASP* 2.8 29.3 + - + +
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Residues in contact with LYS 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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26A PRO* 4.3 17.9 - - + +
27A GLU 3.0 14.5 + - - +
28A THR 3.0 7.8 + - - +
30A VAL* 1.3 75.4 - - - +
32A VAL* 1.3 55.0 + - - +
34A ASP* 2.7 30.3 + - - +
35A ALA* 2.7 34.2 + - - +
275A GLN* 2.9 33.1 + - - +
278A GLU* 2.9 53.6 + - + +
279A ILE* 3.8 11.4 - - + -
282A SER* 4.2 10.3 - - - +
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Residues in contact with VAL 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 THR 2.9 19.5 + - - +
29A LEU* 3.8 9.4 - - + +
30A VAL 3.3 0.2 - - - -
31A LYS* 1.3 75.7 - - - +
33A LYS* 1.3 61.1 + - - +
35A ALA* 3.2 4.5 + - - +
36A GLU* 3.0 20.8 + - - +
43A VAL* 3.5 23.7 - - + +
45A TYR* 3.8 33.7 - - + -
59A PHE* 3.5 29.2 - - + -
279A ILE* 3.7 30.1 - - + -
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Residues in contact with LYS 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 LEU* 3.1 50.0 + - + +
30A VAL* 3.7 5.8 - - - +
32A VAL* 1.3 74.7 - - - +
34A ASP* 1.3 65.5 + - - +
36A GLU* 3.3 8.2 + - - +
37A ASP* 2.9 31.2 + - - +
59A PHE* 3.9 31.0 - - + -
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Residues in contact with ASP 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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26A PRO* 5.8 2.6 - - + +
30A VAL* 2.8 22.6 + - + +
31A LYS* 2.7 37.0 + - + +
33A LYS* 1.3 76.3 - - - +
35A ALA* 1.3 63.3 + - - +
37A ASP* 3.0 9.7 + - - +
38A GLN* 2.6 61.3 + - - +
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Residues in contact with ALA 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 LYS* 2.7 18.5 + - - +
32A VAL 3.3 9.9 - - - +
34A ASP* 1.3 73.7 + - - +
36A GLU* 1.3 57.6 + - - +
38A GLN* 3.1 1.6 + - - +
39A LEU* 2.8 35.5 + - + +
43A VAL* 4.2 10.3 - - + -
262A MET* 6.3 0.2 - - - -
275A GLN* 3.8 33.7 - - + +
279A ILE* 4.2 17.9 - - + -
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Residues in contact with GLU 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 VAL 3.0 12.7 + - - +
33A LYS* 3.6 9.9 - - - +
35A ALA* 1.3 76.2 - - - +
37A ASP* 1.3 58.0 + - - +
40A GLY* 3.0 29.1 + - - -
41A GLY 3.5 18.8 - - - +
42A ARG* 3.3 0.7 - - - -
43A VAL* 2.8 39.2 + - + +
59A PHE* 3.6 10.3 - - + -
60A ARG* 2.6 35.2 + - - -
301A CA 2.4 30.2 - - - -
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Residues in contact with ASP 37 (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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33A LYS* 2.9 23.7 + - - +
34A ASP* 3.0 12.8 + - - +
36A GLU* 1.3 81.6 - - - +
38A GLN* 1.3 72.3 + - - +
40A GLY* 4.4 2.4 + - - -
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Residues in contact with GLN 38 (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 LYS* 5.2 0.2 - - - +
34A ASP* 2.6 47.9 + - - +
35A ALA 3.8 0.4 - - - +
37A ASP* 1.3 87.1 - - - +
39A LEU* 1.3 64.1 + - - +
271A GLU* 5.8 0.7 - - - +
275A GLN* 3.4 28.0 - - - +
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Residues in contact with LEU 39 (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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35A ALA* 2.8 21.4 + - + +
36A GLU* 4.9 0.2 - - - -
38A GLN* 1.3 80.4 - - - +
40A GLY* 1.3 65.1 + - - +
43A VAL* 4.5 7.2 - - + -
262A MET* 3.7 30.5 - - + -
265A SER* 2.7 28.0 + - - +
266A GLN 4.1 2.6 + - - -
267A ALA* 3.5 30.9 + - + +
271A GLU* 4.3 5.2 - - + +
272A ARG* 4.0 15.0 - - + +
275A GLN* 3.7 39.3 - - + +
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Residues in contact with GLY 40 (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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36A GLU* 3.0 18.8 + - - +
37A ASP 4.4 2.3 + - - -
38A GLN 3.6 1.6 - - - -
39A LEU* 1.3 90.4 - - - +
41A GLY* 1.3 69.7 + - - +
42A ARG 3.7 2.1 + - - -
43A VAL* 5.1 1.2 - - - +
263A THR 4.7 0.2 - - - +
265A SER* 4.0 5.8 - - - -
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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