Contacts of the helix formed by residues 33 - 45 (chain L) in PDB entry 4IBL
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 ASP 33 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31L PHE 2.8 10.0 + - - +
32L LYS* 1.3 73.4 - - - +
34L ALA* 1.3 57.6 + - - +
35L CGU 3.2 26.4 + - - +
36L ARG* 3.1 51.1 + - - +
37L THR* 2.8 38.0 + - - -
164T GLY 6.3 0.9 - - - -
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Residues in contact with ALA 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L PHE* 5.7 2.5 - - - -
28L ARG* 5.6 4.0 - - - +
32L LYS 3.5 3.9 + - - -
33L ASP* 1.3 74.3 + - - +
35L CGU 1.3 76.5 + - + +
37L THR* 3.5 6.0 + - - -
38L LYS* 3.0 28.9 + - - +
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Residues in contact with CGU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ASP* 3.2 20.3 + - - +
34L ALA* 1.3 88.0 + - + +
36L ARG* 1.3 65.6 + - - +
38L LYS* 3.8 24.1 + - + +
39L LEU* 2.9 27.2 + - - +
165T LYS* 5.3 15.9 - - - -
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Residues in contact with ARG 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L PHE* 3.9 23.0 + - + -
33L ASP* 3.1 34.3 + - - +
35L CGU 1.3 75.7 + - - +
37L THR* 1.3 64.0 + - - +
39L LEU* 3.3 3.5 + - - +
40L PHE* 3.1 21.8 + - - +
158T TRP* 3.4 66.0 - - + +
159T LYS 3.2 19.6 + - - +
160T SER* 3.5 12.1 + - - +
162T SER 2.8 24.1 + - - -
163T SER* 3.6 1.4 - - - +
164T GLY 3.0 35.0 + - - +
165T LYS* 5.7 5.0 - - + +
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Residues in contact with THR 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L PHE* 3.4 34.5 - - + +
27L ALA* 4.3 6.3 - - + -
28L ARG* 3.5 40.1 - - + +
31L PHE* 3.4 23.5 - - - +
32L LYS 3.9 0.9 + - - -
33L ASP 2.8 22.2 + - - -
34L ALA* 3.7 5.2 - - - -
36L ARG* 1.3 76.7 - - - +
38L LYS* 1.3 56.2 + - - +
40L PHE* 3.2 4.0 + - - +
41L TRP* 2.9 28.0 + - + +
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Residues in contact with LYS 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L PHE* 4.8 6.9 - - + -
34L ALA 3.0 18.5 + - - +
35L CGU 3.8 26.1 + - - +
37L THR* 1.3 76.6 - - - +
39L LEU* 1.3 91.9 + - - +
41L TRP* 3.9 5.5 - - - +
42L ILE* 3.0 38.4 + - + +
204T ASP* 4.5 7.2 + - - -
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Residues in contact with LEU 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L CGU 2.9 17.9 + - - +
36L ARG* 3.6 4.5 - - - +
38L LYS* 1.3 92.8 - - - +
40L PHE* 1.3 62.1 + - - +
42L ILE* 3.3 19.4 - - + +
43L SER* 4.2 2.1 + - - -
156T TYR* 4.6 6.7 - - + -
158T TRP* 3.8 27.8 - - + -
165T LYS* 4.5 11.9 - - - +
188T SER* 3.8 17.9 - - - +
204T ASP* 3.5 41.5 - - + +
205T SER 4.9 3.9 - - - +
207T VAL* 3.7 14.2 + - + +
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Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LEU* 4.0 25.1 - - + -
17L CYS* 4.2 5.4 - - + -
18L LYS* 4.5 13.7 - - - -
22L CYS* 4.4 0.9 - - - -
27L ALA* 3.8 25.8 - - + -
31L PHE* 3.5 34.8 - + + -
36L ARG 3.1 10.1 + - - +
37L THR 3.2 7.4 + - - +
39L LEU* 1.3 77.8 - - - +
41L TRP* 1.3 70.9 + + - +
42L ILE 3.2 1.0 + - - -
43L SER* 3.3 5.5 + - - -
44L TYR* 3.0 67.8 + + + +
207T VAL* 3.5 31.8 + - + +
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Residues in contact with TRP 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L CYS* 3.4 26.0 - - - -
23L SER* 3.6 5.2 - - - -
24L PHE* 3.3 63.8 - + + +
27L ALA* 4.4 3.1 - - + -
37L THR* 2.9 17.1 + - + +
38L LYS* 3.9 4.3 - - - +
40L PHE* 1.3 88.1 - + + +
42L ILE* 1.3 57.5 + - - +
44L TYR* 3.5 26.2 - + - -
45L SER* 2.6 70.4 + - - -
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Residues in contact with ILE 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L LYS* 3.0 29.3 + - + +
39L LEU* 3.3 27.8 - - + +
41L TRP* 1.3 80.4 - - - +
43L SER* 1.3 62.2 + - - +
45L SER* 4.0 3.2 + - - -
46L ASP* 3.3 21.7 + - - +
65L LEU* 3.4 33.5 - - + +
203T THR* 5.8 1.3 - - - -
204T ASP* 5.7 11.7 - - + +
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Residues in contact with SER 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L LEU 4.9 1.3 + - - -
40L PHE 3.3 5.3 + - - -
41L TRP 3.1 0.2 - - - -
42L ILE* 1.3 86.0 - - - +
44L TYR* 1.3 65.4 + - - +
45L SER 3.2 0.4 - - - -
46L ASP* 3.0 20.5 + - - +
47L GLY 4.4 1.7 + - - -
65L LEU* 4.1 3.5 - - - +
110T GLN* 2.9 28.4 + - - -
204T ASP 3.9 4.0 + - - -
205T SER 3.9 0.9 + - - -
206T PRO* 3.6 38.1 - - - +
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Residues in contact with TYR 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L CYS 2.8 29.5 + - - -
18L LYS* 4.9 9.2 - - + -
21L GLN* 3.4 10.3 - - + +
22L CYS* 3.0 50.1 + - - -
40L PHE* 3.0 47.9 + + + +
41L TRP* 3.5 25.1 - + - +
43L SER* 1.3 78.7 - - - +
45L SER* 1.3 60.9 + - - +
46L ASP 3.2 0.9 + - - -
47L GLY 4.6 2.4 + - - -
206T PRO* 6.3 0.7 - - - -
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Residues in contact with SER 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L TRP* 2.6 61.5 + - - -
42L ILE* 4.0 3.5 + - - -
44L TYR* 1.3 77.2 - - - +
46L ASP* 1.3 63.9 + - - +
47L GLY 3.5 1.1 + - - -
66L GLN* 5.3 0.5 + - - -
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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