Contacts of the helix formed by residues 27 - 37 (chain A) in PDB entry 1B43
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 ALA 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 ILE 3.1 3.9 + - - -
26A ASP* 1.3 69.2 - - - +
28A LEU* 1.3 60.8 + - - +
30A ALA* 3.5 1.6 + - - +
31A ILE* 2.9 36.7 + - + +
60A LEU* 5.7 0.8 - - + +
76A TYR* 4.2 14.6 - - + -
77A VAL 2.8 25.7 + - - +
78A PHE* 3.5 43.5 - - + -
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Residues in contact with LEU 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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26A ASP* 3.4 6.9 + - - +
27A ALA* 1.3 78.3 - - - +
29A ASN* 1.3 62.7 + - - +
31A ILE* 3.4 9.6 + - + +
32A TYR* 3.0 45.8 + - + +
77A VAL 4.6 0.8 + - - -
78A PHE* 5.6 1.0 - - - +
79A ASP* 3.6 28.4 - - - +
124A THR* 6.5 1.1 - - + -
127A ASN* 4.4 18.4 - - + +
130A LEU* 6.3 0.2 - - + -
131A ILE* 4.4 26.0 - - + -
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Residues in contact with ASN 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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26A ASP* 3.0 23.9 + - + +
27A ALA 3.4 0.2 - - - -
28A LEU* 1.3 73.0 - - - +
30A ALA* 1.3 66.9 + - - +
32A TYR* 3.3 6.4 + - - +
33A GLN* 3.0 34.3 + - - +
117A ARG* 5.6 3.4 - - - +
153A GLU* 4.8 0.9 - - - +
170A SER* 3.4 18.5 - - - +
171A GLN* 2.9 35.4 + - - +
172A ASP* 3.3 33.7 + - - +
188A THR* 5.2 0.9 + - - -
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Residues in contact with ALA 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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25A ILE* 4.0 10.5 - - + -
26A ASP 3.2 15.8 + - - +
27A ALA 3.7 3.8 - - - +
29A ASN* 1.3 76.8 + - - +
31A ILE* 1.3 63.5 + - - +
33A GLN* 3.0 5.5 + - - +
34A PHE* 2.9 40.7 + - + -
60A LEU* 5.2 0.7 - - + -
76A TYR* 4.3 9.0 - - + -
188A THR* 3.7 29.8 - - + -
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Residues in contact with ILE 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 ALA* 2.9 30.1 + - + +
28A LEU* 3.6 11.0 - - + +
30A ALA* 1.3 76.2 - - - +
32A TYR* 1.3 65.3 + - + +
34A PHE* 3.3 10.4 + - - +
35A LEU* 3.1 27.7 + - + +
56A HIS* 4.0 17.3 - - + +
60A LEU* 4.3 19.7 - - + -
78A PHE* 4.7 3.6 - - + -
130A LEU* 4.1 32.3 - - + +
131A ILE* 4.5 17.0 - - + -
134A ALA* 3.9 24.9 - - + -
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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 LEU* 3.0 35.7 + - + +
29A ASN* 3.9 6.3 - - - +
31A ILE* 1.3 77.6 - - + +
33A GLN* 1.3 65.9 + - - +
35A LEU* 3.3 21.7 + - + +
36A SER* 3.1 24.8 + - - -
104A TRP* 3.0 24.0 + - - -
108A LEU* 5.5 0.2 - - + -
113A ILE* 3.5 26.8 - - + +
116A ALA* 4.5 3.1 - - + +
117A ARG* 3.4 52.3 + - + +
120A ALA* 3.5 7.5 - - + +
127A ASN* 2.6 34.7 + - - -
130A LEU* 4.5 4.0 - - + -
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Residues in contact with GLN 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 ASN* 3.0 27.0 + - - +
30A ALA 3.0 6.9 + - - +
32A TYR* 1.3 77.8 - - - +
34A PHE* 1.3 55.1 + - - +
36A SER* 3.8 8.4 + - - -
37A THR* 2.6 44.0 + - - +
117A ARG* 4.0 22.2 - - - +
171A GLN* 3.5 35.1 - - + +
188A THR* 3.6 25.8 - - - +
189A ILE* 3.8 21.4 - - + +
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Residues in contact with PHE 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 ALA* 2.9 22.9 + - + -
31A ILE* 3.5 10.8 - - - +
33A GLN* 1.3 80.7 - - - +
35A LEU* 1.3 57.6 + - - +
37A THR* 4.2 2.9 - - - -
38A ILE* 3.0 49.4 + - + +
55A SER* 3.8 18.0 - - - +
56A HIS* 3.8 12.1 - - - -
59A GLY* 3.5 33.7 - - - -
60A LEU* 3.6 20.4 - - + -
63A ARG* 3.8 22.2 - - + -
76A TYR* 4.7 5.2 - - - -
188A THR* 3.5 42.4 - - + -
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Residues in contact with LEU 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 ILE* 3.1 20.7 + - + +
32A TYR* 3.3 27.6 + - + +
34A PHE* 1.3 78.7 - - - +
36A SER* 1.3 57.8 + - - +
38A ILE 4.3 1.6 - - - +
39A ARG* 3.9 11.6 + - - +
45A PRO* 5.0 6.0 - - + +
53A ILE* 3.8 29.2 - - + -
55A SER* 3.9 12.7 + - - -
56A HIS* 4.3 11.2 - - + +
108A LEU* 3.9 22.9 - - + -
113A ILE* 3.3 27.2 - - + +
130A LEU* 3.9 27.8 - - + -
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Residues in contact with SER 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 3.1 16.4 + - - -
33A GLN* 3.5 13.9 + - - -
35A LEU* 1.3 79.6 - - - +
37A THR* 1.3 66.4 + - - +
38A ILE 3.8 0.2 - - - -
39A ARG* 2.6 36.1 + - - -
112A GLU* 5.5 2.7 - - - -
113A ILE* 3.8 20.0 - - - -
117A ARG* 4.1 5.2 + - - -
193A ARG* 4.8 2.3 + - - -
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Residues in contact with THR 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 GLN* 2.6 27.0 + - - +
34A PHE* 4.2 0.9 - - - -
36A SER* 1.3 87.5 - - - +
38A ILE* 1.3 71.2 + - - +
39A ARG* 3.8 5.4 + - - -
63A ARG* 5.9 0.3 + - - -
188A THR 4.8 2.6 + - - -
189A ILE* 4.0 23.4 - - + +
193A ARG* 3.4 46.7 + - - +
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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