Contacts of the helix formed by residues 26 - 35 (chain A) in PDB entry 1MBU
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 THR 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.2 8.7 - - + +
25A MET* 1.3 76.9 - - - +
27A VAL* 1.3 60.3 + - - +
28A GLU* 3.0 22.7 + - - +
29A HIS* 2.6 44.7 + - + +
30A LEU* 3.0 25.5 + - - +
61A PHE* 5.7 3.0 - - + -
62A ILE* 4.5 0.9 - - - +
66A THR* 4.4 9.4 - - + +
81A THR* 4.0 14.8 - - + -
84A PHE* 3.8 7.6 - - - -
79C GLU* 3.4 11.2 - - - +
80C VAL* 4.7 11.0 - - + -
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Residues in contact with VAL 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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26A THR* 1.3 75.3 - - - +
28A GLU* 1.3 64.9 + - - +
30A LEU* 3.3 10.6 - - + +
31A LEU* 2.9 26.2 + - - +
83A SER* 3.5 18.8 - - - +
84A PHE* 3.4 33.2 - - + +
87A VAL* 4.2 10.1 - - + -
112A ILE* 4.0 26.2 - - + -
115A GLU* 5.2 0.7 - - + -
118A SER* 4.4 7.4 - - - +
120A ALA* 3.8 18.1 - - + +
79C GLU* 2.9 15.1 + - - +
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Residues in contact with GLU 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 THR* 3.0 13.4 + - - +
27A VAL* 1.3 76.3 - - - +
29A HIS* 1.3 65.0 + - - +
30A LEU 3.0 0.9 - - - -
31A LEU* 3.9 0.9 - - - +
32A LEU* 3.0 24.4 + - - +
58A LEU* 3.9 21.8 - - + +
61A PHE* 3.8 25.8 - - + -
62A ILE* 3.7 19.6 - - + +
118A SER* 3.7 4.7 - - - -
119A GLN* 3.1 17.6 + - + -
120A ALA* 2.8 38.1 + - - +
79C GLU* 2.6 26.4 - - - +
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Residues in contact with HIS 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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13A ALA* 4.5 8.2 - - + +
17A ALA* 4.0 19.0 - - + +
22A HIS* 2.8 32.0 + + - -
24A PHE 3.4 20.4 + - - -
25A MET* 3.9 16.8 - - - -
26A THR* 2.6 43.6 + - + +
28A GLU* 1.3 76.1 - - - +
30A LEU* 1.3 58.2 + - - +
32A LEU* 3.3 5.2 + - + +
33A ALA* 2.9 29.9 + - - +
62A ILE* 3.5 32.5 - - + +
66A THR* 3.8 9.9 - - - -
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Residues in contact with LEU 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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9A SER* 6.5 0.2 - - - -
10A LEU* 3.5 31.9 - - + -
13A ALA* 5.5 2.9 - - + -
26A THR 3.0 12.0 + - - +
27A VAL* 3.3 13.7 - - + +
28A GLU 3.0 0.2 - - - -
29A HIS* 1.3 79.6 - - - +
31A LEU* 1.3 63.2 + - - +
33A ALA* 3.2 8.1 + - + +
34A LEU* 3.0 36.8 + - + +
84A PHE* 3.9 24.2 - - + -
87A VAL* 3.8 19.7 - - + -
88A LEU* 4.1 4.9 - - + -
108A VAL* 3.7 32.5 - - + -
112A ILE* 4.5 7.0 - - + -
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Residues in contact with LEU 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 VAL 2.9 19.5 + - - +
28A GLU 4.0 3.4 - - - +
30A LEU* 1.3 73.9 - - - +
32A LEU* 1.3 62.1 + - - +
34A LEU* 3.1 18.0 + - + -
35A LEU* 3.1 24.7 + - + +
44A LEU* 4.9 1.8 - - + -
54A LEU* 4.5 9.0 - - + -
58A LEU* 3.8 20.4 - - + -
109A LEU* 3.8 28.9 - - + -
112A ILE* 4.1 14.8 - - + -
120A ALA* 3.8 26.7 - - + +
124A LEU* 3.9 26.2 - - + -
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Residues in contact with LEU 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 GLU 3.0 18.3 + - - +
29A HIS* 3.4 6.5 - - + +
31A LEU* 1.3 78.4 - - - +
33A ALA* 1.3 62.3 + - - +
35A LEU* 3.2 21.8 + - + +
36A SER* 4.4 1.9 + - - -
55A ARG* 4.0 56.5 + - + +
58A LEU* 3.7 13.6 - - + +
59A GLU* 3.9 27.6 - - + +
62A ILE* 4.2 15.0 - - + -
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Residues in contact with ALA 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* 3.9 24.4 + - - +
10A LEU* 5.8 0.2 - - - -
13A ALA* 3.6 25.4 - - + -
16A ARG* 6.3 0.9 - - - +
29A HIS 2.9 14.1 + - - +
30A LEU* 3.2 11.6 + - + +
32A LEU* 1.3 77.5 - - - +
34A LEU* 1.3 62.7 + - + +
35A LEU 3.2 0.9 + - - -
36A SER* 3.3 19.2 + - - -
37A ASN 3.6 4.3 + - - -
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Residues in contact with LEU 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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6A LEU* 4.1 15.0 - - + -
9A SER* 4.8 4.5 - - - -
30A LEU* 3.0 25.8 + - + +
31A LEU* 3.1 15.2 + - + +
33A ALA* 1.3 72.9 - - - +
35A LEU* 1.3 66.0 + - - +
36A SER 3.0 2.7 - - - -
37A ASN* 2.9 38.5 + - + +
40A ALA* 3.7 14.1 - - + +
41A ARG 3.8 2.1 + - - -
44A LEU* 5.3 1.1 - - + -
105A GLY* 4.0 28.5 - - - +
108A VAL* 3.8 24.7 - - + -
109A LEU* 4.1 10.8 - - + +
112A ILE* 4.2 16.2 - - + -
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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 LEU* 3.1 21.2 + - + +
32A LEU* 3.4 14.6 - - + +
33A ALA 3.2 1.0 - - - -
34A LEU* 1.3 77.4 - - - +
36A SER* 1.3 57.1 + - - +
41A ARG* 3.4 25.3 - - - +
44A LEU* 3.6 29.4 - - + -
51A LEU* 3.9 21.7 - - + +
54A LEU* 3.7 19.3 - - + -
55A ARG* 3.6 52.9 - - + +
58A LEU* 4.2 8.5 - - + -
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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