Contacts of the helix formed by residues 26 - 35 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 4.3 9.4 - - + +
25B MET* 1.3 77.7 - - - +
27B VAL* 1.3 60.0 + - - +
28B GLU* 2.9 27.0 + - - +
29B HIS* 2.8 37.5 + - + +
30B LEU* 3.0 24.9 + - - +
61B PHE* 5.6 3.1 - - + -
62B ILE* 4.5 0.7 - - - +
66B THR* 4.4 9.9 - - - +
81B THR* 4.0 12.3 - - + -
84B PHE* 3.8 6.3 - - - -
79D GLU* 3.2 18.2 - - - +
80D VAL* 4.8 9.2 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 1.3 73.3 - - - +
28B GLU* 1.3 63.3 + - - +
30B LEU* 3.3 10.2 - - + +
31B LEU* 2.9 25.5 + - - +
83B SER* 3.4 19.1 - - - +
84B PHE* 3.3 33.2 - - - +
87B VAL* 4.1 10.3 - - + -
112B ILE* 4.0 26.2 - - + -
115B GLU* 4.7 1.1 - - + -
118B SER* 4.5 6.3 - - - +
120B ALA* 3.8 17.9 - - + +
79D GLU* 2.7 17.4 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 2.9 13.3 + - - +
27B VAL* 1.3 76.4 - - - +
29B HIS* 1.3 66.5 + - - +
30B LEU 3.0 1.1 - - - -
31B LEU* 3.9 1.3 - - - +
32B LEU* 2.9 24.4 + - - +
58B LEU* 3.6 27.5 - - + +
61B PHE* 3.7 24.9 - - + -
62B ILE* 3.7 19.1 - - + +
118B SER* 3.6 4.5 - - - -
119B GLN* 3.2 21.8 + - + -
120B ALA* 2.8 27.8 + - - +
79D GLU* 2.5 26.8 - - - +
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.8 12.3 - - + +
16B ARG* 5.1 2.7 - - + -
17B ALA* 3.8 23.5 - - + +
22B HIS* 3.0 27.6 + + - -
24B PHE 3.4 19.7 + - - -
25B MET* 4.1 13.0 - - - -
26B THR* 2.8 45.3 + - + +
28B GLU* 1.3 77.0 - - - +
30B LEU* 1.3 58.9 + - - +
32B LEU* 3.3 5.3 + - + +
33B ALA* 3.0 29.8 + - - +
62B ILE* 3.5 34.5 - - + +
66B THR* 3.9 9.9 - - - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER 5.8 0.4 - - - +
10B LEU* 3.7 29.8 - - + -
13B ALA* 4.4 9.4 - - + +
26B THR 3.0 12.6 + - - +
27B VAL* 3.3 13.9 - - + +
28B GLU 3.0 0.2 - - - -
29B HIS* 1.3 75.3 - - - +
31B LEU* 1.3 66.6 + - - +
33B ALA* 3.2 4.9 + - + +
34B LEU* 2.9 46.6 + - + +
84B PHE* 4.0 21.8 - - + -
87B VAL* 3.8 19.5 - - + -
88B LEU* 4.3 3.8 - - + -
108B VAL* 3.8 23.8 - - + -
112B ILE* 4.5 7.4 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL 2.9 20.0 + - - +
28B GLU* 3.9 4.0 - - - +
30B LEU* 1.3 72.3 - - - +
32B LEU* 1.3 64.1 + - - +
34B LEU* 3.1 17.5 + - + -
35B LEU* 3.1 24.6 + - + +
44B LEU* 4.9 2.0 - - + -
54B LEU* 4.6 8.7 - - + -
58B LEU* 3.7 22.4 - - + -
109B LEU* 3.9 28.0 - - + -
112B ILE* 4.0 15.0 - - + -
120B ALA* 3.9 26.2 - - + +
124B LEU* 3.9 26.0 - - + -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 5.7 13.2 - - + +
28B GLU 2.9 17.8 + - - +
29B HIS* 3.4 6.7 - - + +
31B LEU* 1.3 76.5 - - - +
33B ALA* 1.3 63.4 + - - +
35B LEU* 3.2 21.7 + - + +
36B SER* 4.3 2.1 + - - -
55B ARG* 3.7 46.2 - - + +
58B LEU* 3.8 13.1 - - + +
59B GLU* 4.0 23.6 - - + +
62B ILE* 4.1 16.8 - - + -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 3.4 35.9 + - - +
12B MET* 4.6 10.7 - - + +
13B ALA* 3.9 15.5 - - + +
16B ARG* 5.9 3.4 - - - +
29B HIS 3.0 16.2 + - - +
30B LEU* 3.7 5.6 - - + +
32B LEU* 1.3 77.6 - - - +
34B LEU* 1.3 62.3 + - - +
36B SER* 3.2 22.5 + - - -
37B ASN 3.6 4.0 + - - -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.4 9.4 - - + -
9B SER* 4.2 12.6 - - - -
30B LEU* 2.9 29.8 + - + +
31B LEU* 3.1 16.3 + - + +
33B ALA* 1.3 71.1 - - - +
35B LEU* 1.3 66.0 + - - +
36B SER 3.0 2.9 - - - -
37B ASN* 3.0 38.4 + - + +
40B ALA* 3.6 15.0 - - + +
41B ARG 3.8 2.1 + - - -
44B LEU* 5.2 1.2 - - + +
105B GLY* 4.0 27.4 - - - +
108B VAL* 3.9 24.5 - - + -
109B LEU* 4.1 10.5 - - + +
112B ILE* 4.2 12.1 - - + -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 3.1 23.0 + - + +
32B LEU* 3.4 17.5 - - + +
33B ALA 3.1 1.0 - - - -
34B LEU* 1.3 76.6 - - - +
36B SER* 1.3 57.6 + - - +
41B ARG* 3.4 25.2 - - - +
44B LEU* 3.5 30.7 - - + -
51B LEU* 3.9 22.3 - - + +
54B LEU* 4.1 19.3 - - + -
55B ARG* 3.7 42.4 - - + +
58B LEU* 4.4 2.0 - - + -
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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