Contacts of the helix formed by residues 32 - 48 (chain B) in PDB entry 3UXO
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 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 2.6 21.5 + - - +
30B SER* 3.0 15.1 - - - +
31B GLN* 1.3 70.5 - - - +
33B ILE* 1.3 51.3 + - - +
34B HIS* 2.8 5.8 + - - -
35B LYS* 2.6 62.8 + - + +
36B TYR 3.3 2.8 + - - -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU 4.7 1.1 - - - -
27B LYS* 4.4 31.6 - - + +
31B GLN* 3.0 16.5 + - + +
32B ALA* 1.3 74.8 - - - +
34B HIS* 1.3 85.0 + - + +
35B LYS 3.2 0.2 - - - -
36B TYR* 3.3 15.1 + - + +
37B ASN* 3.2 30.4 + - - +
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Residues in contact with HIS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 2.8 1.6 + - - -
33B ILE* 1.3 96.3 - - + +
35B LYS* 1.3 63.4 + - + +
37B ASN* 3.7 18.3 + - - +
38B ALA* 3.6 17.5 + - - +
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 3.6 29.6 + - + +
32B ALA* 2.6 36.6 + - + +
34B HIS* 1.3 74.6 - - + +
36B TYR* 1.3 62.2 + - - -
37B ASN 3.2 0.2 - - - -
38B ALA* 3.3 6.2 + - - +
39B TYR* 3.1 34.0 + - + -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 3.0 48.5 - - + +
24B ASN* 4.4 7.2 - - - -
26B GLU* 4.1 2.1 - - - +
27B LYS* 3.9 47.1 + - + +
32B ALA 3.3 3.2 + - - +
33B ILE* 3.3 18.4 - - + +
35B LYS* 1.3 79.1 - - - +
37B ASN* 1.3 79.8 + - - +
38B ALA 3.3 0.2 + - - -
39B TYR* 3.4 2.1 + - - +
40B ARG* 2.9 62.8 + - + +
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Residues in contact with ASN 37 (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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33B ILE* 3.2 18.4 + - - +
34B HIS* 3.7 24.2 + - - +
35B LYS 3.2 0.2 - - - -
36B TYR* 1.3 96.6 - - - +
38B ALA* 1.3 56.7 + - - +
40B ARG* 3.4 6.4 + - - +
41B LYS* 2.9 28.2 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS 3.6 9.3 + - - +
35B LYS* 3.3 9.3 + - - +
36B TYR 3.2 0.6 - - - -
37B ASN* 1.3 77.3 - - - +
39B TYR* 1.3 67.1 + - - +
41B LYS* 3.5 7.9 + - - +
42B ALA* 3.0 24.6 + - - +
64B GLY 4.6 4.7 - - - +
69B ILE* 3.7 13.1 - - + +
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.7 23.4 - - + +
22B LEU* 3.7 32.8 - - + +
23B ALA* 3.5 35.4 - - + -
26B GLU* 3.7 30.2 + - + -
35B LYS* 3.1 25.0 + - + -
36B TYR 3.7 1.1 - - - +
38B ALA* 1.3 78.5 - - + +
40B ARG* 1.3 57.0 + - - +
42B ALA* 3.3 2.9 + - - +
43B ALA* 2.9 31.8 + - - +
69B ILE* 4.0 24.2 - - + -
72B LYS* 3.3 28.0 + - + -
84B LYS* 5.0 2.9 + - - -
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Residues in contact with ARG 40 (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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20B VAL* 6.2 1.1 - - - +
23B ALA* 4.3 5.8 - - + +
36B TYR* 2.9 56.6 + - + +
37B ASN* 3.7 6.8 + - - +
39B TYR* 1.3 77.8 - - - +
41B LYS* 1.3 61.1 + - - +
43B ALA* 3.6 6.6 + - + +
44B SER* 3.1 24.4 + - - -
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 2.9 18.2 + - - +
38B ALA* 3.9 6.7 - - - +
40B ARG* 1.3 73.7 - - - +
42B ALA* 1.3 60.0 + - - +
44B SER* 3.2 6.1 + - - -
45B VAL* 2.8 44.6 + - + +
63B PRO* 4.5 4.5 - - - -
64B GLY* 4.0 26.0 - - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.7 15.0 - - + -
38B ALA 3.0 18.3 + - - +
39B TYR 3.7 3.1 - - - +
41B LYS* 1.3 74.6 - - - +
43B ALA* 1.3 56.2 + - - +
45B VAL* 3.0 4.4 + - - +
46B ILE* 2.7 38.1 + - - +
64B GLY 4.3 5.6 + - - +
65B VAL* 4.1 22.0 - - + -
69B ILE* 3.7 22.7 - - + -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR* 3.4 24.6 - - - +
19B LEU* 3.4 25.8 - - + +
20B VAL* 4.6 8.1 - - + +
39B TYR 2.9 18.1 + - - +
40B ARG* 3.7 8.1 - - + +
42B ALA* 1.3 74.1 - - - +
44B SER* 1.3 57.6 + - - +
47B ALA* 2.9 28.9 + - - +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG 3.1 15.1 + - - -
41B LYS* 3.6 6.7 - - - -
43B ALA* 1.3 77.9 - - - +
45B VAL* 1.3 64.5 + - - +
47B ALA* 3.6 4.3 + - - +
48B LYS* 3.2 47.9 + - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 2.8 35.0 + - + +
42B ALA* 3.5 5.6 - - - +
44B SER* 1.3 73.6 - - - +
46B ILE* 1.3 67.4 + - - +
48B LYS* 3.3 17.7 + - + +
49B TYR* 3.4 9.9 + - - +
62B LEU* 3.7 30.0 - - + +
63B PRO* 3.3 38.1 - - + +
65B VAL* 4.4 3.1 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.6 30.7 + - + +
15B ILE* 4.0 9.4 - - + -
16B THR* 3.8 11.0 - - + -
19B LEU* 3.9 18.4 - - + -
42B ALA 2.7 19.5 + - - +
43B ALA 3.9 2.9 - - - +
45B VAL* 1.3 72.4 - - - +
47B ALA* 1.3 54.7 + - - +
49B TYR* 2.7 33.4 + - - +
53B ILE* 3.9 19.3 - - + -
59B ALA* 4.9 0.2 - - + -
62B LEU* 3.8 21.1 - - + -
65B VAL* 4.1 10.1 - - + -
73B ILE* 3.7 29.8 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 5.7 3.6 - - - +
16B THR* 3.8 18.4 - - + +
43B ALA 2.9 18.4 + - - +
44B SER* 4.2 4.0 - - - +
46B ILE* 1.3 76.8 - - - +
48B LYS* 1.3 59.8 - - + +
49B TYR 3.2 4.0 + - - +
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Residues in contact with LYS 48 (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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44B SER* 3.2 37.7 + - - +
45B VAL* 3.6 9.6 - - + +
46B ILE 3.1 0.8 - - - -
47B ALA* 1.3 76.1 - - + +
49B TYR* 1.3 60.2 + - - +
50B PRO* 3.4 10.4 - - - +
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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