Contacts of the helix formed by residues 41 - 53 (chain B) in PDB entry 1BXY
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 PRO 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B THR* 1.3 85.2 - - - +
42B ALA* 1.3 64.8 + - - +
44B ARG* 3.3 11.9 + - + +
45B GLY* 3.0 23.9 + - - -
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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
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26B LEU* 5.2 0.2 - - - +
40B THR* 3.3 9.4 + - - +
41B PRO* 1.3 76.9 - - - +
43B ILE* 1.3 69.1 + - + +
45B GLY 4.3 0.2 - - - -
46B ASN* 3.1 34.1 + - - +
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Residues in contact with ILE 43 (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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4B LEU* 4.1 18.6 - - + -
6B VAL* 4.9 1.1 - - + -
25B ALA 5.7 2.2 - - - +
26B LEU* 4.1 13.4 - - + +
37B LEU* 4.0 44.4 - - + -
38B GLU 3.4 22.4 - - - +
39B ASP* 4.9 0.2 - - - -
40B THR* 3.1 16.4 + - + +
42B ALA* 1.3 81.6 - - + +
44B ARG* 1.3 52.1 + - - +
46B ASN* 3.1 4.7 + - - +
47B VAL* 2.8 51.6 + - + +
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Residues in contact with ARG 44 (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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4B LEU* 5.1 6.9 - - + +
39B ASP* 3.3 26.7 + - - +
40B THR 3.0 19.8 + - - +
41B PRO* 3.8 8.7 - - - +
43B ILE* 1.3 72.8 - - - +
45B GLY* 1.3 59.6 + - - +
47B VAL* 3.4 7.6 + - - +
48B GLU* 2.9 59.9 + - - +
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Residues in contact with GLY 45 (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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41B PRO 3.0 16.8 + - - -
42B ALA 4.4 0.2 - - - -
44B ARG* 1.3 76.7 - - - +
46B ASN* 1.3 62.0 + - - +
48B GLU* 3.6 19.0 + - - +
49B LYS* 3.5 21.5 - - - +
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Residues in contact with ASN 46 (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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22B ALA* 3.6 16.8 - - - +
25B ALA* 4.2 20.3 - - - +
26B LEU* 3.9 22.7 - - + -
42B ALA* 3.1 27.1 + - - +
43B ILE 3.1 4.4 + - - +
45B GLY* 1.3 74.6 - - - +
47B VAL* 1.3 65.5 + - - +
49B LYS* 3.2 42.8 + - - +
50B VAL* 3.5 10.4 - - - +
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Residues in contact with VAL 47 (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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4B LEU* 5.2 4.3 - - + -
6B VAL* 4.3 19.1 - - + -
26B LEU* 4.3 10.8 - - + -
43B ILE* 2.8 40.9 + - + +
44B ARG* 3.7 7.9 - - - +
46B ASN* 1.3 71.0 - - - +
48B GLU* 1.3 64.5 + - + +
50B VAL* 3.1 11.5 + - - +
51B ALA* 3.0 23.6 + - + -
54B VAL* 4.1 8.7 - - + -
56B VAL* 3.7 26.9 - - + -
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Residues in contact with GLU 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 ARG* 2.9 48.1 + - - +
45B GLY* 3.6 12.9 - - - +
46B ASN 3.3 0.4 - - - -
47B VAL* 1.3 78.0 - - + +
49B LYS* 1.3 61.5 + - + +
50B VAL 3.2 0.7 + - - -
51B ALA* 3.6 16.6 + - + +
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Residues in contact with LYS 49 (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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18B ASP* 4.2 15.2 + - + +
19B GLN* 3.1 24.3 + - + +
21B ALA* 6.0 1.6 - - - +
22B ALA* 3.8 18.3 - - + +
45B GLY 3.5 17.3 - - - +
46B ASN* 3.2 34.4 + - - +
47B VAL 3.2 1.0 - - - -
48B GLU* 1.3 76.7 - - + +
50B VAL* 1.3 60.0 + - + +
51B ALA 3.6 0.2 - - - -
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Residues in contact with VAL 50 (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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19B GLN* 3.7 35.9 - - + +
22B ALA* 3.9 9.4 - - + -
23B LEU* 3.9 20.2 - - + -
26B LEU* 4.1 9.4 - - + -
46B ASN 3.5 15.0 - - - +
47B VAL* 3.6 4.7 - - - +
49B LYS* 1.3 81.8 - - - +
51B ALA* 1.3 63.4 + - - +
52B HIS 3.1 3.6 - - - -
53B LEU* 2.8 32.6 + - + -
54B VAL* 3.4 25.5 + - + +
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Residues in contact with ALA 51 (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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47B VAL* 3.0 13.2 + - + +
48B GLU* 3.6 17.1 + - - +
49B LYS 3.6 0.2 - - - -
50B VAL* 1.3 75.6 - - - +
52B HIS* 1.3 71.0 + - + +
54B VAL* 3.4 23.6 - - - +
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Residues in contact with HIS 52 (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 VAL* 5.2 2.3 - - - +
10B LYS* 3.4 33.2 - - - +
50B VAL 3.0 1.6 + - - -
51B ALA* 1.3 85.5 - - + +
53B LEU* 1.3 62.8 + - + +
54B VAL 3.6 0.9 - - - -
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Residues in contact with LEU 53 (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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8B LEU* 3.5 15.6 - - + +
9B VAL* 3.0 27.6 + - - -
10B LYS* 3.4 32.5 + - + +
11B SER 4.7 1.1 - - - +
12B PRO* 5.0 3.4 - - + -
15B TYR* 3.2 56.8 - - + +
19B GLN* 4.8 3.1 - - + +
23B LEU* 4.0 24.9 - - + -
50B VAL* 2.8 27.9 + - + +
52B HIS* 1.3 83.2 - - + +
54B VAL* 1.3 57.1 + - + +
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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