Contacts of the helix formed by residues 47 - 56 (chain D) in PDB entry 2BEX
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 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ILE* 4.4 2.0 - - - -
46D THR* 1.3 82.4 + - - +
48D PHE* 1.3 66.4 + - - +
49D ALA* 3.9 8.9 + - - +
50D ASN* 3.1 40.7 + - - +
51D VAL* 3.3 13.6 + - - +
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ALA* 3.9 31.4 - - + -
11D PHE* 4.4 2.2 - + - -
12D GLU* 3.7 44.4 - - + +
16D ILE* 3.9 17.8 - - + +
47D THR* 1.3 73.6 - - - +
49D ALA* 1.3 63.3 + - - +
51D VAL* 2.9 20.2 + - + +
52D VAL* 3.0 30.3 + - + +
120D PRO* 6.5 1.1 - - + -
123D TYR* 3.8 23.8 - + - -
126D VAL* 4.3 4.5 - - + -
127D PRO* 3.6 37.0 - - + -
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D THR* 3.2 10.4 - - - +
48D PHE* 1.3 79.4 - - - +
50D ASN* 1.3 65.3 + - - +
52D VAL* 3.1 9.7 + - - +
53D ASN* 2.9 21.2 + - - +
123D TYR* 3.7 25.9 + - + +
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Residues in contact with ASN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR* 3.2 27.6 + - + +
47D THR* 3.1 18.8 + - - +
48D PHE 3.2 0.4 - - - -
49D ALA* 1.3 77.8 - - - +
51D VAL* 1.3 63.5 + - - +
53D ASN* 3.1 10.8 + - - +
54D VAL* 3.0 24.5 + - + +
107D TYR* 4.1 3.4 - - - +
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.1 8.1 - - + -
16D ILE* 4.0 17.7 - - + -
44D LEU* 4.9 2.7 - - + -
46D THR* 4.0 12.6 - - + -
47D THR 3.4 15.5 - - - +
48D PHE* 2.9 8.9 + - - +
50D ASN* 1.3 75.6 - - - +
52D VAL* 1.3 58.6 + - - +
54D VAL* 2.8 20.3 + - - +
55D CYS* 2.9 11.7 + - - -
107D TYR* 3.3 24.5 - - + +
109D VAL* 4.2 15.0 - - + -
127D PRO* 3.5 34.3 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 3.0 45.0 + - + +
49D ALA* 3.3 8.7 - - - +
51D VAL* 1.3 75.7 - - - +
53D ASN* 1.3 61.7 + - - +
55D CYS* 3.1 23.6 + - - +
56D GLY* 3.3 4.9 + - - -
123D TYR* 3.8 35.4 - - + -
124D PRO* 5.9 0.9 - - + -
125D VAL 3.5 18.6 - - - +
126D VAL* 4.5 1.6 - - + -
127D PRO* 4.2 7.4 - - + -
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ALA 2.9 11.6 + - - +
50D ASN* 3.2 13.9 - - - +
52D VAL* 1.3 75.7 - - - +
54D VAL* 1.3 55.9 + - + +
56D GLY* 2.7 27.3 + - - -
57D ASN* 3.6 7.7 + - - -
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ASN* 3.0 10.9 + - + +
51D VAL 2.8 9.7 + - - +
53D ASN* 1.3 75.1 - - + +
55D CYS* 1.3 56.8 + - - +
57D ASN* 2.8 32.5 + - - +
72D HIS* 3.1 24.3 - - + +
73D HIS 3.2 27.4 - - - +
74D SER* 3.5 20.2 - - - +
107D TYR* 3.0 36.6 - - + +
109D VAL* 4.5 2.7 - - + -
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Residues in contact with CYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL 2.9 13.2 + - - -
52D VAL* 3.1 13.7 - - - +
53D ASN 3.1 0.4 - - - -
54D VAL* 1.3 77.1 - - - +
56D GLY* 1.3 56.6 + - - +
57D ASN 3.2 0.4 - - - +
72D HIS* 3.1 27.6 + - - -
109D VAL* 4.4 1.1 - - - -
111D CYS* 2.0 53.4 - - + -
125D VAL* 4.1 19.7 - - + +
126D VAL* 3.6 2.9 - - - -
127D PRO* 3.4 29.8 - - - -
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Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL 3.3 4.1 + - - -
53D ASN 2.7 13.8 + - - -
55D CYS* 1.3 76.8 - - - +
57D ASN* 1.3 66.1 + - - +
58D PRO* 4.7 0.2 - - - +
125D VAL* 6.1 1.3 - - - -
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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