Contacts of the helix formed by residues 48 - 54 (chain D) in PDB entry 1BHC
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 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D TYR* 3.6 44.3 - - + -
30D CYS* 4.8 1.5 - - + +
47D SER* 1.3 71.4 + - - +
49D GLU* 1.3 64.0 + - - +
51D CYS* 3.1 14.3 + - - +
52D MET* 3.1 17.1 + - - +
48H ALA* 4.0 5.2 - - + -
49H GLU* 3.9 24.7 - - + +
52H MET* 4.6 7.2 - - - -
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Residues in contact with GLU 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 SER* 3.2 8.2 + - - +
48D ALA* 1.3 79.9 - - - +
50D ASP* 1.3 64.8 + - - +
52D MET* 3.4 11.2 - - + +
53D ARG* 2.6 52.5 + - - +
21H TYR* 2.7 41.4 + - + +
32H THR* 3.2 15.2 - - - +
48H ALA* 4.0 6.6 - - + +
20I ARG* 2.5 37.5 + - - -
46I LYS* 3.6 10.4 - - - +
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Residues in contact with ASP 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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45D PHE* 4.0 8.1 - - + -
47D SER* 3.0 10.5 + - - +
49D GLU* 1.3 74.5 - - - +
51D CYS* 1.3 65.6 + - - +
53D ARG* 3.9 12.1 + - - +
54D THR* 2.8 31.6 + - - -
44I ASN 5.4 0.2 - - - -
45I PHE* 3.6 17.6 - - + +
46I LYS* 2.9 27.1 + - - +
47I SER 3.3 15.6 + - - -
50I ASP* 2.6 39.6 - - + +
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Residues in contact with CYS 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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21D TYR* 4.2 4.5 - - + -
22D PHE 3.6 20.0 - - - -
23D TYR* 3.7 4.0 - - - -
30D CYS* 2.0 46.0 - - + -
45D PHE* 3.3 42.3 - - + -
47D SER 3.1 3.6 + - - +
48D ALA 3.1 9.5 + - - +
50D ASP* 1.3 79.2 - - - +
52D MET* 1.3 56.5 + - - +
55D CYS* 2.8 34.8 + - - +
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Residues in contact with MET 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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30D CYS* 3.4 12.3 - - - -
48D ALA 3.2 13.9 - - - +
49D GLU* 3.4 15.9 - - + +
51D CYS* 1.3 78.6 - - - +
53D ARG* 1.3 57.9 + - - +
56D GLY* 2.8 32.4 + - - +
21H TYR* 5.6 2.0 - - + -
29H LEU* 3.7 24.6 - - + +
30H CYS* 2.8 58.1 - - + +
48H ALA* 4.6 9.2 - - + -
52H MET* 3.8 30.5 - - + +
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Residues in contact with ARG 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 GLU* 2.6 53.8 + - - +
50D ASP* 3.9 17.1 + - - +
51D CYS 3.2 0.2 - - - -
52D MET* 1.3 79.2 - - + +
54D THR* 1.3 62.0 + - - +
29H LEU* 5.3 4.7 - - + -
32H THR* 4.9 3.4 - - - +
20I ARG* 3.9 3.8 - - - +
35I TYR* 5.1 0.4 + - - -
40I ALA* 3.9 26.8 - - - +
41I LYS 3.5 22.4 - - - -
42I ARG* 3.1 49.9 + - - +
44I ASN* 2.4 42.4 + - - -
45I PHE* 4.5 0.2 - - - +
46I LYS 4.9 0.2 - - - +
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Residues in contact with THR 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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2D PRO* 3.1 27.3 - - + +
4D PHE* 3.7 30.5 - - + -
45D PHE* 3.8 15.8 - - + -
50D ASP* 2.8 21.6 + - - -
53D ARG* 1.3 80.4 - - - +
55D CYS* 1.3 58.1 + - - +
4I PHE* 4.0 12.4 - - + -
42I ARG* 3.7 15.7 + - - +
45I PHE* 3.8 21.5 - - - -
54I THR* 3.9 12.6 - - + -
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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