Contacts of the helix formed by residues 41 - 49 (chain A) in PDB entry 2B69
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 ARG 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.3 18.7 + - - +
37A PHE* 3.8 13.5 - - - -
39A THR 5.7 0.2 - - - +
40A GLY* 1.3 76.0 - - - +
42A LYS* 1.3 66.3 + - - +
43A ARG* 3.2 39.4 - - + +
44A ASN* 3.1 41.6 + - - +
45A VAL 4.4 0.2 + - - -
181A ARG 3.3 16.7 + - - -
182A MSE 4.0 6.3 + - - -
183A HIS* 3.6 36.8 + - - +
184A MSE 5.3 0.4 - - - +
306A TYR* 3.0 27.1 + - - -
310A GLU* 4.4 4.9 + - - -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.7 20.5 - - + -
41A ARG* 1.3 72.4 - - - +
43A ARG* 1.3 63.1 + - - +
44A ASN 3.1 1.6 + - - -
45A VAL* 3.1 17.6 + - - +
46A GLU* 3.1 14.4 + - + +
49A ILE* 4.0 18.4 - - + -
56A LEU* 3.9 22.7 - - + -
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ARG* 3.1 53.7 - - + +
42A LYS* 1.3 78.1 - - - +
44A ASN* 1.3 60.6 + - - +
45A VAL 3.3 0.9 + - - -
46A GLU* 3.5 40.9 + - - +
47A HIS* 4.9 2.4 + - - -
306A TYR* 3.8 1.8 + - - -
310A GLU* 3.0 33.6 + - - -
313A TYR* 5.7 6.4 - - - +
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 2.9 29.1 + - - +
14A GLY* 3.8 14.5 + - - -
15A PHE 4.4 0.2 - - - +
18A SER* 3.5 25.3 - - - +
40A GLY* 4.7 1.8 - - - -
41A ARG* 3.1 39.8 + - - +
42A LYS 3.1 0.8 + - - -
43A ARG* 1.3 79.4 + - - +
45A VAL* 1.3 59.1 + - - +
46A GLU 3.8 0.2 - - - -
47A HIS* 3.4 16.2 - - - -
181A ARG* 3.8 39.1 + - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 3.5 24.9 - - - +
13A ALA* 4.3 11.4 - - + -
18A SER* 3.9 11.0 - - - +
21A THR* 4.5 14.1 - - + +
22A ASP* 6.1 0.2 - - - +
33A VAL* 5.0 1.8 - - + -
42A LYS 3.7 11.4 - - - +
44A ASN* 1.3 81.2 - - - +
46A GLU* 1.3 66.2 + - - +
47A HIS* 3.2 11.7 - - - -
48A TRP* 3.1 21.7 + - + +
49A ILE* 3.9 5.0 + - + +
54A PHE* 4.1 22.1 - - + -
56A LEU* 4.3 24.9 - - + -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 3.1 14.6 + - + +
43A ARG* 3.5 37.7 + - - +
44A ASN 3.8 0.2 - - - -
45A VAL* 1.3 77.0 - - - +
47A HIS* 1.3 67.6 + - + +
48A TRP 3.2 1.0 + - - -
49A ILE* 3.3 33.2 + - + +
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP* 2.9 24.9 + - - -
43A ARG 4.9 1.4 + - - -
44A ASN 3.4 25.3 - - - -
45A VAL* 4.0 7.6 - - - -
46A GLU* 1.3 85.4 + - + +
48A TRP* 1.3 93.7 + + - +
49A ILE 4.8 2.0 - - - +
181A ARG* 3.6 18.0 + - - -
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Residues in contact with TRP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 3.9 18.4 - - + +
22A ASP* 2.8 41.8 + - + +
25A MSE 3.7 42.8 - - + -
26A MSE 4.0 28.5 - - + -
45A VAL* 3.1 13.2 + - - +
47A HIS* 1.3 105.9 - + - +
49A ILE* 1.3 64.4 + - - +
50A GLY 3.2 0.5 + - - -
51A HIS* 3.0 47.1 + + + +
54A PHE* 3.4 29.1 - - + -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 4.0 28.5 - - + -
45A VAL 4.1 1.8 - - - +
46A GLU* 3.3 34.7 + - + +
47A HIS 4.8 1.9 - - - +
48A TRP* 1.3 76.0 - - - +
50A GLY* 1.3 61.6 + - - +
51A HIS 3.9 0.2 + - - -
54A PHE* 4.1 21.1 - - + -
56A LEU* 4.3 12.1 - - + -
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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