Contacts of the helix formed by residues 27 - 35 (chain A) in PDB entry 1B06
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 LYS 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.1 33.2 - - + +
19A ASP* 3.6 21.1 - - + +
22A GLU* 2.9 31.9 + - - +
25A ILE 3.8 0.4 + - - -
26A SER* 1.3 69.8 - - - +
28A ASP* 1.3 78.6 + - - +
30A ILE* 3.8 0.6 - - - +
31A ASP* 2.9 33.3 + - - +
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Residues in contact with ASP 28 (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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26A SER* 3.1 12.3 + - - +
27A LYS* 1.3 98.9 + - - +
29A ILE* 1.3 60.6 + - - +
31A ASP* 4.0 4.3 - - - +
32A VAL* 3.4 21.8 + - - +
178A LEU* 4.0 18.3 - - + +
181B LYS* 5.1 6.9 + - - +
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Residues in contact with ILE 29 (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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25A ILE* 3.8 15.3 - - + -
26A SER* 3.1 14.4 + - - +
28A ASP* 1.3 77.2 - - - +
30A ILE* 1.3 61.8 + - + +
31A ASP 3.3 0.2 + - - -
32A VAL* 3.4 7.5 - - - +
33A HIS* 2.8 41.7 + - - +
174A HIS 4.0 15.7 - - - +
175A ALA 3.6 17.9 - - - +
176A TYR* 4.0 18.2 - - - -
178A LEU* 3.8 22.4 - - + +
179A GLN* 3.6 41.5 - - + +
180A TYR* 5.3 0.9 - - + -
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Residues in contact with ILE 30 (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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14A LEU* 3.8 23.1 - - + -
16A TYR* 5.2 3.8 - - + -
17A LYS 5.2 0.4 - - - +
18A VAL* 3.3 37.2 - - + +
21A LEU* 3.8 24.9 - - + -
25A ILE* 3.7 27.8 - - + +
26A SER 3.2 13.6 + - - +
27A LYS 3.9 0.7 - - - +
29A ILE* 1.3 77.6 - - + +
31A ASP* 1.3 64.7 + - - +
33A HIS* 3.7 5.1 - - - +
34A TYR* 2.9 30.0 + - + +
87A TYR* 6.0 0.7 - - + +
88A TRP* 4.2 18.8 - - + -
91A MET* 5.0 0.7 - - + -
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Residues in contact with ASP 31 (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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18A VAL* 4.3 17.6 - - + +
27A LYS 2.9 18.2 + - - +
28A ASP* 4.0 6.5 - - - +
29A ILE 3.2 0.2 - - - -
30A ILE* 1.3 77.8 - - - +
32A VAL* 1.3 60.6 + - - +
35A ASN* 2.8 60.8 + - - +
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Residues in contact with VAL 32 (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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28A ASP 3.4 13.0 + - - +
29A ILE* 3.4 12.8 - - - +
31A ASP* 1.3 80.1 - - - +
33A HIS* 1.3 64.0 + - - +
35A ASN* 5.1 0.7 - - - -
36A GLY* 2.8 32.4 + - - +
37A HIS* 3.0 5.1 + - + -
174A HIS 5.6 1.8 - - - +
178A LEU* 4.7 9.0 - - + -
177B TYR* 3.7 23.8 - - + +
181B LYS* 4.9 13.9 - - + +
182B ASN* 3.4 36.1 - - + +
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Residues in contact with HIS 33 (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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29A ILE* 2.8 29.1 + - + +
30A ILE* 3.7 6.0 - - - +
32A VAL* 1.3 77.7 - - + +
34A TYR* 1.3 58.1 + - - +
37A HIS* 3.4 11.6 - - + +
38A HIS* 3.1 25.3 + - - +
84A HIS* 3.1 13.3 + + - -
87A TYR* 3.6 23.1 + + - -
88A TRP* 3.5 16.1 - + + -
170A ASP* 2.9 15.8 + - - -
174A HIS* 3.0 22.6 + + + +
175A ALA* 3.8 17.9 - - + -
322A FE 2.2 27.0 - - - -
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Residues in contact with TYR 34 (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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11A PHE* 3.3 45.6 - + - -
12A PRO 2.5 27.3 + - - -
13A GLN* 3.4 12.2 + - - +
14A LEU* 3.4 50.8 + - + -
18A VAL* 5.4 2.5 - - + -
30A ILE 2.9 18.7 + - - +
31A ASP 4.0 0.2 - - - +
33A HIS* 1.3 75.4 - - - +
35A ASN* 1.3 89.2 + - - +
38A HIS* 3.4 5.1 - + - +
39A LYS 3.4 12.1 + - - -
88A TRP* 3.8 28.9 - + + -
39F LYS* 6.3 0.2 - - - -
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Residues in contact with ASN 35 (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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11A PHE* 4.6 3.8 - - - -
18A VAL* 5.0 4.8 - - - +
31A ASP* 2.8 47.1 + - - +
32A VAL* 5.1 0.4 - - - -
34A TYR* 1.3 99.2 - - - +
36A GLY* 1.3 57.5 + - - +
39A LYS* 3.2 33.6 + - - +
39F LYS* 3.8 25.8 - - - -
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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