Contacts of the helix formed by residues 27 - 35 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 3.1 34.6 - - + +
19B ASP* 3.7 19.7 - - + +
22B GLU* 3.0 32.5 + - - +
25B ILE 3.7 0.6 + - - -
26B SER* 1.3 71.0 - - - +
28B ASP* 1.3 73.7 + - - +
29B ILE 3.2 0.2 - - - -
30B ILE* 3.8 0.4 - - - -
31B ASP* 2.9 32.6 + - - +
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Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LYS* 4.9 8.4 + - - +
26B SER* 3.0 13.5 + - - +
27B LYS* 1.3 102.0 + - - +
29B ILE* 1.3 60.1 + - - +
31B ASP* 4.0 4.1 - - - +
32B VAL* 3.5 21.8 + - - +
178B LEU* 4.1 19.9 - - + +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.9 14.1 - - + -
26B SER* 3.0 11.2 + - - +
28B ASP* 1.3 78.4 - - - +
30B ILE* 1.3 61.4 + - - +
31B ASP 3.3 0.3 + - - -
32B VAL* 3.4 7.6 - - - +
33B HIS* 2.8 42.3 + - - +
174B HIS 4.0 15.5 - - - +
175B ALA 3.7 17.7 - - - +
176B TYR* 3.9 18.6 - - - +
178B LEU* 3.8 21.5 - - + +
179B GLN* 3.6 46.4 - - + +
180B TYR* 5.3 0.7 - - + -
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Residues in contact with ILE 30 (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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14B LEU* 3.8 29.6 - - + -
16B TYR* 5.3 4.0 - - + -
17B LYS 5.2 0.2 - - - +
18B VAL* 3.4 32.5 - - + +
21B LEU* 3.9 23.8 - - + -
25B ILE* 3.6 28.3 - - + +
26B SER 3.2 10.4 + - - +
27B LYS 4.0 0.7 - - - +
29B ILE* 1.3 79.1 - - + +
31B ASP* 1.3 58.4 + - - +
33B HIS* 3.8 4.9 - - - +
34B TYR* 2.9 31.7 + - + +
87B TYR* 5.9 0.7 - - + -
88B TRP* 4.2 20.2 - - + -
91B MET* 5.1 0.7 - - + -
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Residues in contact with ASP 31 (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 VAL* 4.2 19.4 - - + +
27B LYS 2.9 18.6 + - - +
28B ASP* 4.0 6.1 - - - +
30B ILE* 1.3 76.7 - - - +
32B VAL* 1.3 58.9 + - - +
35B ASN* 2.8 66.6 + - - +
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Residues in contact with VAL 32 (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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177A TYR* 3.7 27.4 - - + +
181A LYS* 4.8 12.3 - - + +
182A ASN* 3.6 34.8 - - + +
28B ASP 3.5 12.7 + - - +
29B ILE* 3.4 13.0 - - - +
31B ASP* 1.3 78.9 - - - +
33B HIS* 1.3 62.2 + - + +
35B ASN* 5.0 0.9 - - - -
36B GLY* 2.8 32.7 + - - +
37B HIS* 3.0 6.2 + - - -
174B HIS 5.7 1.6 - - - +
178B LEU* 4.9 5.4 - - + -
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Residues in contact with HIS 33 (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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29B ILE* 2.8 28.2 + - + +
30B ILE* 3.8 6.2 - - - +
32B VAL* 1.3 78.3 - - + +
34B TYR* 1.3 58.3 + - - +
37B HIS* 3.4 11.2 - - + +
38B HIS* 3.1 25.1 + - - +
84B HIS* 2.9 14.1 + + - -
87B TYR* 3.6 23.7 + + - -
88B TRP* 3.6 14.0 - + + -
170B ASP* 2.9 16.5 + - - -
174B HIS* 3.0 22.6 + + + +
175B ALA* 3.8 17.4 + - + -
323B FE 2.3 26.0 - - - -
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Residues in contact with TYR 34 (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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11B PHE* 3.3 37.9 - + - -
12B PRO 2.6 26.5 + - - -
13B GLN* 3.4 11.7 - - - +
14B LEU* 3.5 49.2 + - + -
18B VAL* 5.5 2.2 - - + -
30B ILE 2.9 19.7 + - - +
31B ASP 4.1 0.4 - - - +
33B HIS* 1.3 74.6 - - - +
35B ASN* 1.3 90.5 + - - +
36B GLY 3.2 1.2 + - - -
38B HIS* 3.4 4.3 - + - +
39B LYS 3.3 21.1 + - - -
88B TRP* 3.8 27.3 - + + -
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Residues in contact with ASN 35 (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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11B PHE* 4.6 5.7 - - - -
18B VAL* 5.0 4.4 - - - +
31B ASP* 2.8 45.1 + - - +
32B VAL* 5.0 0.4 - - - -
34B TYR* 1.3 100.2 - - - +
36B GLY* 1.3 58.4 + - - +
39B LYS* 3.3 35.4 + - - +
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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