Contacts of the helix formed by residues 56 - 66 (chain B) in PDB entry 1B3A
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 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B LYS* 1.3 73.2 - - - +
57B TRP* 1.3 64.5 + - - +
58B VAL 3.2 0.3 + - - -
59B ARG* 3.1 34.7 + - - +
60B GLU* 2.9 52.5 + - + +
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Residues in contact with TRP 57 (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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15B ILE* 3.7 31.9 + - + -
16B ALA 5.0 2.4 + - - -
17B ARG 4.0 2.1 - - - -
18B PRO* 3.5 48.2 - - + +
19B LEU* 3.8 12.1 - - + -
41B PHE* 3.5 34.1 - + - -
51B ALA* 4.1 2.9 - - + -
55B LYS* 3.9 27.8 - - + +
56B LYS* 1.3 78.3 - - - +
58B VAL* 1.3 71.6 + - + +
60B GLU* 3.6 15.0 + - - +
61B TYR* 2.9 67.4 + + + -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.8 33.2 - - + -
41B PHE* 4.0 9.3 - - + -
51B ALA* 3.8 11.4 - - + -
52B ASN 3.3 29.6 - - - +
53B PRO* 4.1 4.5 - - + +
55B LYS* 3.1 9.3 + - + +
57B TRP* 1.3 115.4 - - + +
59B ARG* 1.3 61.4 + - - +
61B TYR* 3.3 2.6 + - - +
62B ILE* 3.0 26.9 + - + +
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO 3.6 19.1 - - - +
54B GLU* 3.1 29.0 + - - +
55B LYS 3.1 4.0 + - - +
56B LYS* 3.1 46.5 - - - +
58B VAL* 1.3 74.0 - - - +
60B GLU* 1.3 55.3 + - + +
62B ILE* 3.3 9.5 + - + +
63B ASN* 2.8 44.8 + - - +
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Residues in contact with GLU 60 (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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56B LYS* 2.9 52.6 + - + +
57B TRP* 3.6 16.0 - - - +
59B ARG* 1.3 78.1 - - + +
61B TYR* 1.3 63.3 + - + +
63B ASN* 3.3 15.3 + - - +
64B SER* 2.9 27.2 + - - -
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Residues in contact with TYR 61 (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 PRO* 4.1 8.2 - - + +
19B LEU 2.6 30.5 + - - -
20B PRO* 4.3 0.2 - - - +
21B ARG* 3.3 38.5 + - + +
24B ILE* 3.4 29.2 - - + -
41B PHE* 3.8 12.6 - + + -
57B TRP* 2.9 49.1 + + + +
58B VAL 3.8 4.0 - - - +
60B GLU* 1.3 79.6 - - + +
62B ILE* 1.3 65.7 + - - +
64B SER* 2.8 22.9 + - - -
65B LEU* 2.9 15.6 + - + +
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Residues in contact with ILE 62 (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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27B TYR* 3.4 49.4 - - + +
29B TYR* 3.4 24.9 - - - +
39B VAL* 3.6 30.3 - - + -
41B PHE* 4.5 3.4 - - + -
53B PRO* 5.9 0.9 - - + +
58B VAL* 3.0 23.9 + - + +
59B ARG* 3.7 9.2 - - + +
61B TYR* 1.3 76.5 - - - +
63B ASN* 1.3 66.1 + - - +
65B LEU* 3.1 4.3 + - - +
66B GLU* 2.9 28.3 + - + +
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Residues in contact with ASN 63 (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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59B ARG* 2.8 30.5 + - - +
60B GLU* 3.4 13.9 - - - +
62B ILE* 1.3 76.2 - - - +
64B SER* 1.3 62.8 + - - +
66B GLU* 3.2 9.0 + - - +
67B MET* 3.0 33.2 + - + +
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Residues in contact with SER 64 (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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21B ARG* 2.8 34.0 + - - -
60B GLU 2.9 14.1 + - - -
61B TYR* 2.8 20.2 + - - -
63B ASN* 1.3 76.3 - - - +
65B LEU* 1.3 60.5 + - - +
67B MET* 3.2 15.7 + - - +
68B SER* 3.2 13.5 + - - +
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Residues in contact with LEU 65 (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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21B ARG* 3.4 30.5 - - - +
24B ILE* 4.1 17.5 - - + +
25B LYS 4.1 20.9 - - - +
26B GLU* 4.4 3.4 - - - -
27B TYR* 3.7 42.4 - - + +
41B PHE* 4.2 7.6 - - + -
61B TYR* 2.9 18.1 + - + +
62B ILE 3.1 3.8 + - - +
64B SER* 1.3 81.1 + - - +
66B GLU* 1.3 62.4 + - - +
67B MET 3.6 0.2 + - - -
68B SER* 3.7 13.6 + - - +
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Residues in contact with GLU 66 (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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27B TYR* 3.0 31.7 + - + +
62B ILE* 2.9 23.5 + - + +
63B ASN* 3.6 8.1 - - - +
65B LEU* 1.3 78.7 - - - +
67B MET* 1.3 62.4 + - + +
68B SER* 3.4 5.1 + - - -
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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