Contacts of the helix formed by residues 21 - 30 (chain A) in PDB entry 4A8W
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 ASN 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 2.9 21.8 + - - +
20A ASN* 1.3 73.9 - - - +
22A ILE* 1.3 65.6 + - - +
23A LYS* 3.2 9.1 + - - +
24A ALA* 2.8 31.7 + - - +
25A GLN* 3.0 24.9 + - - +
155A TYR* 3.1 29.7 + - - +
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Residues in contact with ILE 22 (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 ASN* 1.3 73.4 - - - +
23A LYS* 1.3 58.2 + - + +
25A GLN* 3.4 5.9 + - + +
26A GLN* 2.8 57.0 + - + +
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Residues in contact with LYS 23 (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 ASN* 3.2 7.7 + - - +
22A ILE* 1.3 77.1 - - + +
24A ALA* 1.4 58.3 + - - +
26A GLN* 3.5 15.8 + - - +
27A ALA* 3.0 28.1 + - - +
155A TYR 4.6 0.4 - - - +
156A PHE* 3.2 26.4 + - + +
157A SER* 4.5 1.8 - - - +
158A ASN* 3.1 42.0 + - - +
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Residues in contact with ALA 24 (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 PHE* 3.4 14.2 - - + -
19A ALA 3.5 21.1 - - - +
21A ASN* 2.8 20.6 + - - +
23A LYS* 1.4 72.5 - - - +
25A GLN* 1.3 61.7 + - - +
27A ALA* 3.2 2.4 + - - +
28A SER 3.1 18.0 + - - -
154A PRO 3.3 26.2 - - - +
155A TYR 4.0 3.1 - - - +
156A PHE* 3.7 17.4 - - + +
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Residues in contact with GLN 25 (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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15A GLN* 4.4 19.1 + - - +
18A PHE* 3.4 19.4 - - - +
19A ALA 3.1 19.3 - - - +
20A ASN* 4.6 7.9 - - - +
21A ASN 3.0 25.1 + - - +
22A ILE* 3.9 5.6 - - + +
24A ALA* 1.3 72.9 - - - +
26A GLN* 1.4 62.6 + - + +
28A SER* 2.6 29.1 + - - -
29A LYS* 3.3 33.0 + - - +
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Residues in contact with GLN 26 (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 ILE* 2.8 44.6 + - + +
23A LYS* 3.7 19.0 - - - +
25A GLN* 1.4 71.6 - - - +
27A ALA* 1.4 53.8 + - - +
29A LYS* 3.4 6.4 + - - +
30A ARG* 2.8 69.4 + - - +
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Residues in contact with ALA 27 (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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23A LYS 3.0 14.5 + - - +
24A ALA 3.2 8.9 + - - +
26A GLN* 1.4 76.9 - - - +
28A SER* 1.3 63.1 + - - +
29A LYS 3.5 0.2 + - - -
30A ARG* 3.7 12.4 + - - +
156A PHE* 3.6 37.2 - - + -
200A TYR* 2.7 32.2 + - + +
366A TYR* 4.7 0.5 - - - -
368A GLY* 5.7 1.4 - - - -
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Residues in contact with SER 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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9A LEU* 3.5 13.8 - - - +
15A GLN* 5.4 0.7 + - - -
18A PHE* 3.5 48.4 - - - -
24A ALA 3.1 6.5 + - - -
25A GLN* 2.6 29.4 + - - -
27A ALA* 1.3 77.9 - - - +
29A LYS* 1.3 61.5 + - - +
366A TYR* 2.7 23.3 + - - -
368A GLY* 5.7 0.2 - - - -
376A HIS* 3.1 12.0 - - - -
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Residues in contact with LYS 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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9A LEU* 4.0 13.2 - - + -
25A GLN* 3.3 40.9 + - - +
26A GLN* 4.2 4.5 - - - +
28A SER* 1.3 85.9 + - - +
30A ARG* 1.4 66.2 + - - +
31A SER* 3.1 5.5 + - - -
376A HIS* 3.2 15.1 + - - -
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Residues in contact with ARG 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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26A GLN* 2.8 62.5 + - - +
27A ALA* 3.7 12.2 + - - +
28A SER 3.6 2.4 - - - -
29A LYS* 1.4 67.0 - - - +
31A SER* 1.3 67.8 + - - +
33A LYS* 5.1 19.5 - - + +
200A TYR* 4.6 6.7 - - - +
368A GLY* 4.7 2.9 - - - -
369A ALA* 3.8 8.3 - - - +
376A HIS* 2.8 21.5 + - - -
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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