Contacts of the helix formed by residues 21 - 26 (chain P) in PDB entry 2AIZ
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 SER 21 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15P GLN* 2.7 34.6 + - - -
16P THR* 4.4 3.9 - - - +
17P PHE* 4.7 1.1 - - - +
20P TYR* 1.3 76.0 - - - +
22P VAL* 1.3 57.6 + - - +
23P ALA* 3.2 6.3 - - - -
24P ASP* 2.6 33.0 + - - +
25P LEU* 2.9 12.8 + - - -
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Residues in contact with VAL 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P GLN* 4.9 8.1 - - + +
17P PHE* 4.1 16.3 - - + -
21P SER* 1.3 71.8 - - - +
23P ALA* 1.3 58.7 + - - +
24P ASP 2.9 0.5 + - - -
25P LEU* 3.1 11.7 + - - +
26P GLN* 2.9 57.3 + - + +
55P TYR* 4.0 38.1 - - + +
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Residues in contact with ALA 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P SER* 3.2 7.0 - - - -
22P VAL* 1.3 78.4 - - - +
24P ASP* 1.3 60.4 + - - +
26P GLN* 4.3 2.5 - - - -
27P GLN* 3.7 35.8 + - - +
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Residues in contact with ASP 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P TYR* 4.2 7.5 - - + +
21P SER* 2.6 27.4 + - - +
23P ALA* 1.3 73.2 - - - +
25P LEU* 1.3 59.7 + - - +
26P GLN 3.0 1.3 - - - -
28P ARG* 2.5 52.7 + - - +
29P TYR* 3.1 38.2 + - - -
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Residues in contact with LEU 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P PHE* 4.2 16.8 - - + +
20P TYR* 3.5 48.7 - - + +
21P SER 2.9 22.9 + - - +
22P VAL* 3.9 9.2 - - - +
24P ASP* 1.3 76.1 - - - +
26P GLN* 1.3 59.6 + - + +
29P TYR* 3.2 17.7 - - - +
30P ASN* 3.3 10.1 - - - +
48P ILE* 5.0 2.0 - - + -
51P ALA* 3.5 21.1 - - + +
52P HIS* 3.0 41.0 - - + +
55P TYR* 4.6 14.4 - - + -
134P TYR* 4.5 1.1 - - + -
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Residues in contact with GLN 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P VAL* 2.9 35.9 + - + +
23P ALA* 4.9 1.6 - - - +
25P LEU* 1.3 79.7 - - + +
27P GLN* 1.3 68.4 + - + +
30P ASN* 3.8 11.8 + - - +
55P TYR* 4.5 9.4 + - + +
134P TYR* 3.0 50.6 + - + +
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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