Contacts of the helix formed by residues 1046 - 1054 (chain A) in PDB entry 1ATZ
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 ASP1046 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1044A SER* 3.1 19.8 + - - +
1045A VAL* 1.3 82.3 + - - +
1047A ALA* 1.3 62.0 + - - +
1049A ALA* 3.4 3.3 + - - +
1050A ASP* 3.0 23.4 + - - +
1075A ILE* 3.9 33.3 - - + +
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Residues in contact with ALA1047 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1044A SER* 4.9 5.8 + - - +
1045A VAL 3.4 0.4 - - - -
1046A ASP* 1.3 77.6 - - - +
1048A ALA* 1.3 59.2 + - - +
1050A ASP* 3.1 8.0 + - - +
1051A ALA* 2.9 27.1 + - - +
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Residues in contact with ALA1048 (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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1008A GLY* 3.1 33.4 - - - +
1011A LEU* 3.9 14.3 - - + +
1012A GLY* 3.4 20.0 - - - +
1015A VAL* 4.3 1.6 - - - +
1044A SER 5.4 0.6 + - - -
1045A VAL 3.6 6.0 + - - +
1046A ASP 3.4 0.2 - - - -
1047A ALA* 1.3 76.0 - - - +
1049A ALA* 1.3 60.3 + - - +
1051A ALA* 3.5 8.9 - - - +
1052A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA1049 (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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1011A LEU* 3.8 10.7 - - + +
1045A VAL 3.1 18.8 + - - +
1046A ASP 3.6 5.6 - - - +
1048A ALA* 1.3 75.8 - - - +
1050A ASP* 1.3 61.9 + - - +
1052A ALA* 3.3 5.8 + - - +
1053A ARG* 3.1 19.8 + - - +
1075A ILE* 3.4 34.8 - - + +
1076A LEU* 4.1 11.5 - - - +
1078A GLY* 5.1 8.0 - - - +
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Residues in contact with ASP1050 (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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1046A ASP 3.0 13.6 + - - +
1047A ALA* 3.1 10.1 + - - +
1049A ALA* 1.3 75.4 - - - +
1051A ALA* 1.3 60.0 + - - +
1053A ARG* 3.0 39.0 + - - +
1054A SER* 2.9 33.8 + - - -
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Residues in contact with ALA1051 (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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1012A GLY* 5.6 3.4 - - - -
1015A VAL* 4.0 11.2 - - + -
1047A ALA 2.9 13.2 + - - +
1048A ALA* 3.1 13.4 + - - +
1050A ASP* 1.3 73.5 + - - +
1052A ALA* 1.3 66.4 + - - +
1054A SER* 3.5 7.4 + - - -
1055A ASN* 2.8 38.8 + - - +
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Residues in contact with ALA1052 (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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1011A LEU* 4.8 1.1 - - + -
1015A VAL* 3.6 21.5 - - + +
1048A ALA 2.9 12.5 + - - +
1049A ALA* 3.4 11.7 - - - +
1050A ASP 3.2 0.2 - - - -
1051A ALA* 1.3 76.7 - - - +
1053A ARG* 1.3 63.3 + - - +
1055A ASN 3.2 6.6 + - - -
1057A VAL* 2.9 34.8 + - + +
1059A VAL* 3.7 30.3 - - + -
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Residues in contact with ARG1053 (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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1049A ALA 3.1 9.2 + - - +
1050A ASP* 3.0 39.4 + - - +
1052A ALA* 1.3 79.1 - - - +
1054A SER* 1.3 84.1 + - - +
1056A ARG* 3.1 13.7 + - - -
1057A VAL 4.3 4.2 + - - +
1079A PRO* 3.8 44.4 - - + +
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Residues in contact with SER1054 (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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1050A ASP* 2.9 23.3 + - - -
1051A ALA* 3.5 11.1 + - - -
1053A ARG* 1.3 95.6 - - - +
1055A ASN* 1.3 64.2 + - - +
1056A ARG* 3.4 1.7 + - - +
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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