Contacts of the helix formed by residues 1007 - 1019 (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 ILE1007 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972A TYR* 3.7 24.2 - - + +
1005A SER* 3.9 8.3 - - - +
1006A GLN* 1.3 69.9 - - - +
1008A GLY* 1.3 67.1 + - - +
1010A ALA* 3.5 4.4 - - - +
1011A LEU* 2.9 23.0 + - - +
1035A ILE* 3.5 27.1 - - + -
1037A VAL* 3.7 19.7 - - + -
1039A ASP 3.6 24.2 - - - +
1041A SER* 3.1 31.3 + - - +
1045A VAL* 4.0 6.5 - - + -
1072A GLN* 4.6 2.9 - - - +
1076A LEU* 4.1 17.7 - - + -
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Residues in contact with GLY1008 (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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1007A ILE* 1.3 72.5 - - - +
1009A ASP* 1.3 62.9 + - - +
1011A LEU* 4.9 0.2 - - - -
1012A GLY* 2.9 19.6 + - - -
1043A ASP* 2.8 17.9 + - - -
1044A SER 3.6 19.5 - - - -
1045A VAL* 3.6 16.6 - - - +
1048A ALA* 3.1 16.5 - - - +
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Residues in contact with ASP1009 (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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976A THR* 4.6 1.6 - - - -
1006A GLN* 3.7 18.8 + - + +
1008A GLY* 1.3 75.8 - - - +
1010A ALA* 1.3 57.4 + - - +
1012A GLY* 3.3 2.0 + - - +
1013A PHE* 2.9 29.5 + - - +
1016A ARG* 4.9 2.4 + - - -
1043A ASP* 2.9 23.1 + - - +
1044A SER 5.7 0.2 - - - +
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Residues in contact with ALA1010 (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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932A LEU* 3.8 8.5 - - + +
972A TYR* 3.4 41.1 - - + -
976A THR* 3.3 16.9 + - - +
1006A GLN 3.1 19.8 + - - +
1007A ILE* 3.5 5.8 - - - +
1008A GLY 3.2 0.2 - - - -
1009A ASP* 1.3 74.2 - - - +
1011A LEU* 1.3 65.5 + - - +
1013A PHE* 3.2 4.5 + - - +
1014A ALA* 3.0 21.5 + - - +
1035A ILE* 5.2 0.2 - - + -
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Residues in contact with LEU1011 (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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932A LEU* 4.1 6.8 - - - +
1007A ILE 2.9 17.3 + - - +
1008A GLY 3.8 3.1 - - - +
1010A ALA* 1.3 75.2 - - - +
1012A GLY* 1.3 57.5 + - - +
1014A ALA* 3.1 1.8 + - + -
1015A VAL* 2.8 38.0 + - + +
1033A VAL* 4.4 22.4 - - + -
1035A ILE* 4.3 11.4 - - + -
1048A ALA* 3.9 9.9 - - + +
1049A ALA* 3.8 28.0 - - + +
1059A VAL* 4.1 32.1 - - + -
1076A LEU* 3.7 28.5 - - + +
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Residues in contact with GLY1012 (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 2.9 15.1 + - - -
1009A ASP* 3.7 4.0 - - - -
1011A LEU* 1.3 76.3 - - - +
1013A PHE* 1.3 62.1 + - - +
1015A VAL* 3.3 8.0 + - - +
1016A ARG* 3.1 38.1 + - - +
1048A ALA* 3.4 13.6 - - - +
1051A ALA* 5.6 2.9 - - - -
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Residues in contact with PHE1013 (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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970A LEU* 3.9 12.8 - - + -
976A THR* 3.5 44.2 - - + +
977A THR* 5.2 0.2 - - - -
978A ILE* 3.8 37.5 - - + -
1009A ASP 2.9 14.1 + - - +
1010A ALA 3.4 8.7 - - - +
1012A GLY* 1.3 75.4 - - - +
1014A ALA* 1.3 63.6 + - - +
1016A ARG* 3.2 32.1 + - - +
1017A TYR* 2.9 24.4 + + + +
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Residues in contact with ALA1014 (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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930A ILE* 3.4 27.1 - - + +
932A LEU* 4.2 9.0 - - + -
970A LEU* 4.3 6.3 - - + -
1010A ALA 3.0 13.6 + - - +
1011A LEU* 3.1 8.0 + - - +
1013A PHE* 1.3 80.0 - - - +
1015A VAL* 1.3 63.7 + - - +
1017A TYR* 3.1 3.8 + - - -
1018A LEU* 2.9 22.5 + - - +
1033A VAL* 4.0 24.7 - - + -
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Residues in contact with VAL1015 (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* 2.8 28.7 + - + +
1012A GLY* 3.6 9.6 - - - +
1013A PHE 3.3 0.2 - - - -
1014A ALA* 1.3 75.9 - - - +
1016A ARG* 1.3 59.1 + - + +
1018A LEU* 3.2 8.7 + - - +
1019A THR* 2.8 33.1 + - - +
1033A VAL* 5.3 0.2 - - + -
1048A ALA 4.3 3.6 - - - +
1051A ALA* 3.7 26.2 - - + +
1052A ALA* 3.6 31.4 - - + +
1055A ASN* 3.8 22.7 - - + +
1057A VAL* 4.3 11.9 - - + -
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Residues in contact with ARG1016 (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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1009A ASP 4.9 1.8 + - - -
1012A GLY* 3.1 23.8 + - - +
1013A PHE* 3.2 43.1 + - - +
1015A VAL* 1.3 78.1 - - + +
1017A TYR* 1.3 59.4 + - - +
1019A THR* 4.3 2.0 - - - -
1020A SER* 2.8 49.6 + - - +
1022A MET* 3.6 10.6 - - + +
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Residues in contact with TYR1017 (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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930A ILE* 3.8 17.9 - - + -
968A SER* 3.9 11.9 - - - -
970A LEU* 4.1 9.4 - - + -
978A ILE* 3.5 38.0 - - + +
981A PRO* 3.3 14.7 - - - +
982A TRP* 3.0 76.3 + + - +
1013A PHE* 2.9 20.4 + + + +
1014A ALA* 3.1 8.9 + - - +
1016A ARG* 1.3 76.2 - - - +
1018A LEU* 1.3 60.9 + - - +
1022A MET* 3.2 39.1 - - + +
1023A HIS 5.2 1.4 + - - -
1025A ALA* 4.4 0.2 - - - +
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Residues in contact with LEU1018 (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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928A ASP* 3.5 24.5 - - + +
930A ILE* 3.5 12.6 - - + -
982A TRP* 3.5 25.8 - - + -
1014A ALA 2.9 13.6 + - - +
1015A VAL 3.6 3.8 - - - +
1017A TYR* 1.3 78.1 - - - +
1019A THR* 1.3 64.9 + - + +
1020A SER 4.0 0.2 - - - -
1022A MET* 5.5 0.2 - - - -
1025A ALA* 4.3 5.0 - - - +
1031A LYS* 2.8 46.2 + - + -
1032A ALA 3.6 11.2 - - - +
1033A VAL* 3.2 35.2 - - + -
1057A VAL* 3.7 16.8 - - + -
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Residues in contact with THR1019 (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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1015A VAL* 2.8 19.7 + - - +
1016A ARG* 4.3 1.6 - - - -
1018A LEU* 1.3 85.8 - - + +
1020A SER* 1.3 58.7 + - - +
1021A GLU* 3.3 10.7 + - - +
1031A LYS* 4.2 12.8 - - + +
1055A ASN* 3.5 45.9 + - - +
1057A VAL* 3.8 17.5 - - + -
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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