Contacts of the helix formed by residues 1007 - 1019 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972B TYR* 3.9 20.9 - - + +
1005B SER* 3.8 9.9 - - - +
1006B GLN* 1.3 69.5 - - - +
1008B GLY* 1.3 65.4 + - - +
1010B ALA* 3.3 4.7 + - - +
1011B LEU* 2.9 23.2 + - - +
1035B ILE* 3.6 26.5 - - + -
1037B VAL* 3.7 19.3 - - + -
1039B ASP 3.6 24.0 - - - +
1040B VAL 4.4 0.4 - - - -
1041B SER* 3.1 33.8 + - - +
1045B VAL* 3.9 6.3 - - + -
1072B GLN* 4.6 4.0 - - + +
1076B LEU* 4.1 18.2 - - + -
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Residues in contact with GLY1008 (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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1007B ILE* 1.3 72.8 - - - +
1009B ASP* 1.3 61.7 + - - +
1011B LEU* 5.0 0.2 - - - -
1012B GLY* 2.9 20.6 + - - -
1041B SER* 3.7 1.4 + - - -
1043B ASP* 2.8 21.0 + - - -
1044B SER 3.7 17.0 - - - -
1045B VAL* 3.7 13.9 - - - +
1048B ALA* 3.1 16.9 - - - +
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Residues in contact with ASP1009 (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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974B SER 5.1 0.7 - - - +
975B ILE* 4.8 5.5 - - - -
976B THR* 4.1 17.5 + - - -
1006B GLN* 3.9 18.9 - - + +
1008B GLY* 1.3 74.3 - - - +
1010B ALA* 1.3 57.5 + - - +
1012B GLY* 3.4 1.7 + - - -
1013B PHE* 2.9 30.1 + - - +
1016B ARG* 4.9 8.3 + - - -
1043B ASP* 2.9 17.1 + - - +
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Residues in contact with ALA1010 (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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932B LEU* 3.9 8.7 - - + +
972B TYR* 3.4 29.8 - - + -
976B THR* 3.2 27.3 + - - +
1006B GLN 3.0 18.3 + - - +
1007B ILE* 3.6 5.6 - - - +
1008B GLY 3.2 0.2 - - - -
1009B ASP* 1.3 78.1 - - - +
1011B LEU* 1.3 58.5 + - - +
1013B PHE* 3.2 4.2 + - - +
1014B ALA* 3.0 26.7 + - - +
1035B ILE* 5.3 0.7 - - + -
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Residues in contact with LEU1011 (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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932B LEU* 4.1 6.6 - - - +
1007B ILE 2.9 17.5 + - - +
1010B ALA* 1.3 75.0 - - - +
1012B GLY* 1.3 57.0 + - - +
1014B ALA* 3.1 2.5 + - + +
1015B VAL* 2.8 42.2 + - + +
1033B VAL* 4.4 22.7 - - + -
1035B ILE* 4.4 11.4 - - + -
1048B ALA* 3.9 12.1 - - + +
1049B ALA* 3.8 27.6 - - - +
1059B VAL* 4.1 27.4 - - + -
1076B LEU* 3.6 35.0 - - + +
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Residues in contact with GLY1012 (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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1008B GLY 2.9 16.5 + - - -
1009B ASP* 3.8 2.0 - - - -
1011B LEU* 1.3 75.9 - - - +
1013B PHE* 1.3 61.0 + - - +
1015B VAL* 3.4 7.0 + - - +
1016B ARG* 3.1 38.6 + - - +
1048B ALA* 3.5 13.8 - - - +
1051B ALA* 5.7 2.7 - - - -
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Residues in contact with PHE1013 (chain B).
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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970B LEU* 3.6 13.0 - - + -
976B THR* 3.5 44.0 - - + -
977B THR* 5.2 0.2 - - - -
978B ILE* 3.5 42.2 - - + -
1009B ASP* 2.9 19.0 + - - +
1010B ALA 3.4 5.2 - - - +
1012B GLY* 1.3 76.3 - - - +
1014B ALA* 1.3 55.7 + - - +
1016B ARG* 3.3 32.9 + - - +
1017B TYR* 2.9 29.1 + + + +
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Residues in contact with ALA1014 (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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930B ILE* 3.4 26.7 - - + +
932B LEU* 4.1 16.8 - - + -
970B LEU* 4.2 11.2 - - + -
1010B ALA 3.0 13.4 + - - +
1011B LEU* 3.5 7.4 - - - +
1013B PHE* 1.3 74.4 - - - +
1015B VAL* 1.3 65.8 + - - +
1017B TYR* 3.1 2.0 + - - -
1018B LEU* 2.9 22.6 + - - +
1033B VAL* 4.1 17.5 - - + -
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Residues in contact with VAL1015 (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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1011B LEU* 2.8 34.0 + - + +
1012B GLY* 3.7 7.0 - - - +
1014B ALA* 1.3 71.4 - - - +
1016B ARG* 1.3 63.2 + - + +
1018B LEU* 3.1 10.8 + - - +
1019B THR* 2.8 36.8 + - - +
1033B VAL* 5.3 0.2 - - + -
1048B ALA 4.3 3.8 - - - +
1051B ALA* 3.9 27.4 - - + +
1052B ALA* 3.7 33.4 - - + +
1055B ASN* 4.2 11.2 - - + +
1057B VAL* 4.4 10.5 - - + -
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Residues in contact with ARG1016 (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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1009B ASP* 4.9 8.1 + - - -
1012B GLY* 3.1 29.6 + - - +
1013B PHE* 3.4 43.7 + - - +
1015B VAL* 1.3 77.4 - - + +
1017B TYR* 1.3 59.1 + - - +
1019B THR* 4.3 1.3 - - - -
1020B SER* 2.9 49.7 + - - +
1022B MET* 3.7 8.5 - - + +
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Residues in contact with TYR1017 (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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930B ILE* 3.9 11.7 - - + -
968B SER* 3.3 24.9 - - - -
970B LEU* 4.1 7.4 - - + -
978B ILE* 3.6 32.9 - - + +
981B PRO* 3.2 14.6 - - - +
982B TRP* 3.0 70.6 + + - +
1013B PHE* 2.9 22.3 + + + +
1014B ALA* 3.5 9.4 - - - +
1016B ARG* 1.3 76.5 - - - +
1018B LEU* 1.3 59.1 + - - +
1022B MET* 3.2 49.0 - - + +
1023B HIS 4.4 3.7 + - - -
1025B ALA* 4.4 1.2 - - - +
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Residues in contact with LEU1018 (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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928B ASP* 3.4 26.2 - - + +
930B ILE* 3.5 12.3 - - + -
982B TRP* 3.5 24.0 - - + +
1014B ALA 2.9 10.0 + - - +
1015B VAL 3.6 6.5 - - - +
1017B TYR* 1.3 77.8 - - - +
1019B THR* 1.3 65.3 + - + +
1020B SER 4.0 0.4 - - - -
1025B ALA* 4.6 3.3 - - - +
1031B LYS* 2.8 48.2 + - + -
1032B ALA 3.6 10.5 - - - +
1033B VAL* 3.2 35.2 - - + -
1057B VAL* 3.8 18.6 - - + -
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Residues in contact with THR1019 (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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1015B VAL* 2.8 20.3 + - - +
1016B ARG* 4.3 1.4 - - - -
1018B LEU* 1.3 86.2 - - + +
1020B SER* 1.3 60.9 + - - +
1021B GLU 3.8 2.7 - - - -
1031B LYS* 4.2 12.1 - - + +
1055B ASN* 3.6 46.3 + - + +
1057B VAL* 3.9 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