Contacts of the helix formed by residues 1040 - 1047 (chain A) in PDB entry 1OBO
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 GLU1040 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A PHE* 5.0 0.3 - - - -
1038A GLN 4.7 5.2 - - - +
1039A ALA* 1.3 89.0 - - - +
1041A VAL* 1.3 69.0 + - + +
1042A THR* 3.8 16.8 - - + +
1043A ASP* 2.8 32.3 + - - +
1044A LEU* 4.2 1.9 + - - +
1069A LEU* 4.5 2.9 - - - -
1072A GLU* 5.3 4.2 - - - +
2165B SER 5.4 2.9 - - - +
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Residues in contact with VAL1041 (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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1040A GLU* 1.3 73.4 + - + +
1042A THR* 1.3 73.2 + - + +
1044A LEU* 3.2 35.9 + - + +
1069A LEU* 4.0 18.8 - - + +
1072A GLU* 3.5 51.6 + - + +
1073A LEU* 4.2 9.0 - - + -
1075A ASP* 4.6 8.1 - - + -
1076A VAL* 3.3 27.9 - - + +
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Residues in contact with THR1042 (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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1040A GLU* 3.8 14.1 - - + +
1041A VAL* 1.3 84.0 - - + +
1043A ASP* 1.3 66.1 + - - +
1044A LEU 3.0 2.7 - - - -
1045A ASN* 3.0 36.7 + - - +
1046A ASP* 4.2 4.3 + - - +
1075A ASP* 5.6 3.6 - - + +
1076A VAL* 4.7 2.7 - - + -
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Residues in contact with ASP1043 (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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1007A PHE* 3.7 25.6 - - + -
1034A HIS* 4.9 12.1 + - + -
1038A GLN 4.7 0.7 - - - +
1039A ALA* 3.4 10.6 - - - +
1040A GLU* 2.8 41.9 + - - +
1042A THR* 1.3 82.0 + - - +
1044A LEU* 1.3 61.4 + - - +
1045A ASN 3.0 0.2 - - - -
1046A ASP* 3.1 33.1 + - - +
1047A TYR* 3.7 3.8 - - - -
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Residues in contact with LEU1044 (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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1007A PHE* 3.6 46.4 - - + -
1040A GLU 5.0 0.2 - - - +
1041A VAL* 3.4 32.8 - - + +
1042A THR 3.0 0.4 - - - -
1043A ASP* 1.3 78.3 - - - +
1045A ASN* 1.3 60.0 + - - +
1046A ASP 3.2 0.9 + - - -
1047A TYR 3.6 16.0 + - - +
1050A LEU* 4.0 19.4 - - + +
1052A ILE* 4.6 8.7 - - + -
1066A TRP* 4.9 9.6 - - + -
1069A LEU* 6.0 3.4 - - + -
1073A LEU* 4.0 9.0 - - + -
1076A VAL* 4.6 4.0 - - + -
1078A PHE* 3.6 34.8 - - + -
1081A LYS* 3.7 7.3 - - - -
1109A ILE* 5.9 0.2 - - + -
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Residues in contact with ASN1045 (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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1042A THR* 3.0 33.0 + - - +
1044A LEU* 1.3 78.4 - - - +
1046A ASP* 1.3 60.4 + - - +
1047A TYR 3.2 5.1 + - - -
1048A GLN* 5.0 1.0 - - - +
1075A ASP 5.4 1.9 - - - +
1076A VAL* 3.4 31.0 - - - +
1077A ASP 4.5 9.7 + - - +
1081A LYS* 3.5 18.1 + - - +
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Residues in contact with ASP1046 (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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1001A ALA* 3.9 18.8 - - + +
1002A LYS 4.8 0.7 - - - +
1034A HIS* 5.9 1.6 - - - -
1042A THR 4.3 3.9 - - - +
1043A ASP* 3.1 31.6 + - - +
1045A ASN* 1.3 80.3 - - - +
1047A TYR* 1.3 76.2 + - + +
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Residues in contact with TYR1047 (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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1001A ALA* 3.8 18.9 - - + +
1002A LYS 3.2 31.0 - - - -
1003A LYS 4.0 2.0 - - - +
1004A ILE 3.6 5.6 - - - -
1005A GLY* 3.3 31.0 - - - -
1007A PHE* 3.9 9.2 - + - -
1032A THR* 3.5 14.5 + - - +
1034A HIS* 2.6 37.0 + + - -
1043A ASP 3.7 19.3 - - - -
1044A LEU 3.6 1.8 + - - +
1045A ASN 3.2 2.0 - - - -
1046A ASP* 1.3 87.1 - - + +
1048A GLN* 1.3 61.2 + - - +
1049A TYR 3.4 15.7 - - - +
1050A LEU* 3.8 9.3 - - + +
1081A LYS* 2.6 36.6 + - - +
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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