Contacts of the helix formed by residues 1045 - 1054 (chain H) in PDB entry 3AOI
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 ALA1045 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040H LEU* 3.2 24.8 + - + +
1041H GLU* 4.0 1.1 + - - -
1043H TYR* 3.1 1.8 - - - -
1044H GLY* 1.3 73.5 - - - +
1046H ALA* 1.3 67.9 + - - +
1048H THR* 3.6 15.9 - - - +
1049H LEU* 3.0 19.1 + - - +
758I GLU* 3.1 13.7 - - + -
762I GLN* 5.1 0.9 - - - -
763I MET* 3.6 30.3 - - + -
1472I ILE* 4.4 1.7 - - - +
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Residues in contact with ALA1046 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044H GLY 2.7 9.0 + - - -
1045H ALA* 1.3 75.2 - - - +
1047H HIS* 1.3 64.3 + - + +
1049H LEU* 3.3 3.3 - - - +
1050H GLN* 2.8 22.3 + - - +
758I GLU* 3.0 4.2 + - - +
1471I LEU* 3.3 22.7 - - + -
1472I ILE* 3.4 17.7 - - + +
1476I THR* 3.4 35.0 - - - +
1477I GLY 3.9 4.9 - - - +
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Residues in contact with HIS1047 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046H ALA* 1.3 82.4 - - + +
1048H THR* 1.3 59.3 + - - +
1049H LEU 3.0 2.0 - - - -
1050H GLN* 3.8 15.3 - - + +
1051H GLU* 2.6 38.4 + - + +
1078H GLU* 4.9 13.3 + - - -
1079H PRO* 6.0 4.5 - - + +
752I SER* 4.9 6.5 + - - -
754I PHE* 3.8 42.5 - + + +
755I ALA* 4.2 14.1 - - + +
758I GLU* 3.0 18.4 + - - +
1471I LEU* 3.4 33.6 - - + +
1476I THR* 4.7 1.0 - - + +
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Residues in contact with THR1048 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040H LEU* 3.9 12.3 - - + +
1045H ALA* 3.6 10.3 - - - -
1047H HIS* 1.3 72.6 - - - +
1049H LEU* 1.3 58.1 + - - +
1051H GLU* 3.7 6.8 - - - +
1052H MET* 3.5 25.4 + - + +
1056H LYS* 5.1 1.3 + - - +
701I LEU* 3.7 20.0 - - + -
750I PRO* 5.2 6.1 - - + -
755I ALA* 3.3 17.5 + - - +
758I GLU* 2.7 38.5 + - - +
759I ALA* 4.4 0.5 - - - +
763I MET* 3.5 25.3 - - + +
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Residues in contact with LEU1049 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032H PHE* 5.0 1.6 - - + -
1037H VAL* 3.2 47.1 - - + +
1040H LEU* 3.8 20.8 - - + +
1041H GLU* 4.5 13.0 - - + -
1045H ALA 3.0 18.3 + - - +
1046H ALA 3.0 2.5 + - - +
1047H HIS 3.0 0.2 - - - -
1048H THR* 1.3 75.2 - - - +
1050H GLN* 1.3 66.5 + - - +
1051H GLU 3.2 1.3 - - - -
1052H MET* 3.1 9.6 + - + +
1053H LEU* 3.0 42.2 + - + +
1466I VAL* 5.2 6.5 - - + -
1472I ILE* 3.3 33.4 - - + -
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Residues in contact with GLN1050 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046H ALA 2.8 18.4 + - - +
1047H HIS* 3.7 17.3 - - + +
1049H LEU* 1.3 72.5 - - - +
1051H GLU* 1.3 55.7 + - - +
1053H LEU* 3.0 10.2 + - - -
1054H THR* 2.7 47.2 + - + +
1079H PRO* 2.9 39.8 - - + +
1469I GLY 3.7 11.0 + - - +
1470I ARG* 3.4 8.1 + - - +
1471I LEU* 3.1 43.8 - - + +
1472I ILE* 5.6 0.7 - - + -
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Residues in contact with GLU1051 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047H HIS* 2.6 17.6 + - + +
1048H THR* 3.7 7.1 - - - +
1050H GLN* 1.3 74.8 - - - +
1052H MET* 1.3 59.2 + - - +
1054H THR* 3.3 7.5 + - - -
1055H LEU* 3.4 26.2 + - + -
1056H LYS* 3.0 41.5 + - - +
750I PRO* 3.3 10.0 - - - +
751I LEU* 2.7 35.1 + - + +
752I SER* 2.5 32.4 + - - -
755I ALA* 2.7 22.0 - - - +
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Residues in contact with MET1052 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032H PHE* 3.3 46.2 - - + -
1040H LEU* 4.8 2.0 - - + -
1048H THR* 3.5 18.5 + - + +
1049H LEU* 3.1 13.3 + - + +
1051H GLU* 1.3 80.4 - - - +
1053H LEU* 1.3 65.5 + - + +
1056H LYS* 3.5 22.8 - - - +
1057H SER* 3.9 14.4 - - - -
621I LYS* 4.9 3.3 + - - +
623I VAL* 2.7 60.2 - - + +
701I LEU* 5.5 2.2 - - + -
748I HIS* 4.2 15.7 - - + -
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Residues in contact with LEU1053 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032H PHE* 5.9 1.1 - - + -
1037H VAL* 4.8 12.6 - - + -
1049H LEU* 3.0 46.7 - - + +
1050H GLN* 3.0 8.3 + - - +
1052H MET* 1.3 83.8 - - + +
1054H THR* 1.3 68.4 + - + +
1057H SER* 4.1 6.4 + - - -
1058H ASP* 4.0 17.2 + - - +
1082H PRO* 5.2 2.6 - - - +
617I ASN 4.9 12.3 - - - +
620I GLY* 6.0 6.5 - - - -
621I LYS 6.4 0.2 - - - +
1466I VAL* 4.8 27.8 - - + +
1469I GLY* 5.4 8.7 - - - -
1470I ARG 5.7 3.6 - - - +
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Residues in contact with THR1054 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050H GLN* 2.7 39.0 + - + +
1051H GLU* 3.3 1.6 + - - -
1053H LEU* 1.3 87.1 - - + +
1055H LEU* 1.3 65.6 + - - +
1056H LYS 2.5 4.5 + - - -
1057H SER 2.5 30.3 + - - -
1058H ASP* 3.4 9.2 + - - +
1059H ASP* 4.0 19.4 + - - +
1063H ARG* 5.1 0.2 - - - +
1079H PRO* 4.3 9.7 - - + +
1080H SER 5.7 0.2 - - - -
1082H PRO* 3.4 33.2 - - + -
1469I GLY* 3.9 11.2 - - - +
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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