Contacts of the helix formed by residues 1066 - 1073 (chain O) in PDB entry 5X0X
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 GLU1066 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1063O PHE* 3.0 28.9 + - + +
1064O VAL* 3.3 15.6 - - - +
1065O PHE* 1.3 75.7 - - - +
1067O GLU* 1.3 59.9 + - - +
1068O VAL 3.0 3.1 - - - +
1069O GLU* 3.0 14.7 + - + +
1070O ASP* 2.9 31.3 + - - +
1076O ARG* 5.7 6.7 + - - -
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Residues in contact with GLU1067 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065O PHE* 2.7 33.0 - - - +
1066O GLU* 1.3 73.4 - - - +
1068O VAL* 1.3 57.2 + - - +
1070O ASP* 3.2 19.1 - - + +
1071O GLN* 2.9 31.1 + - - +
1346O TYR* 3.5 48.1 - - + +
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Residues in contact with VAL1068 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018O LEU* 4.3 24.9 - - + -
1023O TYR* 3.6 23.3 - - - +
1063O PHE* 3.5 29.6 - - + +
1065O PHE* 6.1 3.1 - - + -
1066O GLU 3.0 1.4 - - - +
1067O GLU* 1.3 75.5 - - - +
1069O GLU* 1.3 65.1 + - - +
1071O GLN* 2.9 35.9 + - - +
1072O ILE* 2.9 16.6 + - + +
1343O ALA* 5.9 3.4 - - + -
1346O TYR* 5.4 9.6 - - + -
1347O ASN* 5.0 3.6 - - - +
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Residues in contact with GLU1069 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063O PHE* 3.3 43.8 - - + +
1066O GLU* 3.0 17.5 + - + +
1068O VAL* 1.3 76.7 - - - +
1070O ASP* 1.3 66.4 + - - +
1072O ILE* 3.0 8.5 + - - +
1073O ASN* 2.3 71.7 + - - +
1074O PRO 4.5 2.1 - - - +
1076O ARG* 3.1 39.7 + - + -
1082O ILE* 4.6 11.2 - - + +
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Residues in contact with ASP1070 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066O GLU* 2.9 17.5 + - - +
1067O GLU* 3.2 28.4 + - - +
1069O GLU* 1.3 89.8 - - - +
1071O GLN* 1.3 65.3 + - - +
1072O ILE 3.2 2.3 + - - +
1073O ASN* 3.2 19.1 + - - +
1074O PRO* 3.9 17.8 - - + +
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Residues in contact with GLN1071 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018O LEU* 5.8 2.4 - - - +
1067O GLU 2.9 20.4 + - - +
1068O VAL* 2.9 30.1 + - + +
1070O ASP* 1.3 75.0 - - - +
1072O ILE* 1.3 62.7 + - + +
1339O GLU* 3.9 40.2 - - + +
1342O SER* 2.8 41.0 + - - +
1343O ALA* 3.7 4.7 - - - +
1346O TYR* 3.5 22.9 - - + -
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Residues in contact with ILE1072 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018O LEU* 5.3 6.7 - - + -
1063O PHE* 4.9 7.2 - - + -
1068O VAL* 2.9 20.7 + - + +
1069O GLU* 3.3 9.6 - - - +
1070O ASP 3.5 1.7 - - - +
1071O GLN* 1.3 82.1 - - + +
1073O ASN* 1.3 63.1 + - + +
1074O PRO* 4.4 2.1 - - - +
1079O ASN* 4.1 12.6 - - - +
1080O ASP 4.7 3.6 - - - +
1081O ASP* 3.5 32.8 - - + +
1082O ILE* 3.4 36.6 - - + -
1318O LEU* 5.7 0.4 - - + -
1339O GLU* 5.6 2.0 - - - +
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Residues in contact with ASN1073 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069O GLU* 2.3 61.1 + - - +
1070O ASP* 3.2 5.4 - - - -
1072O ILE* 1.3 80.4 - - + +
1074O PRO* 1.3 68.5 - - - +
1075O THR* 2.4 37.5 + - - +
1076O ARG 2.9 3.4 - - - +
1077O GLU* 2.8 36.7 + - - +
1079O ASN* 4.3 11.9 - - - +
1082O ILE* 4.4 3.6 - - + -
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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