Contacts of the helix formed by residues 1060 - 1071 (chain A) in PDB entry 1WUE
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 THR1060 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1050A ALA* 3.6 4.3 - - - -
1051A PHE 3.0 9.9 - - - -
1052A GLU 4.4 6.7 - - - -
1053A GLN* 3.8 3.8 - - - -
1054A PRO* 3.6 37.0 - - + -
1058A GLN 3.5 7.1 + - - +
1059A GLU* 1.3 77.7 - - - +
1061A LEU* 1.3 65.8 + - - +
1062A VAL* 3.9 2.2 + - - -
1063A THR* 2.7 34.6 + - - +
1064A GLU* 3.0 23.7 + - - +
2066B PHE* 4.5 5.7 - - - -
2067B ILE* 4.0 14.2 - - + +
2071B HIS* 4.6 2.5 - - - +
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Residues in contact with LEU1061 (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 VAL 5.3 0.2 - - - +
1012A ARG* 5.3 0.4 - - - +
1030A ALA* 3.4 42.0 - - + +
1031A PHE* 3.8 5.8 - - - +
1032A ASP* 3.7 22.4 - - - +
1048A LEU* 3.6 30.3 - - + +
1050A ALA* 3.4 20.0 - - - +
1051A PHE 2.9 10.8 + - - +
1052A GLU* 4.4 14.7 - - + +
1060A THR* 1.3 71.4 - - - +
1062A VAL* 1.3 60.4 + - + +
1064A GLU 3.6 0.2 + - - -
1065A ARG* 3.0 54.2 + - - +
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Residues in contact with VAL1062 (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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1052A GLU* 5.9 4.2 - - + +
1060A THR* 3.3 3.1 + - - +
1061A LEU* 1.3 79.7 - - + +
1063A THR* 1.3 64.3 + - + +
1065A ARG* 3.4 29.1 + - - +
1066A PHE* 3.2 20.0 + - + +
2066B PHE* 3.7 47.3 - - + -
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Residues in contact with THR1063 (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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1059A GLU* 4.8 1.0 - - - -
1060A THR* 2.7 37.0 + - - +
1062A VAL* 1.3 75.2 - - + +
1064A GLU* 1.3 70.5 + - - +
1066A PHE* 3.1 6.4 + - - +
1067A ILE* 3.0 25.2 + - - +
1097A HIS* 6.1 0.4 - - - -
2063B THR* 3.7 46.7 - - + +
2066B PHE* 3.8 19.3 - - + -
2067B ILE* 4.2 8.5 - - + +
2097B HIS* 4.9 5.1 + - - +
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Residues in contact with GLU1064 (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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1048A LEU* 3.7 26.5 - - + -
1050A ALA* 4.3 2.0 - - + -
1059A GLU* 3.5 30.8 - - + +
1060A THR 3.0 19.7 + - - +
1063A THR* 1.3 77.2 + - - +
1065A ARG* 1.3 59.8 + - - +
1067A ILE* 3.2 4.0 + - - +
1068A ILE* 2.9 34.8 + - - +
1097A HIS* 2.8 47.8 - - - +
1100A GLY* 2.8 30.8 + - - +
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Residues in contact with ARG1065 (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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1010A GLN* 3.6 38.9 + - - +
1032A ASP* 2.6 43.1 + - - +
1034A PHE* 5.5 3.8 - - + -
1048A LEU* 3.8 7.8 - - + +
1061A LEU* 3.0 41.3 + - - +
1062A VAL* 3.4 26.8 - - - +
1064A GLU* 1.3 75.9 - - - +
1066A PHE* 1.3 61.6 + - - +
1068A ILE* 3.6 7.6 - - - +
1069A GLN* 3.4 33.8 + - - +
1364A GLN* 6.1 0.9 - - - +
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Residues in contact with PHE1066 (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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1062A VAL* 3.2 9.9 + - + +
1063A THR* 3.1 11.5 + - - +
1065A ARG* 1.3 78.6 - - - +
1067A ILE* 1.3 66.0 + - + +
1068A ILE 3.3 0.2 + - - -
1069A GLN* 3.3 4.3 + - + +
1070A GLN* 2.9 72.1 + - + +
1071A HIS* 4.7 8.5 - - - -
2052B GLU 6.0 0.7 - - - -
2060B THR* 4.8 4.0 - - - -
2062B VAL* 3.8 44.2 - - + -
2063B THR* 3.9 19.1 - - + -
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Residues in contact with ILE1067 (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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1063A THR 3.0 14.1 + - - +
1064A GLU* 3.8 7.0 - - - +
1066A PHE* 1.3 77.7 - - + +
1068A ILE* 1.3 58.4 + - - +
1071A HIS* 2.8 55.4 + - + +
1072A LEU* 3.1 24.5 + - + -
1094A VAL* 4.7 5.2 - - + -
1097A HIS* 3.4 53.2 - - + +
1100A GLY* 6.2 0.2 - - - -
2054B PRO* 5.0 0.7 - - + -
2060B THR* 4.1 13.0 - - + +
2063B THR* 3.9 18.6 - - + -
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Residues in contact with ILE1068 (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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1034A PHE* 3.6 41.5 - - + -
1048A LEU* 4.0 11.7 - - + -
1064A GLU 2.9 20.6 + - - +
1065A ARG* 3.6 6.5 - - - +
1066A PHE 3.1 0.2 - - - -
1067A ILE* 1.3 77.4 - - - +
1069A GLN* 1.3 61.0 + - + +
1072A LEU* 4.0 13.5 - - + -
1073A ILE* 2.8 54.5 + - + +
1100A GLY* 3.6 33.9 - - - +
1103A ALA* 4.0 4.9 - - + -
1104A LEU* 4.0 8.5 - - + -
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Residues in contact with GLN1069 (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 THR* 4.7 1.2 - - - +
1034A PHE* 5.6 1.7 - - + -
1065A ARG* 3.4 24.4 + - - +
1066A PHE* 3.3 5.7 + - + +
1068A ILE* 1.3 83.1 - - + +
1070A GLN* 1.3 68.6 + - + +
1073A ILE* 4.4 6.5 - - + +
1074A PRO* 3.5 16.9 - - - +
1364A GLN* 3.3 36.3 + - - +
1366A ILE* 4.0 33.2 - - + +
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Residues in contact with GLN1070 (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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1066A PHE* 2.9 56.2 + - + +
1069A GLN* 1.3 84.2 + - + +
1071A HIS* 1.3 84.6 + - + +
1074A PRO* 3.8 11.1 - - - +
2023B TYR* 4.3 6.1 - - - +
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Residues in contact with HIS1071 (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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1066A PHE* 4.7 5.9 - - - -
1067A ILE* 2.8 45.1 + - + +
1070A GLN* 1.3 98.1 + - + +
1072A LEU* 1.3 64.5 + - - +
1073A ILE 3.6 0.7 - - - -
1074A PRO* 3.5 3.5 - - - +
1075A LEU* 3.3 24.1 + - - +
1094A VAL* 4.5 5.6 - - + -
2023B TYR* 3.4 43.8 - + + +
2052B GLU 3.4 25.0 + - - -
2053B GLN* 3.7 12.8 - - + -
2054B PRO* 3.7 17.7 - - + +
2060B THR* 4.4 2.8 - - - +
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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