Contacts of the helix formed by residues 1094 - 1107 (chain D) in PDB entry 4TU6
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 ASP1094 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1092D GLU 3.8 3.8 + - - -
1093D LEU* 1.3 78.0 - - - +
1095D GLU* 1.3 67.3 + - - +
1096D ASP* 2.9 36.6 + - - +
1097D PHE* 3.1 26.2 + - + +
1098D GLU 3.1 9.9 + - - -
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Residues in contact with GLU1095 (chain D).
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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1093D LEU* 3.3 7.1 + - - +
1094D ASP* 1.3 75.7 + - - +
1096D ASP* 1.3 64.2 + - - +
1098D GLU* 3.2 8.1 + - - +
1099D GLN* 2.9 28.8 + - - +
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Residues in contact with ASP1096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094D ASP* 2.9 14.8 + - - +
1095D GLU* 1.3 81.2 - - - +
1097D PHE* 1.3 57.6 + - - +
1099D GLN* 3.7 11.1 - - - +
1100D LEU* 3.0 26.0 + - - +
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Residues in contact with PHE1097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985D THR* 3.5 38.8 - - + -
988D GLU* 3.2 43.3 - - + -
989D LEU* 3.9 22.4 - - + -
992D PHE* 6.1 2.2 - + + -
1093D LEU* 4.2 17.7 - - + -
1094D ASP* 3.1 23.5 + - + +
1096D ASP* 1.3 74.9 - - - +
1098D GLU* 1.3 69.3 + - - +
1099D GLN 3.1 1.1 - - - -
1100D LEU* 3.2 12.0 + - + +
1101D CYS* 3.0 37.0 + - - -
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Residues in contact with GLU1098 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989D LEU* 4.8 0.7 - - - +
1045D THR* 3.5 6.9 - - - -
1046D VAL* 2.7 51.0 + - + +
1047D LYS* 3.5 6.4 + - - +
1093D LEU* 3.9 22.2 - - + -
1094D ASP 3.1 5.7 + - - +
1095D GLU* 3.2 8.7 + - - +
1097D PHE* 1.3 83.8 - - - +
1099D GLN* 1.3 63.0 + - - +
1101D CYS* 3.3 5.2 + - - +
1102D GLU* 2.5 58.0 + - - +
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Residues in contact with GLN1099 (chain D).
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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1095D GLU 2.9 15.8 + - - +
1096D ASP* 3.7 13.7 - - - +
1097D PHE 3.1 0.2 - - - -
1098D GLU* 1.3 79.2 - - - +
1100D LEU* 1.3 61.9 + - - +
1102D GLU* 3.5 18.3 + - - +
1103D GLU* 2.9 60.4 + - - +
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Residues in contact with LEU1100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982D GLU* 6.0 1.8 - - + -
985D THR* 3.5 33.2 - - + +
1096D ASP 3.0 17.4 + - - +
1097D PHE* 3.2 12.3 + - + +
1099D GLN* 1.3 76.3 - - - +
1101D CYS* 1.3 62.1 + - - +
1103D GLU* 3.2 7.2 + - + +
1104D ILE* 3.1 38.8 + - + +
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Residues in contact with CYS1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985D THR* 3.9 14.1 - - - -
986D PHE* 4.4 6.1 - - - -
989D LEU* 4.3 13.9 - - - -
1044D LEU 3.4 21.4 - - - +
1045D THR* 3.9 5.0 - - - +
1097D PHE* 3.0 44.8 + - - +
1098D GLU* 3.3 17.7 + - - +
1100D LEU* 1.3 78.2 - - - +
1102D GLU* 1.3 60.8 + - - +
1103D GLU 3.2 1.0 + - - -
1104D ILE* 3.4 10.0 + - - +
1105D GLN* 3.3 21.0 + - - +
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Residues in contact with GLU1102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045D THR* 3.8 16.8 - - + +
1047D LYS* 3.8 25.6 - - + +
1098D GLU* 2.5 56.1 + - - +
1099D GLN* 4.0 22.3 + - - +
1100D LEU 3.4 0.2 - - - -
1101D CYS* 1.3 75.2 - - - +
1103D GLU* 1.3 56.7 + - + +
1105D GLN* 3.5 7.3 + - - +
1106D GLU* 3.3 24.9 + - - +
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Residues in contact with GLU1103 (chain D).
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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1099D GLN* 2.9 48.0 + - - +
1100D LEU* 3.2 8.6 + - + +
1101D CYS 3.2 0.4 - - - -
1102D GLU* 1.3 74.3 - - - +
1104D ILE* 1.3 64.4 + - + +
1105D GLN 3.2 1.1 - - - -
1106D GLU* 4.0 9.8 + - - +
1107D SER* 3.2 14.7 + - - -
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Residues in contact with ILE1104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982D GLU* 3.7 50.3 - - + +
985D THR* 4.3 12.6 - - + -
986D PHE* 3.6 32.8 - - + -
1100D LEU* 3.1 36.9 + - + +
1101D CYS* 3.7 8.3 - - - +
1103D GLU* 1.3 79.1 - - - +
1105D GLN* 1.3 58.2 + - - +
1107D SER* 2.9 11.9 + - - -
1108D ARG* 2.9 37.6 + - + +
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Residues in contact with GLN1105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986D PHE* 5.3 0.9 - - + -
1044D LEU* 3.8 28.1 - - + +
1045D THR* 3.7 18.5 + - + +
1048D ASP* 2.9 34.2 + - - -
1101D CYS 3.3 14.1 + - - +
1102D GLU* 3.5 9.1 + - - +
1103D GLU 3.2 0.6 - - - -
1104D ILE* 1.3 78.0 - - - +
1106D GLU* 1.3 65.1 + - - +
1107D SER 3.2 2.0 + - - -
1108D ARG* 3.6 16.5 + - - +
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Residues in contact with GLU1106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102D GLU 3.3 15.6 + - - +
1103D GLU* 4.4 8.1 - - + +
1104D ILE 3.5 0.2 - - - -
1105D GLN* 1.3 78.6 + - - +
1107D SER* 1.3 59.5 + - - +
1108D ARG 4.0 0.2 + - - -
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Residues in contact with SER1107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982D GLU* 5.7 0.2 + - - -
1103D GLU 3.2 13.3 + - - -
1104D ILE* 2.9 14.7 + - - -
1106D GLU* 1.3 78.6 - - - +
1108D ARG* 1.3 56.8 + - - +
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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