Contacts of the helix formed by residues 103 - 111 (chain 1) in PDB entry 1QJX
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 MET 103 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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761 CYS* 3.2 53.8 - - + +
771 ILE* 3.4 17.4 + - - +
781 HIS* 3.8 11.9 - - - +
791 GLU* 3.8 24.5 - - + +
1001 LEU 4.7 1.6 + - - +
1011 GLN 3.5 0.2 - - - -
1021 GLU* 1.3 90.0 - - - +
1041 ALA* 1.3 64.5 - - - +
1051 GLN* 3.4 5.1 + - + +
1061 ILE* 3.7 7.8 + - + +
1071 ARG* 3.2 22.5 + - - +
2323 GLN* 3.8 10.3 - - - +
2363 ILE* 4.4 0.7 - - - -
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Residues in contact with ALA 104 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031 MET* 1.3 71.4 - - - +
1051 GLN* 1.3 66.6 + - + +
1071 ARG* 4.2 0.7 - - - -
1081 ARG* 2.9 27.8 + - - +
2561 TYR* 3.9 26.8 - - + -
2303 HIS* 4.0 16.2 - - + +
2313 LYS 4.6 1.1 - - - +
2323 GLN* 3.0 36.2 + - + +
2363 ILE* 3.8 6.1 - - + +
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Residues in contact with GLN 105 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761 CYS 6.2 0.2 - - - +
1031 MET* 3.4 4.4 + - + +
1041 ALA* 1.3 79.4 - - + +
1061 ILE* 1.3 67.5 + - + +
1081 ARG* 4.1 3.2 - - - +
1091 LYS* 3.5 23.4 + - - +
1053 TYR* 4.6 2.9 + - - -
2263 ASP* 3.4 48.2 + - - +
2273 THR 5.2 4.0 + - - -
2323 GLN* 4.7 0.4 + - - -
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Residues in contact with ILE 106 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731 ARG 5.2 4.0 - - - +
751 GLY* 3.8 34.5 - - - +
761 CYS 4.5 5.8 - - - +
771 ILE* 3.6 29.2 - - + -
1001 LEU* 4.1 24.7 - - + +
1031 MET* 3.7 9.7 + - + +
1041 ALA 3.5 0.2 - - - -
1051 GLN* 1.3 79.8 - - + +
1071 ARG* 1.3 70.4 + - - +
1091 LYS* 3.2 15.4 + - - +
1101 PHE* 3.2 50.2 + - + -
2381 HIS* 4.9 4.7 - - - +
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Residues in contact with ARG 107 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001 LEU 3.7 16.6 - - - +
1011 GLN* 3.0 57.1 + - - +
1031 MET 3.2 17.5 + - - +
1041 ALA* 3.3 3.1 + - - +
1061 ILE* 1.3 83.7 - - - +
1081 ARG* 1.3 63.3 + - - +
1101 PHE* 3.3 4.1 + - - +
1111 GLU* 2.9 47.7 + - + +
2561 TYR* 3.2 40.2 - - + -
2581 HIS 2.9 20.4 + - - -
2611 THR 3.1 28.3 + - - +
2621 THR* 5.1 1.6 - - - +
2363 ILE* 3.7 8.3 - - - +
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Residues in contact with ARG 108 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041 ALA 2.9 17.2 + - - +
1051 GLN* 4.1 2.7 - - - +
1071 ARG* 1.3 77.8 - - - +
1091 LYS* 1.3 63.2 + - - +
1111 GLU* 3.4 9.1 + - - +
1121 MET* 3.6 15.0 + - + +
2511 PRO* 3.5 14.1 - - + +
2521 ARG* 2.9 38.8 + - + +
2531 ALA* 5.1 0.2 - - - +
2561 TYR* 3.2 21.1 + - + +
1013 GLU* 2.8 36.2 + - - -
1053 TYR* 3.1 36.9 + - - +
2273 THR* 3.5 18.1 + - - +
2293 LEU 4.3 4.8 + - - -
2303 HIS* 3.4 36.1 - - - +
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Residues in contact with LYS 109 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701 PHE* 2.8 58.3 + - + -
711 LEU* 3.9 17.2 - - + +
731 ARG* 4.5 21.5 + - - +
1051 GLN 3.5 17.0 - - - +
1061 ILE* 3.2 15.4 + - - +
1071 ARG 3.2 0.8 - - - -
1081 ARG* 1.3 73.6 - - - +
1101 PHE* 1.3 68.7 + - + +
1121 MET* 3.1 20.3 + - - +
1131 PHE* 3.9 9.5 - - - -
1053 TYR* 3.8 25.9 - - + +
2263 ASP* 5.5 6.0 + - - +
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Residues in contact with PHE 110 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711 LEU* 4.1 35.4 - - + -
1001 LEU* 4.9 9.0 - - + -
1061 ILE* 3.2 48.6 + - + +
1071 ARG* 3.9 7.0 - - - +
1091 LYS* 1.3 80.3 - - + +
1111 GLU* 1.3 60.2 + - + +
1121 MET 2.9 6.2 + - - -
1131 PHE* 3.2 22.0 + - - +
1161 ALA* 5.0 3.9 - - + +
1181 PHE* 3.4 38.4 - + - -
1921 MET* 3.8 25.9 - - - +
2381 HIS* 4.0 18.2 - + - -
2401 ALA* 3.9 20.2 - - + -
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Residues in contact with GLU 111 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011 GLN* 3.2 18.0 + - - +
1071 ARG* 2.9 48.5 + - + +
1081 ARG 3.7 7.4 - - - +
1091 LYS 3.1 1.0 - - - -
1101 PHE* 1.3 76.3 - - + +
1121 MET* 1.3 56.0 + - - +
1131 PHE 3.1 7.4 - - - -
1921 MET* 4.6 12.7 - - + +
1931 PHE* 3.5 44.4 - - + -
2491 ARG* 3.7 5.7 - - - +
2501 PRO 4.3 6.8 - - - +
2511 PRO* 5.5 0.6 - - - +
2521 ARG* 5.0 5.6 + - + +
2561 TYR* 2.9 28.7 + - - +
2621 THR* 5.9 0.3 - - - +
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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