Contacts of the helix formed by residues 1069 - 1075 (chain K) in PDB entry 6R8Y
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 GLU1069 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58K TYR* 4.2 0.9 - - - -
1059K ASN* 3.6 22.6 + - - +
1067K LYS 4.0 5.5 + - - +
1068K ILE* 1.3 78.7 - - - +
1070K HIS* 1.3 64.3 + - - +
1071K SER* 3.9 15.3 + - - +
1072K PHE* 3.2 13.5 + - + +
1073K TRP* 3.2 21.0 + - - +
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Residues in contact with HIS1070 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K TYR* 3.5 46.2 - + + -
1055K GLN* 4.1 10.4 + - - +
1059K ASN* 3.4 25.9 + - - +
1068K ILE 3.7 3.2 + - - -
1069K GLU* 1.3 72.4 + - - +
1071K SER* 1.3 66.7 + - - +
1073K TRP* 3.1 3.5 + + - +
1074K ARG* 3.0 37.4 + - + +
1090K ASP* 2.3 42.5 + - + -
1093K LEU* 3.3 29.5 - - + +
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Residues in contact with SER1071 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059K ASN* 4.1 8.3 + - - +
1069K GLU* 3.9 13.3 + - - +
1070K HIS* 1.3 83.1 + - - +
1072K PHE* 1.3 54.2 + - - +
1074K ARG* 3.4 2.7 + - - +
1075K SER* 2.3 41.0 + - - -
1085K ALA* 5.3 3.5 + - - +
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Residues in contact with PHE1072 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K TYR 5.7 0.2 - - - -
83K LYS* 2.4 68.4 + - + -
85K ASN* 3.1 38.4 - - - -
107K ASN* 4.9 6.1 - - + -
109K GLN* 5.3 9.0 - - - -
1068K ILE* 4.4 6.7 - - + -
1069K GLU* 3.2 19.8 + - + +
1071K SER* 1.3 82.5 + - - +
1073K TRP* 1.3 54.3 + - - +
1075K SER* 3.3 15.0 - - - -
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Residues in contact with TRP1073 (chain K).
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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37K THR* 4.3 15.0 - - + -
57K MET 4.5 1.9 + - - -
58K TYR* 3.3 55.9 - + + +
59K GLY* 3.5 28.9 - - - -
60K LYS* 3.8 18.4 - - + -
82K ALA* 6.3 0.9 - - + -
83K LYS* 2.9 27.0 + - + +
999K HIS* 3.2 27.5 - + - -
1000K LEU 4.3 0.7 - - - -
1001K GLY* 3.6 25.8 - - - -
1068K ILE* 4.8 0.7 - - + -
1069K GLU 3.2 4.3 + - - +
1070K HIS* 3.1 7.0 + + - +
1072K PHE* 1.3 84.7 - - - +
1074K ARG* 1.3 104.6 + - + +
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Residues in contact with ARG1074 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 5.7 1.4 - - - +
58K TYR* 6.3 0.2 - - - -
998K PHE* 3.3 39.7 - - + -
999K HIS* 3.0 30.2 + - - -
1000K LEU* 3.3 26.1 + - - +
1070K HIS* 3.0 36.9 + - + +
1071K SER* 3.7 3.4 - - - +
1073K TRP* 1.3 104.8 - - + +
1075K SER* 1.3 64.0 + - - +
1076K PHE 3.4 1.0 + - - -
1085K ALA* 3.8 18.6 - - + +
1090K ASP* 2.7 32.9 + - - +
1092K ASP* 4.4 13.7 + - - +
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Residues in contact with SER1075 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K LYS* 3.0 19.4 + - - -
999K HIS* 3.3 8.7 - - - +
1071K SER* 2.3 30.9 + - - -
1072K PHE* 3.3 16.6 - - - -
1073K TRP 3.2 1.2 - - - -
1074K ARG* 1.3 76.9 - - - +
1076K PHE* 1.3 67.8 + - - +
1077K HIS* 3.4 1.3 + - - +
1083K GLU 3.7 12.8 - - - -
1084K PRO* 4.1 10.4 - - - +
1085K ALA 4.2 6.6 + - - +
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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