Contacts of the helix formed by residues 1032 - 1039 (chain A) in PDB entry 3KSS
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 PRO1032 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A TYR* 5.7 2.0 - - - +
529A LEU* 6.1 3.1 - - + -
532A VAL* 5.3 5.6 - - + -
533A LEU* 3.7 27.8 - - + -
973A LEU* 4.3 21.4 - - + +
1028A LEU 3.0 24.5 - - - +
1029A PHE* 3.5 13.0 - - + -
1031A ILE* 1.3 96.6 - - + +
1033A ALA* 1.3 74.3 + - - +
1035A TYR* 2.9 13.2 + - + +
1036A LYS* 3.1 16.3 + - - +
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Residues in contact with ALA1033 (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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532A VAL* 5.4 4.2 - - + +
536A PRO* 4.4 7.2 - - + +
539A THR* 3.7 26.9 - - + +
540A LEU* 6.2 0.9 - - + -
1029A PHE* 3.8 13.0 - - + +
1032A PRO* 1.3 84.1 - - + +
1034A ALA* 1.3 64.9 + - - +
1035A TYR 3.0 0.2 + - - -
1036A LYS* 3.1 24.8 - - - +
1037A LEU* 2.9 28.9 + - + +
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Residues in contact with ALA1034 (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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899A LEU* 3.5 28.7 - - + -
1029A PHE 4.7 0.4 + - - -
1030A ILE* 3.0 27.7 + - - +
1032A PRO 3.4 0.4 - - - -
1033A ALA* 1.3 79.8 - - - +
1035A TYR* 1.3 55.7 + - - +
1037A LEU* 3.7 8.3 - - - +
1038A MET* 3.0 30.7 + - + +
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Residues in contact with TYR1035 (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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893A ARG* 6.1 0.7 - - - -
896A GLU* 5.1 3.5 + - + -
945A LEU* 3.8 22.4 - - + +
948A LEU* 3.1 40.2 - - + -
949A ARG* 2.9 38.8 + - - -
952A ILE* 4.2 19.5 - - + -
973A LEU* 5.7 4.7 - - + -
1030A ILE 4.2 0.4 + - - -
1031A ILE 3.1 17.1 + - - +
1032A PRO* 2.9 7.6 + - + +
1034A ALA* 1.3 75.9 - - - +
1036A LYS* 1.3 68.2 + - - +
1038A MET* 3.0 19.2 + - + +
1039A TRP* 3.2 18.0 + + + +
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Residues in contact with LYS1036 (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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532A VAL 4.2 1.2 + - - -
533A LEU* 2.6 52.7 + - + +
536A PRO* 3.4 34.9 - - + +
969A LEU* 5.2 19.1 - - + -
970A ASP* 6.6 0.2 - - - -
973A LEU* 5.9 3.8 - - + +
1032A PRO 3.1 6.1 + - - +
1033A ALA* 3.1 28.6 - - - +
1035A TYR* 1.3 81.0 - - - +
1037A LEU* 1.3 63.8 + - + +
1039A TRP* 3.3 21.0 - - - +
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Residues in contact with LEU1037 (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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536A PRO* 3.2 39.7 - - + -
537A LYS* 5.2 11.9 - - + +
540A LEU* 5.5 10.1 - - + -
1033A ALA* 2.9 33.6 + - + +
1034A ALA* 3.7 8.3 - - - +
1036A LYS* 1.3 85.1 - - + +
1038A MET* 1.3 64.3 + - - +
1039A TRP* 3.4 2.1 + - - -
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Residues in contact with MET1038 (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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893A ARG* 4.7 18.7 + - - +
894A VAL* 6.0 0.9 - - - -
895A GLY* 3.4 44.9 - - - +
898A LEU* 5.1 6.5 - - + -
899A LEU* 5.1 6.5 - - + +
1034A ALA 3.0 15.7 + - - +
1035A TYR* 3.0 15.0 + - + +
1037A LEU* 1.3 78.7 - - - +
1039A TRP* 1.3 63.1 + - + +
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Residues in contact with TRP1039 (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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893A ARG* 6.2 2.0 - - - +
1035A TYR* 3.2 18.1 + + + +
1036A LYS* 3.3 19.1 - - - -
1037A LEU 4.5 1.9 - - - +
1038A MET* 1.3 85.1 - - + +
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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