Contacts of the helix formed by residues 908 - 918 (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 LEU 908 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550A VAL* 5.0 0.2 - - - -
904A VAL* 3.5 27.6 - - + +
905A PRO* 3.3 25.1 - - + +
906A PHE 3.0 0.8 - - - -
907A ALA* 1.3 76.8 - - - +
909A VAL* 1.3 64.3 + - - +
910A GLY 3.6 0.2 - - - -
911A GLY* 3.4 9.0 + - - -
912A ILE* 3.0 19.2 + - + +
930A PHE* 4.2 34.8 - - + +
933A LEU* 3.5 30.0 - - + +
934A ALA* 4.1 9.6 - - + -
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Residues in contact with VAL 909 (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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546A SER* 4.1 20.0 - - - +
547A VAL* 4.3 6.5 - - + -
549A THR* 4.9 2.2 - - + -
550A VAL* 3.4 39.3 - - + -
905A PRO 4.1 2.9 - - - +
906A PHE* 3.0 31.9 + - + +
907A ALA 3.1 0.2 - - - -
908A LEU* 1.3 74.1 - - - +
910A GLY* 1.3 71.3 + - - +
912A ILE* 2.9 16.1 + - - +
913A TRP* 2.9 23.7 + - + +
1022A THR* 4.4 5.2 - - + +
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Residues in contact with GLY 910 (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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908A LEU 3.6 0.4 - - - -
909A VAL* 1.3 81.1 - - - +
911A GLY* 1.3 56.4 + - - +
913A TRP* 3.4 7.3 + - - +
914A LEU* 3.0 24.1 + - - +
1018A GLY* 3.0 32.4 + - - -
1021A ILE* 4.6 4.7 - - - -
1022A THR* 3.3 14.8 + - - -
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Residues in contact with GLY 911 (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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908A LEU 3.4 6.4 + - - -
909A VAL 2.9 1.2 + - - -
910A GLY* 1.3 77.0 - - - +
912A ILE* 1.3 57.3 + - - +
914A LEU* 3.0 22.3 + - - +
915A LEU* 3.4 11.1 + - - +
930A PHE* 4.4 3.1 - - - -
933A LEU* 4.7 0.4 - - - -
1015A PRO* 3.3 38.0 - - - +
1018A GLY* 3.6 3.6 - - - -
1019A GLY 3.1 8.7 - - - +
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Residues in contact with ILE 912 (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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550A VAL* 3.1 32.8 - - + +
553A PRO* 3.2 33.9 - - + -
554A LEU* 3.6 25.1 - - + -
908A LEU* 3.0 21.9 + - + +
909A VAL* 3.0 6.5 - - - +
911A GLY* 1.3 69.7 - - - +
913A TRP* 1.3 62.6 + - + +
914A LEU 3.0 4.7 - - - -
915A LEU* 2.9 43.4 + - + +
916A TRP* 3.6 5.2 + - + -
930A PHE* 3.8 15.8 - - + -
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Residues in contact with TRP 913 (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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549A THR* 2.8 64.0 + - + +
550A VAL* 3.3 11.6 - - + +
552A TRP* 4.6 18.4 - + - -
553A PRO* 4.0 3.3 - - + +
909A VAL* 2.9 20.1 + - + +
910A GLY* 3.8 9.0 - - - +
912A ILE* 1.3 93.2 - - + +
914A LEU* 1.3 60.8 + - - +
916A TRP* 3.1 38.0 + + + +
917A TRP* 4.0 3.1 + - - +
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Residues in contact with LEU 914 (chain A).
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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910A GLY 3.0 11.7 + - - +
911A GLY 3.0 14.6 - - - +
912A ILE 3.0 0.2 - - - -
913A TRP* 1.3 74.8 - - - +
915A LEU* 1.3 54.5 + - - +
916A TRP 2.8 9.0 + - - -
917A TRP* 3.8 5.5 + - + +
918A MET* 2.8 56.9 + - + +
999A LEU* 6.2 0.9 - - + -
1014A ALA* 2.8 41.1 - - + +
1017A ILE* 3.9 19.3 - - + -
1018A GLY* 3.7 13.5 - - - +
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Residues in contact with LEU 915 (chain A).
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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554A LEU* 5.4 3.8 - - + -
557A VAL* 5.8 3.1 - - - +
911A GLY 3.9 7.2 - - - +
912A ILE* 2.9 41.1 + - + +
914A LEU* 1.3 76.9 - - - +
916A TRP* 1.3 73.5 + - + +
919A GLY* 2.8 7.7 + - - -
920A PHE* 2.7 62.3 + - + +
921A HIS 5.4 0.4 - - - +
922A LEU* 5.1 11.7 - - + +
926A THR* 4.9 18.2 - - + -
930A PHE* 4.8 7.4 - - + -
1014A ALA* 5.0 4.3 - - + -
1015A PRO* 4.9 13.9 - - + -
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Residues in contact with TRP 916 (chain A).
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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552A TRP* 3.1 42.6 - + - -
553A PRO* 3.0 54.0 - - + +
556A LYS* 3.5 26.4 - - + +
557A VAL* 3.9 2.9 - - - -
558A GLY* 3.4 29.8 - - - -
912A ILE 3.7 8.3 - - - -
913A TRP* 3.1 36.1 - + + +
914A LEU 2.8 4.8 - - - -
915A LEU* 1.3 118.0 - - + +
917A TRP* 1.3 66.7 + - - +
918A MET 3.3 0.2 - - - -
919A GLY* 3.4 7.4 + - - -
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Residues in contact with TRP 917 (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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913A TRP 4.0 3.6 + - - +
914A LEU* 3.8 5.8 + - + +
916A TRP* 1.3 77.4 - - - +
918A MET* 1.3 113.4 + - + +
919A GLY* 3.0 6.2 + - - -
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Residues in contact with MET 918 (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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914A LEU* 2.8 52.7 - - + +
916A TRP 3.3 0.2 - - - -
917A TRP* 1.3 116.5 - - + +
919A GLY* 1.3 63.5 + - - +
920A PHE* 3.1 53.1 + - + -
921A HIS* 5.5 0.9 - - - -
999A LEU* 5.5 14.8 - - + -
1010A SER* 5.5 1.6 - - - -
1014A ALA* 4.5 9.0 - - + -
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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