Contacts of the helix formed by residues 901 - 918 (chain D) in PDB entry 3O33
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 THR 901 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899D LYS 3.4 4.0 + - - +
900D LEU* 1.3 78.3 - - - +
902D PRO* 1.3 74.8 - - - +
903D ILE* 3.3 10.2 + - - +
904D ASP* 2.8 35.7 + - - +
905D LYS* 3.1 16.6 + - - +
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Residues in contact with PRO 902 (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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900D LEU 4.2 2.7 - - - +
901D THR* 1.3 88.0 - - - +
903D ILE* 1.3 57.0 + - + +
905D LYS* 3.3 9.5 + - + +
906D ARG* 3.0 60.6 + - - +
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Residues in contact with ILE 903 (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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873D LEU* 3.7 24.7 - - + +
874D SER* 4.3 19.3 - - - +
901D THR* 3.2 9.3 - - - +
902D PRO* 1.3 79.9 - - + +
904D ASP* 1.3 61.8 + - - +
906D ARG* 3.3 12.6 + - - +
907D LYS* 2.9 52.4 + - + +
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Residues in contact with ASP 904 (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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900D LEU* 4.5 9.2 - - + -
901D THR* 2.8 37.2 + - - +
903D ILE* 1.3 78.4 - - - +
905D LYS* 1.3 65.8 + - - +
907D LYS* 3.2 8.6 + - - +
908D CYS* 3.0 23.2 + - - +
962D PRO* 3.6 21.0 - - + +
965D PHE* 3.7 6.4 - - + -
1005D TYR* 2.8 38.3 + - - +
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Residues in contact with LYS 905 (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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855D PRO* 5.1 3.8 - - - +
900D LEU* 4.3 11.3 - - + +
901D THR 3.1 12.3 + - - +
902D PRO* 3.3 12.3 + - + +
904D ASP* 1.3 74.6 - - - +
906D ARG* 1.3 59.3 + - + +
908D CYS* 3.2 3.1 + - - +
909D GLU* 2.8 60.9 + - - +
952D LEU* 3.6 47.3 - - + +
953D GLN* 4.9 6.9 - - - +
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Residues in contact with ARG 906 (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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868D THR* 4.8 2.6 - - - +
871D ARG* 3.5 25.2 - - - +
872D ASP 4.3 1.1 - - - -
873D LEU* 2.8 51.1 + - + +
874D SER 3.7 8.3 + - - -
876D PRO* 3.0 33.9 - - - +
902D PRO* 3.0 58.3 + - - +
903D ILE* 3.5 9.9 - - - +
905D LYS* 1.3 78.4 - - + +
907D LYS* 1.3 56.6 + - - +
909D GLU* 3.4 14.9 + - - +
910D ARG* 3.0 26.3 + - - +
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Residues in contact with LYS 907 (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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873D LEU* 4.1 28.5 - - + -
903D ILE* 2.9 37.6 + - - +
904D ASP* 3.2 11.2 + - - +
906D ARG* 1.3 74.3 - - - +
908D CYS* 1.3 60.6 + - - +
910D ARG* 3.3 3.2 + - - +
911D LEU* 2.9 33.2 + - - +
965D PHE* 5.1 0.2 - - - -
1004D LEU* 2.9 42.1 + - + +
1005D TYR* 3.6 41.6 - - + +
1006D PRO* 5.6 0.4 - - - +
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Residues in contact with CYS 908 (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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904D ASP 3.0 12.8 + - - +
905D LYS 3.6 7.6 - - - +
907D LYS* 1.3 74.2 - - - +
909D GLU* 1.3 60.2 + - - +
911D LEU* 3.6 5.5 - - - +
912D LEU* 2.8 35.2 + - - +
948D ILE* 4.2 10.3 - - - -
952D LEU* 3.7 24.5 - - + -
965D PHE* 3.5 48.6 - - + -
969D PHE* 3.9 12.3 - - - -
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Residues in contact with GLU 909 (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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854D VAL* 3.4 32.0 - - + +
855D PRO* 3.5 33.9 - - - +
868D THR* 3.8 7.8 + - + +
871D ARG* 3.9 15.8 + - - -
905D LYS* 2.8 56.7 + - - +
906D ARG* 3.5 18.1 - - - +
907D LYS 3.2 0.2 - - - -
908D CYS* 1.3 77.9 - - - +
910D ARG* 1.3 60.0 + - - +
913D LEU* 3.1 22.0 + - - +
952D LEU* 3.5 15.6 - - + +
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Residues in contact with ARG 910 (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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868D THR* 3.2 25.7 + - + +
869D PHE* 3.3 26.6 + - + -
870D CYS 4.5 0.4 + - - -
871D ARG 2.7 30.1 + - - -
872D ASP* 4.9 0.2 - - - +
873D LEU* 3.8 34.4 - - - +
906D ARG 3.0 13.0 + - - +
907D LYS* 3.5 10.1 - - - +
908D CYS 3.2 0.2 - - - -
909D GLU* 1.3 75.4 - - - +
911D LEU* 1.3 64.6 + - - +
913D LEU* 3.3 2.4 + - - +
914D PHE* 2.9 58.0 + - + -
1004D LEU* 4.2 22.3 - - + +
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Residues in contact with LEU 911 (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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907D LYS 2.9 21.6 + - - +
908D CYS* 3.3 5.4 + - - +
910D ARG* 1.3 77.9 - - - +
912D LEU* 1.3 63.1 + - - +
914D PHE* 3.3 5.2 + - + +
915D LEU* 3.1 28.7 + - - +
965D PHE* 3.9 22.9 - - + -
969D PHE* 4.1 12.3 - - + -
997D PHE* 4.0 20.0 - - + -
1000D LEU* 3.7 34.8 - - + -
1001D LEU* 3.9 24.2 - - + +
1004D LEU* 3.6 21.1 - - + -
1005D TYR* 5.0 2.7 - - + -
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Residues in contact with LEU 912 (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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854D VAL* 3.9 23.6 - - + -
908D CYS* 2.8 20.7 + - - +
909D GLU 3.7 4.0 - - - +
910D ARG 3.3 0.2 - - - -
911D LEU* 1.3 76.9 - - - +
913D LEU* 1.3 57.4 + - - +
915D LEU* 3.2 4.5 + - - +
916D TYR* 2.8 37.6 + - + -
945D LEU* 3.9 25.7 - - + +
948D ILE* 3.8 15.9 - - + -
949D LYS* 3.6 30.1 - - + +
952D LEU* 4.0 14.1 - - + -
969D PHE* 3.4 29.2 - - + -
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Residues in contact with LEU 913 (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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831D VAL* 4.2 8.3 - - + -
848D PHE* 4.0 19.3 - - + -
852D CYS 4.1 9.4 - - - +
853D HIS* 4.0 13.9 - - + +
854D VAL* 3.9 28.0 - - + +
868D THR* 3.6 29.2 - - + -
869D PHE* 3.3 34.3 - - + +
909D GLU 3.1 14.4 + - - +
910D ARG* 3.3 5.1 + - - +
912D LEU* 1.3 76.1 - - - +
914D PHE* 1.3 66.1 - - - +
916D TYR* 3.2 2.7 + - + +
917D CYS* 2.9 28.6 + - - -
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Residues in contact with PHE 914 (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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869D PHE* 3.5 29.8 - + + -
910D ARG* 2.9 55.0 + - + +
911D LEU* 3.6 2.9 - - + +
913D LEU* 1.3 76.7 - - - +
915D LEU* 1.3 62.7 + - - +
917D CYS* 3.4 3.6 + - - +
918D HIS* 3.2 20.8 + - - +
996D TYR* 3.2 29.2 + - - -
1000D LEU* 3.3 42.0 - - + -
1004D LEU* 5.7 3.1 - - + -
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Residues in contact with LEU 915 (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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911D LEU 3.1 12.2 + - - +
912D LEU 3.7 5.8 - - - +
914D PHE* 1.3 74.9 - - - +
916D TYR* 1.3 64.3 + - - +
918D HIS* 3.0 12.3 + - - +
921D SER* 2.8 24.1 + - - -
945D LEU* 3.9 19.3 - - + -
969D PHE* 3.5 36.1 - - + -
973D PHE* 4.6 8.7 - - + -
993D LEU* 3.7 21.3 - - + -
996D TYR* 3.7 26.2 - - + -
997D PHE* 4.1 26.0 - - + -
1000D LEU* 4.3 5.8 - - + -
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Residues in contact with TYR 916 (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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831D VAL* 3.9 38.1 - - + +
852D CYS 5.0 3.6 - - - -
854D VAL* 4.0 21.1 - - + -
912D LEU* 2.8 36.7 + - + +
913D LEU* 3.6 6.7 - - + +
915D LEU* 1.3 74.7 - - - +
917D CYS* 1.3 61.0 + - - +
918D HIS 3.5 1.2 + - - +
921D SER* 3.5 4.2 + - - -
925D GLN* 3.5 56.4 + - + -
926D ASP* 5.3 1.0 + - - -
945D LEU* 3.8 23.3 - - + -
946D SER* 3.2 34.0 + - - -
949D LYS* 4.0 16.9 - - + +
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Residues in contact with CYS 917 (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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830D ALA* 3.7 35.6 - - + +
831D VAL* 3.7 21.8 - - - -
833D GLN* 5.7 1.0 + - - -
846D LYS* 4.9 5.6 - - - -
848D PHE* 4.3 0.4 - - - -
869D PHE* 4.0 23.1 - - + -
913D LEU* 2.9 22.9 + - - +
914D PHE* 3.8 5.4 - - - +
916D TYR* 1.3 75.5 - - - +
918D HIS* 1.3 60.4 + - - +
919D GLU* 3.7 1.9 + - - -
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Residues in contact with HIS 918 (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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914D PHE 3.2 11.5 + - - +
915D LEU 3.0 10.1 + - - +
916D TYR 4.1 1.2 - - - +
917D CYS* 1.3 78.2 - - - +
919D GLU* 1.3 70.7 + - + +
920D MET* 3.0 49.4 + - + +
921D SER* 2.9 25.3 + - - -
922D LEU* 5.3 0.5 - - - +
925D GLN* 4.9 0.3 + - - -
992D LYS* 5.2 5.9 + - + +
993D LEU* 4.1 10.5 - - + +
996D TYR* 3.5 50.2 - + + +
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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