Contacts of the helix formed by residues 865 - 877 (chain K) in PDB entry 5ANC
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 865 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845K ASN* 3.3 21.8 - - + +
846K SER* 4.3 0.2 - - - -
864K ASP* 1.3 89.2 + - - +
866K GLY* 1.3 64.0 + - - +
867K ASN 3.3 3.8 + - - -
868K SER* 3.8 16.8 - - - -
869K ILE* 3.1 21.5 + - + +
897K TRP* 3.9 18.6 - - + -
899K LEU* 4.3 10.1 - - + -
933K GLY 5.2 2.5 - - - +
934K CYS 3.3 24.2 - - - +
935K SER* 3.2 25.1 - - - +
936K GLU 4.4 0.4 - - - -
952K ASP* 3.4 29.2 - - + +
961K LEU* 5.6 1.1 - - + -
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Residues in contact with GLY 866 (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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824K TRP* 3.8 21.8 - - - -
849K THR 4.4 0.9 - - - -
851K PRO* 3.8 10.2 - - - +
864K ASP* 4.8 0.2 + - - -
865K LEU* 1.3 75.6 - - - +
867K ASN* 1.3 62.1 + - - +
869K ILE* 4.0 1.6 - - - -
870K VAL* 3.3 30.3 + - - +
936K GLU* 3.6 25.5 + - - +
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Residues in contact with ASN 867 (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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198J GLU* 4.5 19.6 + - - +
851K PRO* 4.7 8.5 - - - +
865K LEU 3.3 1.2 + - - -
866K GLY* 1.3 77.8 - - - +
868K SER* 1.3 64.3 + - - +
870K VAL* 3.9 14.2 - - - +
871K SER* 3.9 13.5 + - - -
934K CYS* 4.2 14.5 - - + +
935K SER 2.9 32.0 + - - +
936K GLU* 3.6 12.1 - - - +
939K GLU* 4.8 14.5 - - - +
958K SER* 5.7 0.7 - - - -
962K ILE* 4.9 2.9 - - - +
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Residues in contact with SER 868 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865K LEU* 3.7 23.8 + - - -
866K GLY 3.6 0.2 - - - -
867K ASN* 1.3 76.7 - - - +
869K ILE* 1.3 63.5 + - - +
872K GLY 3.6 9.1 + - - -
897K TRP* 4.1 6.1 - - - -
934K CYS 4.2 6.0 + - - -
958K SER* 4.1 8.6 + - - -
961K LEU* 3.5 31.4 - - - +
962K ILE* 3.8 20.5 - - - +
965K MET* 3.4 21.1 - - - +
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Residues in contact with ILE 869 (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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824K TRP* 3.4 62.4 - - + +
836K LEU* 4.4 0.7 - - + -
847K VAL* 3.9 15.7 - - + +
864K ASP* 4.3 3.4 - - - +
865K LEU 3.1 26.4 + - - +
866K GLY* 4.2 0.7 - - - +
867K ASN 3.3 0.6 - - - -
868K SER* 1.3 76.6 - - - +
870K VAL* 1.3 60.2 + - - +
872K GLY 3.2 1.7 + - - -
873K PHE* 3.0 49.1 + - + +
894K LEU* 5.7 1.8 - - + -
897K TRP* 3.3 27.6 - - + -
965K MET* 3.8 6.5 - - + -
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Residues in contact with VAL 870 (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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777K GLU* 4.7 8.3 - - + +
824K TRP* 3.6 30.7 - - + +
825K SER* 2.9 33.4 + - - +
830K LYS* 4.3 13.5 + - - +
851K PRO* 3.8 20.9 - - + -
866K GLY 3.3 19.6 + - - +
867K ASN* 3.9 9.0 - - - +
869K ILE* 1.3 79.6 - - - +
871K SER* 1.3 68.7 + - - +
874K GLN* 3.4 12.5 + - - +
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Residues in contact with SER 871 (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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244J GLU* 5.0 9.3 + - - -
867K ASN 3.9 14.7 + - - -
869K ILE 3.4 0.4 - - - -
870K VAL* 1.3 83.5 - - - +
872K GLY* 1.3 64.9 + - - +
874K GLN* 3.8 5.7 + - - +
875K LEU* 3.6 25.5 + - - +
962K ILE* 4.3 19.3 - - - -
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Residues in contact with GLY 872 (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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868K SER 3.6 10.8 + - - -
869K ILE 3.2 5.2 + - - -
871K SER* 1.3 79.1 - - - +
873K PHE* 1.3 57.6 + - - +
875K LEU* 3.3 20.3 + - - +
876K ALA* 3.3 9.7 + - - +
962K ILE* 3.8 26.6 - - - +
965K MET* 4.0 11.4 - - - -
966K LYS* 4.3 7.3 + - - +
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Residues in contact with PHE 873 (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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751K LEU* 3.7 14.8 - - + -
753K VAL* 4.0 10.5 - - + -
825K SER* 4.4 5.7 - - - -
836K LEU* 3.4 40.7 - - + +
869K ILE* 3.0 27.1 + - + +
872K GLY* 1.3 72.2 - - - +
874K GLN* 1.3 63.4 + - - +
876K ALA* 3.8 7.7 - - + +
877K THR* 3.5 27.7 + - + +
892K PHE* 4.6 3.4 - + - -
894K LEU* 3.5 35.0 - - + -
897K TRP* 5.1 4.9 - - + -
965K MET* 3.6 28.7 - - + -
969K CYS* 3.5 31.4 - - - -
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Residues in contact with GLN 874 (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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825K SER* 2.9 20.1 + - - -
827K GLY 3.4 9.3 + - - -
828K PRO* 2.7 36.8 + - - +
830K LYS* 2.9 39.0 + - - +
870K VAL 3.4 16.2 + - - +
871K SER* 3.8 8.3 - - - +
872K GLY 3.3 0.6 - - - -
873K PHE* 1.3 77.3 - - - +
875K LEU* 1.3 63.6 + - + +
877K THR* 2.7 19.8 + - - -
878K LEU* 3.3 25.7 - - + +
1101K TYR* 4.3 16.6 - - + -
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Residues in contact with LEU 875 (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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244J GLU* 5.9 3.4 - - + -
871K SER 3.6 15.0 - - - +
872K GLY 3.3 8.1 + - - +
874K GLN* 1.3 80.2 - - + +
876K ALA* 1.3 61.2 + - - +
878K LEU* 3.5 13.3 + - + +
879K SER* 3.4 16.8 + - - -
962K ILE* 4.9 6.5 - - + +
963K ALA* 6.4 0.2 - - - -
966K LYS* 3.6 31.7 - - + +
1103K GLU* 3.2 43.7 - - + +
1104K GLU* 4.5 0.9 - - - -
1105K LYS* 3.7 45.5 - - + +
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Residues in contact with ALA 876 (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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872K GLY 3.3 7.0 + - - +
873K PHE* 3.8 20.9 - - + +
874K GLN 3.3 0.6 - - - -
875K LEU* 1.3 78.2 - - - +
877K THR* 1.3 59.8 + - + +
878K LEU 3.6 0.3 + - - -
879K SER* 3.7 18.5 + - - +
887K LEU* 3.9 5.4 - - - +
892K PHE* 4.8 6.0 - - + -
965K MET 4.5 0.2 - - - +
966K LYS* 4.2 8.9 - - - +
969K CYS* 3.4 40.9 - - + +
973K LEU* 4.0 8.3 - - - +
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Residues in contact with THR 877 (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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825K SER 4.9 5.6 - - - +
827K GLY 3.6 16.9 + - - +
828K PRO* 3.6 17.1 - - - +
834K ASN* 4.1 30.3 - - + +
836K LEU* 5.9 4.5 - - + -
873K PHE* 3.5 14.4 + - + +
874K GLN* 2.7 22.2 + - - -
876K ALA* 1.3 77.4 - - + +
878K LEU* 1.3 58.3 + - - +
886K PRO* 3.8 2.4 - - - +
887K LEU* 3.2 35.3 + - - +
892K PHE* 4.9 13.2 - - + -
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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