Contacts of the helix formed by residues 869 - 886 (chain A) in PDB entry 3F2B
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 PHE 869 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A LEU* 4.3 14.6 - - + -
864A ILE* 2.8 25.8 + - + +
867A HIS* 3.3 29.4 - - + -
868A GLY* 1.3 74.7 - - - +
870A ALA* 1.3 67.8 + - - +
871A VAL 3.2 4.0 + - - -
872A ILE* 3.3 33.7 + - + +
873A TYR* 3.3 18.5 + + + -
963A PHE* 4.5 13.2 - + - -
964A LEU* 3.8 19.7 - - + -
968A GLY 5.9 0.2 - - - -
970A LYS 4.9 1.6 - - - -
971A VAL* 4.5 2.7 - - - -
972A PRO* 3.4 48.5 - - + -
1095A LEU* 3.7 22.9 - - + -
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Residues in contact with ALA 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ALA* 4.0 7.0 - - - +
830A ASP* 3.3 40.8 - - - +
833A ILE* 3.6 15.8 - - + +
864A ILE* 3.7 12.3 + - + -
865A ILE* 4.2 15.2 - - + +
868A GLY* 3.5 2.2 - - - -
869A PHE* 1.3 77.6 - - - +
871A VAL* 1.3 63.9 + - - +
873A TYR* 3.2 5.6 + - - +
874A LEU* 3.2 18.0 + - - +
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Residues in contact with VAL 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A PRO* 3.7 32.1 - - + +
825A ARG* 4.1 1.1 - - - -
826A ILE* 3.6 50.7 - - + +
829A ALA* 3.7 20.9 - - + -
830A ASP* 5.1 1.8 + - - +
868A GLY 5.0 2.1 + - - +
869A PHE 3.2 1.4 - - - -
870A ALA* 1.3 78.0 - - + +
872A ILE* 1.3 58.7 + - - +
874A LEU* 3.2 3.5 + - - +
875A ILE* 2.8 31.7 + - + +
994A PHE* 3.9 21.1 - - + -
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Residues in contact with ILE 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A PRO* 4.6 11.7 - - + -
869A PHE* 3.3 40.7 + - + +
871A VAL* 1.3 75.7 - - + +
873A TYR* 1.3 62.0 + - - +
875A ILE* 4.1 6.9 - - - +
876A SER* 2.8 34.7 + - - -
973A ASP* 5.0 2.0 - - - -
974A ILE* 3.8 26.2 - - + +
994A PHE* 4.9 3.1 - - + -
1056A VAL* 4.8 10.8 - - + -
1095A LEU* 3.9 35.7 - - + -
1096A LYS 4.7 10.8 - - - +
1097A LEU* 4.0 16.1 - - + +
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Residues in contact with TYR 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A ILE* 4.1 12.6 - - + -
864A ILE* 3.4 36.2 - - + +
869A PHE* 3.3 25.4 + + + +
870A ALA* 3.2 9.7 + - - +
872A ILE* 1.3 78.3 - - + +
874A LEU* 1.3 50.5 + - - +
876A SER* 3.1 5.6 + - - -
877A HIS* 2.7 33.5 + - - +
896A VAL* 4.2 6.1 - - + +
899A SER* 3.0 25.6 + - - -
901A VAL* 4.1 9.4 - - + -
902A ALA* 3.7 28.7 - - + -
905A THR* 4.0 18.4 - - + +
907A ILE* 3.7 7.2 - - + +
960A PHE* 4.4 0.2 - - - -
963A PHE* 3.5 33.9 - + - -
974A ILE* 3.8 16.6 - - + -
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Residues in contact with LEU 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ILE* 6.0 4.7 - - + -
829A ALA* 4.6 16.8 - - + -
832A GLU* 3.4 44.6 - - + +
833A ILE* 3.3 28.0 - - + -
836A MET* 4.3 13.0 - - - -
870A ALA 3.2 5.8 + - - +
871A VAL* 3.2 8.9 + - - +
873A TYR* 1.3 76.7 - - - +
875A ILE* 1.3 72.8 + - + +
877A HIS* 3.0 16.8 + - + +
878A LYS* 3.0 37.1 + - - +
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Residues in contact with ILE 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ILE* 3.9 24.9 - - + -
871A VAL* 2.8 25.2 + - + +
872A ILE* 4.1 3.1 - - - +
874A LEU* 1.3 80.6 - - + +
876A SER* 1.3 64.2 + - - +
878A LYS* 3.1 19.0 + - + +
879A LEU* 3.0 31.5 + - + +
990A THR* 5.1 1.8 - - + -
993A LEU* 4.2 22.8 - - + +
994A PHE* 3.5 40.2 - - + -
1097A LEU* 3.7 19.3 - - + -
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Residues in contact with SER 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A ILE 2.8 26.0 + - - -
873A TYR 3.3 5.8 - - - -
875A ILE* 1.3 73.3 - - - +
877A HIS* 1.3 61.8 + - - +
879A LEU* 3.6 10.5 + - - +
880A VAL* 3.2 23.4 + - - +
907A ILE* 3.3 20.3 - - - +
974A ILE* 3.4 24.8 - - - +
976A LEU* 3.9 13.4 - - - +
1097A LEU* 3.6 13.2 - - - +
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Residues in contact with HIS 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A GLU* 5.7 0.9 - - - -
836A MET* 3.6 35.2 - - + +
873A TYR 2.7 13.7 + - - +
874A LEU* 3.0 19.5 + - + +
876A SER* 1.3 72.9 - - - +
878A LYS* 1.3 69.9 + - + +
880A VAL* 3.3 4.2 + - - +
881A LYS* 2.9 49.4 + - + +
905A THR* 2.7 25.0 + - - +
906A GLU* 4.4 17.6 + - + +
907A ILE* 2.7 19.0 - - + +
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Residues in contact with LYS 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A GLU* 3.9 11.1 + - - -
874A LEU* 3.0 40.9 + - - +
875A ILE* 3.1 12.1 + - + +
877A HIS* 1.3 82.3 - - + +
879A LEU* 1.3 61.2 + - - +
881A LYS* 3.8 8.2 - - + +
882A LYS* 2.8 32.9 + - - +
989A TYR* 3.7 19.7 - - + +
993A LEU* 4.0 28.0 - - + -
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Residues in contact with LEU 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ILE* 3.0 36.5 + - + +
876A SER* 3.8 11.4 - - - +
878A LYS* 1.3 76.6 - - - +
880A VAL* 1.3 63.4 + - - +
882A LYS* 3.6 2.0 + - + +
883A SER* 3.1 23.6 + - - -
976A LEU* 5.0 3.8 - - + -
978A PHE* 3.9 15.8 - - + -
982A TYR* 5.0 1.4 + - - -
986A ALA* 3.3 38.1 - - + +
989A TYR* 3.7 22.9 - - + -
990A THR* 4.1 8.1 - - + +
993A LEU* 4.8 1.1 - - + -
1097A LEU* 4.6 4.9 - - + -
1099A ILE* 3.8 25.6 - - + -
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Residues in contact with VAL 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A SER 3.2 14.0 + - - +
877A HIS 3.7 6.3 - - - +
879A LEU* 1.3 79.7 - - - +
881A LYS* 1.3 65.0 + - - +
883A SER* 3.2 4.0 + - - -
884A LEU* 3.1 40.8 + - + +
890A VAL* 4.1 36.3 - - + -
906A GLU* 3.7 25.6 - - + +
907A ILE* 4.7 2.7 - - + +
976A LEU* 4.1 20.2 - - + -
978A PHE* 4.6 0.7 - - + -
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Residues in contact with LYS 881 (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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877A HIS* 2.9 43.0 + - + +
878A LYS* 3.8 7.2 - - + +
880A VAL* 1.3 75.8 - - - +
882A LYS* 1.3 58.0 + - - +
884A LEU* 3.2 10.3 + - + +
885A ASP* 2.9 47.9 + - - +
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Residues in contact with LYS 882 (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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1A PO4 2.9 35.8 + - - -
878A LYS 2.8 21.2 + - - +
879A LEU* 4.0 2.7 - - + +
881A LYS* 1.3 72.2 - - - +
883A SER* 1.3 57.9 + - - +
885A ASP* 3.2 9.3 + - + +
886A ASP* 2.7 54.6 + - - +
982A TYR* 3.4 12.0 + - - +
985A ARG* 5.1 4.2 - - - +
986A ALA* 5.9 0.7 - - - -
989A TYR* 3.4 55.9 - - + +
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Residues in contact with SER 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A LEU 3.1 15.2 + - - -
880A VAL 3.2 8.3 + - - -
882A LYS* 1.3 76.9 - - - +
884A LEU* 1.3 59.7 + - - +
886A ASP* 3.1 4.0 + - - +
887A GLY 3.1 5.7 + - - -
888A TYR* 2.6 55.8 + - - +
889A LEU 4.5 0.2 + - - -
890A VAL* 3.5 17.7 - - - +
978A PHE* 3.9 3.5 - - - -
982A TYR* 3.5 29.2 + - - -
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Residues in contact with LEU 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A VAL* 3.1 35.7 + - + +
881A LYS* 3.5 10.3 - - + +
883A SER* 1.3 71.0 - - - +
885A ASP* 1.3 64.8 + - - +
887A GLY* 2.8 20.8 + - - -
888A TYR 3.8 4.3 - - - +
889A LEU* 3.8 29.8 - - + +
890A VAL* 4.7 3.4 - - + +
1120A LYS* 5.8 6.7 - - - +
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Residues in contact with ASP 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A LYS* 2.9 41.9 + - - +
882A LYS* 3.7 8.2 - - + +
884A LEU* 1.3 77.7 - - - +
886A ASP* 1.3 65.2 + - - +
887A GLY* 3.2 0.9 + - - -
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Residues in contact with ASP 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PO4 3.8 5.0 + - - -
882A LYS* 2.7 36.9 + - - +
883A SER 3.5 4.5 - - - +
884A LEU 3.0 0.4 - - - -
885A ASP* 1.3 82.9 - - - +
887A GLY* 1.3 59.2 + - - +
888A TYR* 3.5 10.8 - - - -
982A TYR* 2.8 31.9 + - + -
985A ARG* 3.3 28.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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