Contacts of the helix formed by residues 828 - 846 (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 GLY 828 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826A ILE 3.2 0.2 + - - -
827A GLU* 1.3 77.3 - - - +
829A ALA* 1.3 58.9 + - - +
830A ASP 3.5 2.2 - - - -
831A GLU* 3.4 14.3 + - - +
832A GLU* 2.8 37.4 + - - +
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Residues in contact with ALA 829 (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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826A ILE* 3.1 21.0 + - + +
827A GLU 3.4 0.6 + - - -
828A GLY* 1.3 75.9 - - - +
830A ASP* 1.3 68.8 + - - +
832A GLU* 4.0 3.9 - - - +
833A ILE* 3.1 30.1 + - - +
870A ALA* 4.2 2.2 - - - +
871A VAL* 3.7 34.8 - - + +
874A LEU* 4.6 15.5 - - + -
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Residues in contact with ASP 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A ARG* 4.8 12.8 + - - -
828A GLY 3.5 0.2 - - - -
829A ALA* 1.3 79.6 - - - +
831A GLU* 1.3 64.6 + - + +
833A ILE* 3.4 3.1 + - - +
834A ARG* 3.2 19.8 + - - +
865A ILE* 3.7 42.4 - - + +
868A GLY* 5.9 1.0 - - - -
870A ALA* 3.3 23.4 + - - +
871A VAL* 5.1 1.6 + - - +
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Residues in contact with GLU 831 (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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828A GLY* 3.4 15.8 + - - +
829A ALA 3.2 0.4 - - - -
830A ASP* 1.3 83.3 - - + +
832A GLU* 1.3 64.2 + - - +
834A ARG* 3.4 24.9 + - - +
835A GLU* 3.1 25.9 + - - +
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Residues in contact with GLU 832 (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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827A GLU 5.6 0.5 - - - +
828A GLY* 2.8 21.7 + - - +
829A ALA 4.0 3.1 - - - +
831A GLU* 1.3 79.5 - - + +
833A ILE* 1.3 56.5 + - - +
835A GLU* 3.3 17.0 + - + +
836A MET* 2.8 41.1 + - + +
874A LEU* 3.4 39.5 - - + +
877A HIS* 5.7 1.4 - - - -
878A LYS* 3.9 9.6 + - - -
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Residues in contact with ILE 833 (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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829A ALA 3.1 21.2 + - - +
830A ASP 3.8 3.8 - - - +
831A GLU 3.4 0.2 - - - -
832A GLU* 1.3 77.0 - - - +
834A ARG* 1.3 53.9 + - - +
836A MET* 3.8 2.3 - - - +
837A SER* 2.5 35.7 + - - -
861A LEU* 3.9 18.6 - - + -
864A ILE* 5.1 4.5 - - + -
865A ILE* 5.5 1.1 - - + -
870A ALA* 3.6 27.6 - - + +
873A TYR* 4.1 11.9 - - + -
874A LEU* 3.3 44.9 - - + +
901A VAL* 4.0 15.5 - - + -
905A THR* 4.3 15.4 - - + +
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Residues in contact with ARG 834 (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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830A ASP 3.2 13.8 + - - +
831A GLU* 3.4 27.0 + - - +
832A GLU 3.2 0.2 - - - -
833A ILE* 1.3 78.0 - - - +
835A GLU* 1.3 84.4 + - - +
837A SER* 3.3 3.9 + - - -
838A TYR* 3.0 48.9 + - + +
861A LEU* 3.7 26.6 - - + +
865A ILE* 5.0 6.3 - - + -
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Residues in contact with GLU 835 (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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831A GLU* 3.1 20.0 + - - +
832A GLU* 3.7 16.7 - - + +
834A ARG* 1.3 97.8 - - - +
836A MET* 1.3 89.1 + - - +
838A TYR* 4.6 1.6 - - - +
839A ARG* 2.9 54.4 + - + +
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Residues in contact with MET 836 (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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832A GLU* 2.8 31.2 + - + +
833A ILE* 3.8 4.3 - - - +
835A GLU* 1.3 86.1 - - - +
837A SER* 1.3 62.8 + - - +
839A ARG* 3.9 20.2 + - - +
840A ARG* 3.1 30.7 + - + +
874A LEU* 4.3 14.1 - - - -
877A HIS* 3.6 42.4 - - + -
904A MET 4.0 5.6 - - - +
905A THR* 3.6 38.8 - - + -
906A GLU* 5.7 1.1 - - - +
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Residues in contact with SER 837 (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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833A ILE 2.5 23.3 + - - -
834A ARG 3.3 5.4 + - - -
836A MET* 1.3 80.4 - - - +
838A TYR* 1.3 60.3 + - - +
841A ALA* 3.0 26.4 + - - +
857A LEU* 4.0 16.2 - - - -
861A LEU* 3.8 16.5 - - - +
901A VAL* 4.0 13.4 - - - +
904A MET* 3.8 26.6 - - - +
905A THR* 4.4 3.1 - - - -
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Residues in contact with TYR 838 (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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834A ARG* 3.0 51.3 + - + +
835A GLU* 4.3 3.4 - - - +
837A SER* 1.3 76.8 - - - +
839A ARG* 1.3 61.8 + - - +
841A ALA* 3.9 0.7 - - - +
842A LYS* 3.0 45.3 + - - +
849A LEU* 3.9 12.1 - - + -
854A GLU* 3.4 23.5 + - - -
857A LEU* 3.8 28.9 - - + +
858A GLU* 3.2 37.4 + - - +
861A LEU* 3.5 23.3 - - + -
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Residues in contact with ARG 839 (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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835A GLU* 2.9 48.9 + - - +
836A MET* 3.9 25.3 + - - +
838A TYR* 1.3 73.1 - - - +
840A ARG* 1.3 70.0 + - - +
842A LYS* 3.3 7.7 + - - +
843A GLU* 3.0 49.3 + - - +
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Residues in contact with ARG 840 (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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836A MET* 3.1 21.0 + - + +
837A SER 4.1 2.2 - - - +
839A ARG* 1.3 85.0 - - - +
841A ALA* 1.3 61.3 + - - +
843A GLU* 2.8 51.9 + - - +
844A ILE* 3.3 40.0 + - + +
903A THR 5.5 0.2 - - - +
904A MET* 3.4 37.0 - - + +
906A GLU* 3.6 31.8 + - - +
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Residues in contact with ALA 841 (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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837A SER 3.0 19.7 + - - +
838A TYR 3.9 2.5 - - - +
840A ARG* 1.3 72.8 - - - +
842A LYS* 1.3 56.5 + - - +
844A ILE 3.3 0.3 + - - -
845A TYR* 2.7 43.0 + - + +
849A LEU* 3.8 9.4 - - + -
853A VAL* 4.3 2.0 - - + -
857A LEU* 3.8 23.1 - - + -
900A PHE* 4.2 7.9 - - + -
904A MET* 3.5 20.9 - - + -
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Residues in contact with LYS 842 (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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838A TYR* 3.0 40.9 + - - +
839A ARG* 3.7 7.4 - - - +
840A ARG 3.3 0.2 - - - -
841A ALA* 1.3 77.8 - - - +
843A GLU* 1.3 60.7 + - - +
846A GLY* 2.6 38.8 + - - +
847A ASP* 3.6 34.6 + - + +
848A PRO* 5.6 0.4 - - - -
849A LEU* 3.7 28.7 - - + +
854A GLU* 6.1 0.4 - - - -
923A LYS* 4.3 2.3 - - - +
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Residues in contact with GLU 843 (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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839A ARG* 3.0 39.2 + - - +
840A ARG* 2.8 55.8 + - - +
842A LYS* 1.3 77.3 - - - +
844A ILE* 1.3 58.3 + - - +
923A LYS* 3.2 30.3 + - - +
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Residues in contact with ILE 844 (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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840A ARG* 3.3 44.0 - - - +
841A ALA 3.3 0.6 + - - -
842A LYS 3.0 0.4 - - - -
843A GLU* 1.3 82.1 - - - +
845A TYR* 1.3 84.7 + - + +
846A GLY 3.6 0.9 - - - -
904A MET* 4.0 26.0 - - + -
918A VAL* 3.7 23.7 - - + +
919A CYS 4.6 2.4 - - - +
923A LYS* 3.4 15.7 - - - +
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Residues in contact with TYR 845 (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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841A ALA* 2.7 26.9 + - - +
844A ILE* 1.3 95.5 - - + +
846A GLY* 1.3 56.8 + - - +
848A PRO 4.5 0.7 - - - +
849A LEU* 4.2 5.4 - - + -
850A PRO* 3.4 31.9 - - + +
853A VAL* 4.2 14.1 - - + -
900A PHE* 4.0 25.6 - + - -
904A MET* 4.8 0.7 - - + -
911A ASN* 3.1 16.7 + - - -
913A LEU* 3.7 6.3 - - + +
916A HIS* 2.8 33.6 + + - -
918A VAL* 3.7 24.2 - - + +
923A LYS* 3.7 16.3 - - - +
925A SER* 4.6 6.7 + - - -
927A PHE* 3.9 17.0 - + - -
954A ASP* 5.3 0.7 + - - +
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Residues in contact with GLY 846 (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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842A LYS* 2.6 25.2 + - - +
844A ILE 3.6 1.2 - - - -
845A TYR* 1.3 70.2 - - - +
847A ASP* 1.3 61.1 + - - +
848A PRO 3.0 20.4 - - - +
849A LEU* 3.2 18.5 + - - +
923A LYS* 3.6 18.3 - - - +
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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
------------------------------------------------------------
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