Contacts of the helix formed by residues 850 - 869 (chain A) in PDB entry 4B87
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 SER 850 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A ARG* 3.8 9.4 - - - +
849A PRO* 1.3 79.4 - - - +
851A GLN* 1.3 64.8 + - - +
852A GLN* 3.5 10.2 + - - +
853A GLU* 3.1 35.9 + - - +
854A VAL* 3.1 20.0 + - - +
999A GLU* 5.3 0.9 - - - -
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Residues in contact with GLN 851 (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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792A ASN* 4.9 16.4 + - - +
793A HIS 5.2 1.0 + - - -
817A ARG* 3.4 29.5 - - - +
849A PRO 3.9 0.6 + - - -
850A SER* 1.3 73.8 - - - +
852A GLN* 1.3 58.0 + - - +
854A VAL* 3.2 4.5 + - - +
855A ILE* 2.9 37.4 + - + +
885A LYS* 4.4 12.8 - - + +
991A TYR* 3.3 38.9 + - + +
992A SER 3.0 21.2 + - - +
993A GLU* 4.0 13.9 - - - +
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Residues in contact with GLN 852 (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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850A SER* 3.2 8.3 + - - +
851A GLN* 1.3 78.9 - - - +
853A GLU* 1.3 68.8 + - - +
855A ILE* 3.3 9.7 + - - +
856A ARG* 3.0 35.3 + - + +
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Residues in contact with GLU 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A PRO* 3.7 20.7 - - + +
850A SER* 3.1 38.7 + - - +
852A GLN* 1.3 83.8 - - - +
854A VAL* 1.3 63.1 + - - +
856A ARG* 3.5 16.1 + - - +
857A PHE* 3.1 22.2 + - - +
974A ALA* 4.5 14.5 - - + +
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Residues in contact with VAL 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A PRO* 4.0 20.6 - - + +
850A SER 3.1 16.4 + - - +
851A GLN* 3.2 6.7 + - - +
853A GLU* 1.3 78.4 - - - +
855A ILE* 1.3 56.2 + - - +
857A PHE* 3.3 4.9 + - + +
858A ALA* 2.9 24.8 + - - +
886A VAL* 5.8 0.2 - - + -
974A ALA 4.5 8.1 - - - +
989A ILE* 3.9 32.5 - - + -
990A PRO* 3.6 27.1 - - + +
991A TYR* 3.9 26.5 - - + +
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Residues in contact with ILE 855 (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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851A GLN* 2.9 24.9 + - + +
852A GLN* 3.7 7.6 - - + +
854A VAL* 1.3 73.4 - - - +
856A ARG* 1.3 58.0 + - - +
858A ALA* 3.0 7.4 + - + +
859A ILE* 2.7 41.0 + - + +
885A LYS* 3.9 33.7 - - + +
886A VAL* 4.2 16.4 - - + +
889A ALA* 3.6 28.0 - - + -
991A TYR* 4.1 17.7 - - + +
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Residues in contact with ARG 856 (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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852A GLN* 3.0 28.1 + - + +
853A GLU* 3.5 16.5 - - - +
855A ILE* 1.3 74.6 - - - +
857A PHE* 1.3 67.0 + - - +
859A ILE* 3.5 11.2 - - + +
860A ASN* 3.0 48.3 + - - +
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Residues in contact with PHE 857 (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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853A GLU 3.1 13.7 + - - +
854A VAL 3.3 8.0 + - - +
856A ARG* 1.3 76.9 - - - +
858A ALA* 1.3 58.8 + - - +
860A ASN* 3.4 3.7 + - - +
861A THR* 2.8 56.3 + - - -
959A PHE* 4.6 3.6 - + - -
974A ALA* 3.9 23.3 - - + +
975A ASP* 4.1 19.1 - - - -
976A VAL* 4.2 22.4 - - + -
987A TYR* 4.2 26.2 - + - -
989A ILE* 3.9 29.4 - - + -
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Residues in contact with ALA 858 (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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854A VAL 2.9 14.4 + - - +
855A ILE* 3.0 11.2 + - - +
857A PHE* 1.3 80.3 - - - +
859A ILE* 1.3 59.0 + - + +
861A THR* 3.3 2.4 + - - -
862A ALA* 2.9 30.5 + - - +
886A VAL* 4.6 4.3 - - + -
890A ILE* 4.1 22.4 - - + +
959A PHE* 3.7 23.1 - - + -
989A ILE* 4.4 14.8 - - + -
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Residues in contact with ILE 859 (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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855A ILE* 2.7 30.5 + - + +
856A ARG* 3.5 13.7 - - + +
858A ALA* 1.3 74.6 - - + +
860A ASN* 1.3 67.4 + - - +
862A ALA* 3.9 2.9 - - - +
863A PHE* 2.9 32.3 + - - +
889A ALA* 3.6 42.4 - - + +
890A ILE* 3.9 7.2 - - + +
893A VAL* 3.7 27.1 - - + +
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Residues in contact with ASN 860 (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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856A ARG* 3.0 42.8 + - - +
857A PHE* 4.0 4.4 - - + +
859A ILE* 1.3 79.4 - - - +
861A THR* 1.3 65.1 + - - +
863A PHE* 3.8 7.0 - - - +
864A GLU* 3.1 25.5 + - - +
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Residues in contact with THR 861 (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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857A PHE* 2.8 42.8 + - - -
858A ALA 3.7 4.3 - - - -
860A ASN* 1.3 79.5 - - - +
862A ALA* 1.3 61.1 + - - +
864A GLU* 3.5 11.1 + - - +
865A ALA* 3.0 22.0 + - - +
957A LEU* 4.1 5.2 - - + -
959A PHE* 4.1 15.7 - - + -
987A TYR* 3.8 39.7 - - + +
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Residues in contact with ALA 862 (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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858A ALA 2.9 17.0 + - - +
859A ILE* 3.9 3.6 - - - +
861A THR* 1.3 78.0 - - - +
863A PHE* 1.3 63.1 + - - +
865A ALA* 3.3 7.7 + - - +
866A VAL* 3.0 28.4 + - - +
874A VAL* 4.0 15.9 - - + -
890A ILE* 3.9 26.7 - - + -
893A VAL* 4.9 1.1 - - + -
894A LEU* 4.1 7.0 - - + -
957A LEU* 5.0 1.6 - - - -
959A PHE* 4.5 8.7 - - + -
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Residues in contact with PHE 863 (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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859A ILE 2.9 18.6 + - - +
860A ASN* 3.8 7.2 - - - +
862A ALA* 1.3 74.1 - - - +
864A GLU* 1.3 69.4 + - + +
866A VAL* 3.3 6.5 + - + +
867A THR* 3.0 44.9 + - + -
893A VAL* 4.2 31.6 - - + -
894A LEU* 4.2 11.1 - - + +
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Residues in contact with GLU 864 (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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860A ASN 3.1 15.8 + - - +
861A THR* 3.9 10.8 - - - +
863A PHE* 1.3 83.9 - - + +
865A ALA* 1.3 63.4 + - - +
867A THR* 3.3 7.6 + - - -
868A LEU* 3.0 26.3 + - + +
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Residues in contact with ALA 865 (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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861A THR 3.0 18.6 + - - +
862A ALA* 3.4 6.3 - - - +
863A PHE 3.2 0.2 - - - -
864A GLU* 1.3 79.7 - - - +
866A VAL* 1.3 60.1 - - + +
868A LEU* 3.3 8.7 + - - +
869A ASN* 3.0 26.7 + - - +
872A ALA* 4.4 8.0 - - + +
874A VAL* 5.7 1.1 - - + -
955A GLN* 5.2 7.2 + - - +
957A LEU* 3.4 28.9 - - + -
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Residues in contact with VAL 866 (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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862A ALA 3.0 7.9 + - - +
863A PHE* 3.4 15.7 - - + +
865A ALA* 1.3 75.1 - - + +
867A THR* 1.3 65.2 + - - +
869A ASN 3.1 25.9 - - - +
870A PRO* 3.3 12.5 - - + +
872A ALA* 4.2 23.3 - - + +
874A VAL* 4.5 7.4 - - + -
894A LEU* 3.3 40.8 - - + -
928A LEU* 5.8 8.3 - - + -
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Residues in contact with THR 867 (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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863A PHE* 3.0 39.9 + - + -
864A GLU* 3.6 8.5 - - - -
866A VAL* 1.3 80.3 - - - +
868A LEU* 1.3 60.1 + - - +
869A ASN 3.5 0.2 + - - -
870A PRO* 4.9 3.5 - - - +
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Residues in contact with LEU 868 (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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864A GLU* 3.0 18.5 + - + +
865A ALA* 3.3 6.7 + - - +
867A THR* 1.3 76.9 - - - +
869A ASN* 1.3 61.6 + - + +
870A PRO* 4.3 3.8 - - - +
955A GLN* 5.8 5.8 - - - +
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Residues in contact with ASN 869 (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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865A ALA 3.0 9.2 + - - +
866A VAL* 3.1 10.9 - - - +
867A THR 3.3 0.6 - - - -
868A LEU* 1.3 83.5 - - + +
870A PRO* 1.3 63.5 - - - +
871A HIS* 2.8 28.1 + - - +
872A ALA* 3.0 26.3 + - + +
954A ASN* 2.8 28.9 + - - +
955A GLN* 2.6 34.4 + - - +
2043A EDO 4.2 9.6 - - - -
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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