Contacts of the helix formed by residues 818 - 831 (chain B) in PDB entry 1B0P
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 818 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700B PRO* 2.6 33.5 + - - +
806B MET* 3.8 16.3 - - + +
809B SER* 3.8 9.6 - - - +
811B ALA* 3.7 20.2 - - + -
815B CYS* 3.8 5.9 - - - +
817B GLU* 1.3 71.9 - - - +
819B PRO* 1.4 71.9 - - - +
821B VAL* 3.2 4.9 + - - -
822B ARG* 3.0 25.5 + - - +
844B TRP* 3.5 31.9 - - + +
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Residues in contact with PRO 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B PHE 4.3 2.7 - - - +
698B VAL 3.6 27.6 - - - +
699B CYS 4.1 9.6 - - - +
700B PRO* 3.8 10.1 - - + -
815B CYS 3.2 23.8 - - - +
816B GLY* 3.7 7.9 - - - +
817B GLU 3.5 4.3 - - - -
818B THR* 1.4 93.3 - - - +
820B TYR* 1.3 62.3 + - + +
822B ARG* 3.5 2.9 + - + +
823B VAL* 3.2 27.0 + - - +
1042B MET* 3.7 21.3 - - + -
1084B GLN* 4.7 4.7 - - - +
1087B MET* 5.6 2.5 - - + -
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Residues in contact with TYR 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B GLY 3.1 27.8 - - - -
817B GLU* 3.6 9.0 - - - +
818B THR 3.2 0.6 - - - -
819B PRO* 1.3 78.8 - - + +
821B VAL* 1.3 63.9 + - - +
822B ARG 3.3 0.2 + - - -
823B VAL 3.3 2.4 + - - -
824B ILE* 3.2 26.4 + - - +
987B PHE* 3.5 24.5 - + + -
989B MET* 5.3 2.0 - - + -
1040B VAL* 3.9 9.9 - - + -
1041B SER* 3.4 8.7 - - - -
1042B MET* 3.1 46.0 + - + +
1049B PHE* 3.6 29.4 - + + -
1067B ALA* 3.6 18.6 - - + -
1068B TYR 2.7 30.3 + - - -
1069B ALA* 4.7 1.3 - - + -
1087B MET* 4.0 9.7 - - + -
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Residues in contact with VAL 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B MET* 3.6 30.5 - - + -
817B GLU 3.3 16.8 - - - +
818B THR 3.2 1.8 + - - +
820B TYR* 1.3 76.0 - - - +
822B ARG* 1.3 64.1 + - - +
824B ILE* 3.2 10.0 + - - +
825B THR* 3.2 24.8 + - + +
844B TRP* 3.7 15.3 - - + -
853B TYR* 3.8 13.9 - - + +
960B PHE* 4.0 20.6 - - + -
987B PHE* 4.6 4.9 - - + -
989B MET* 3.5 28.0 - - + -
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Residues in contact with ARG 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B ALA 2.9 23.7 + - - -
697B PHE* 3.5 10.3 + - - +
699B CYS 4.3 8.4 + - - +
702B SER* 3.2 44.3 + - - +
704B ILE 4.6 8.5 + - - -
800B GLN* 2.6 43.2 + - - +
804B PRO* 3.6 16.0 - - + +
806B MET* 3.4 24.5 - - + +
818B THR 3.0 16.5 + - - +
819B PRO* 4.0 4.2 + - + +
820B TYR 3.2 0.2 - - - -
821B VAL* 1.3 79.5 - - - +
823B VAL* 1.3 60.8 + - - +
825B THR* 2.6 24.6 + - - +
826B GLN* 3.2 26.2 + - - +
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Residues in contact with VAL 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B PHE* 3.8 41.3 - - + +
799B SER* 5.5 0.9 - - - +
800B GLN* 4.7 0.4 - - - +
819B PRO 3.2 17.7 - - - +
820B TYR 3.3 1.2 + - - -
822B ARG* 1.3 77.1 - - - +
824B ILE* 1.3 65.8 + - - +
826B GLN* 3.0 27.5 + - + +
827B LEU* 3.3 17.2 - - + +
1042B MET* 4.0 4.9 - - + -
1049B PHE* 3.1 29.6 - - + -
1050B LEU* 4.2 9.2 - - + -
1053B LEU* 4.0 9.9 - - + -
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Residues in contact with ILE 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B TYR 3.2 17.9 + - - +
821B VAL* 3.2 11.6 + - - +
823B VAL* 1.3 75.4 - - - +
825B THR* 1.3 64.2 + - - +
827B LEU* 3.1 2.8 + - - -
828B PHE* 2.9 42.7 + - + +
829B GLY 3.9 0.3 + - - -
832B MET* 3.9 22.4 - - + -
958B TRP* 4.4 12.1 - - + -
960B PHE* 4.2 11.2 - - + -
987B PHE* 3.8 42.4 - - + -
1049B PHE* 4.4 1.1 - - + -
1053B LEU* 3.8 27.6 - - + -
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Residues in contact with THR 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ARG* 4.4 2.3 + - - -
803B GLU 4.5 0.9 - - - +
805B LEU* 3.2 36.8 + - + +
806B MET* 4.3 16.2 - - + -
821B VAL* 3.2 12.1 + - + +
822B ARG* 2.6 22.9 + - - -
824B ILE* 1.3 79.1 - - + +
826B GLN* 1.3 57.0 + - - +
829B GLY* 2.7 31.0 + - - +
832B MET* 4.2 9.6 - - + -
834B ILE* 5.3 0.4 - - + -
853B TYR* 4.4 8.5 - - + -
862B PRO* 4.1 20.9 - - + -
960B PHE* 6.0 1.1 - - + -
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Residues in contact with GLN 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ARG* 3.0 26.8 + - - +
799B SER* 3.2 25.4 + - - +
800B GLN* 2.9 36.0 + - - +
802B GLN* 3.4 26.0 + - + +
803B GLU 3.6 10.5 - - - +
804B PRO* 3.5 24.3 - - + +
822B ARG* 3.4 24.3 + - - +
823B VAL* 3.0 25.6 + - - +
825B THR* 1.3 79.6 + - - +
827B LEU* 1.3 62.1 + - + +
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Residues in contact with LEU 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ARG* 3.0 54.2 + - + +
794B ASP* 4.0 20.9 - - + -
799B SER* 4.4 7.2 - - - -
823B VAL* 3.3 20.2 - - + +
824B ILE 3.1 6.8 + - - +
826B GLN* 1.3 82.1 - - - +
828B PHE* 1.3 87.0 + - + +
831B ARG* 5.6 0.5 + - - -
1050B LEU* 3.8 24.0 - - + +
1053B LEU* 3.8 26.2 - - + -
1054B LYS* 4.8 3.1 - - + +
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Residues in contact with PHE 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824B ILE* 2.9 29.3 + - + -
827B LEU* 1.3 99.3 - - + +
829B GLY* 1.3 67.5 + - - +
830B GLU* 3.3 9.6 - - - +
831B ARG* 3.0 35.1 + - - +
832B MET* 3.4 17.4 + - - +
956B SER* 4.4 10.8 - - - +
958B TRP* 3.8 21.5 - + - -
1053B LEU* 3.6 25.6 - - + -
1054B LYS* 4.5 4.0 - - - -
1057B GLU* 3.3 41.1 - - + -
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Residues in contact with GLY 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805B LEU* 3.6 14.8 - - - -
825B THR* 2.7 31.3 + - - -
828B PHE* 1.3 71.1 - - - +
830B GLU* 1.3 63.0 + - - +
831B ARG 3.3 0.7 + - - -
832B MET* 3.4 22.4 + - - +
861B GLY 3.3 21.1 - - - -
862B PRO* 3.3 5.0 - - - -
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Residues in contact with GLU 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PRO* 3.2 24.1 - - - +
211A GLU* 3.8 9.5 - - - +
793B ARG* 2.7 44.5 + - - +
805B LEU* 3.8 4.2 - - - +
827B LEU 4.7 0.2 - - - +
828B PHE 3.3 7.1 - - - -
829B GLY* 1.3 71.6 - - - -
831B ARG* 1.3 82.0 + - + +
832B MET 3.6 0.2 - - - -
856B ASN* 3.7 10.1 - - - +
860B GLN* 3.3 42.4 - - + +
861B GLY* 4.2 3.1 - - - +
924B LYS* 6.1 2.3 - - + +
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Residues in contact with ARG 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO* 3.5 13.7 - - - +
211A GLU* 4.9 2.0 - - - +
793B ARG* 5.8 0.4 - - - +
827B LEU 5.6 0.6 + - - -
828B PHE* 3.0 23.8 + - - +
830B GLU* 1.3 99.3 + - + +
832B MET* 1.3 60.8 + - - +
920B PRO* 3.6 35.2 - - - +
924B LYS* 6.5 0.9 - - - -
953B THR* 4.0 15.3 - - - +
954B LYS* 2.8 46.7 + - - +
955B LYS* 3.4 23.0 + - - +
956B SER* 2.8 29.3 + - - +
1057B GLU* 3.0 33.1 + - - -
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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