Contacts of the helix formed by residues 795 - 812 (chain B) in PDB entry 1MQB
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 795 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B VAL* 3.2 17.9 - - - +
764B LEU* 4.0 10.5 - - - +
787B GLU* 4.6 3.8 - - - +
793B LYS* 3.9 8.3 - - - +
794B PHE* 1.3 77.1 + - - +
796B SER* 1.3 61.2 + - - +
797B ALA* 3.0 28.7 - - + +
798B SER* 2.7 32.4 - - - +
799B ASP 3.2 3.5 + - - -
858B ARG* 4.4 25.3 + - - +
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Residues in contact with SER 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ALA* 3.2 33.7 - - - +
735B TYR 4.6 2.8 + - - -
736B VAL* 4.3 1.7 - - - +
764B LEU* 4.1 18.1 - - - +
795B THR* 1.3 73.6 - - - +
797B ALA* 1.3 56.5 + - - +
799B ASP* 3.2 14.3 + - - +
800B VAL* 3.0 31.5 + - - +
863B LYS* 5.6 7.6 - - - -
864B PHE* 3.7 7.3 - - - -
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Residues in contact with ALA 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B THR* 3.0 15.2 - - + +
796B SER* 1.3 74.7 - - - +
798B SER* 1.3 59.7 + - - +
800B VAL* 3.2 10.0 + - - +
801B TRP 3.0 18.5 + - - -
858B ARG* 3.5 35.4 - - + +
861B ARG* 3.0 24.5 + - + +
862B PRO 5.5 0.9 - - - +
863B LYS* 5.5 10.2 - - - +
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Residues in contact with SER 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B VAL* 4.7 1.3 - - - -
784B THR* 5.4 0.5 - - - +
785B ALA* 4.1 6.6 + - - +
787B GLU* 3.7 11.6 + - - -
788B ALA* 3.7 15.2 - - - +
793B LYS 3.6 12.0 + - - -
794B PHE* 3.6 14.4 - - - -
795B THR* 2.7 35.7 + - - +
797B ALA* 1.3 73.7 - - - +
799B ASP* 1.3 61.1 + - - -
801B TRP* 3.1 21.1 - - - +
802B SER* 3.3 8.7 + - - -
861B ARG* 3.8 2.4 - - - +
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Residues in contact with ASP 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B MET* 3.4 19.5 - - + +
735B TYR 4.3 2.3 - - - +
736B VAL* 3.5 16.1 - - - +
737B HIS* 2.9 24.5 + - - +
738B ARG* 3.1 26.6 + - - -
740B LEU* 3.7 5.1 - - + +
795B THR 3.2 0.8 + - - +
796B SER* 3.2 13.8 + - - +
798B SER* 1.3 80.8 - - - +
800B VAL* 1.3 57.5 + - - +
802B SER* 3.2 12.0 + - - -
803B PHE* 2.8 27.5 + - - +
864B PHE* 3.6 16.7 - - + -
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Residues in contact with VAL 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B SER* 3.0 19.2 + - - +
797B ALA* 3.4 14.4 - - - +
798B SER 3.2 0.2 - - - -
799B ASP* 1.3 73.3 - - - +
801B TRP* 1.3 68.8 + - - +
803B PHE* 3.2 3.0 + - - +
804B GLY 3.1 14.7 + - - -
853B CYS* 3.2 29.5 - - + +
861B ARG* 3.8 13.5 - - + -
862B PRO* 3.4 28.3 - - + +
863B LYS* 4.8 0.7 - - - -
864B PHE* 3.5 36.1 - - + +
867B ILE* 4.1 4.0 - - + -
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Residues in contact with TRP 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B ARG 5.2 1.0 + - - -
783B TRP 3.5 14.2 + - - -
784B THR 3.6 9.4 + - - -
785B ALA* 3.4 27.6 - - + -
786B PRO* 3.5 27.8 - - + -
797B ALA 3.0 10.1 + - - +
798B SER 3.1 12.1 - - - +
800B VAL* 1.3 75.5 - - - +
802B SER* 1.3 53.1 + - - +
804B GLY* 2.8 24.6 + - - -
805B ILE* 3.2 22.1 + - + +
818B TYR* 4.7 4.1 + - - -
830B ILE* 4.0 22.4 - - + -
835B ARG* 3.7 24.5 - - - -
853B CYS 3.5 9.6 + - - +
854B TRP* 2.8 57.5 + + + -
855B GLN 3.9 0.9 - - - -
861B ARG* 3.5 22.9 - - - +
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Residues in contact with SER 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B ARG 5.2 4.7 + - - -
740B LEU* 3.3 36.8 + - - +
783B TRP* 2.7 25.7 + - - +
784B THR* 4.6 1.9 - - - -
798B SER 3.3 8.9 + - - -
799B ASP* 3.2 14.6 + - - -
801B TRP* 1.3 78.1 - - - +
803B PHE* 1.3 58.5 + - - +
805B ILE* 2.9 8.4 + - - +
806B VAL* 2.9 28.9 + - - +
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Residues in contact with PHE 803 (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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720B LEU* 3.6 37.2 - - + -
723B ILE* 3.7 22.0 - - + -
724B ALA* 3.7 20.6 - - + -
740B LEU* 3.6 11.4 - - + -
799B ASP 2.8 17.2 + - - +
800B VAL* 3.5 4.9 - - - +
801B TRP 3.1 0.4 - - - -
802B SER* 1.3 77.5 - - - +
804B GLY* 1.3 55.0 + - - +
806B VAL* 3.5 5.1 - - + +
807B MET* 2.7 62.0 + - + +
853B CYS* 4.2 2.9 - - - -
864B PHE* 3.7 19.7 - + + -
867B ILE* 3.6 33.9 - - + -
871B LEU* 4.4 2.0 - - + -
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Residues in contact with GLY 804 (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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800B VAL 3.1 6.5 + - - -
801B TRP 2.8 9.5 + - - -
803B PHE* 1.3 77.2 - - - +
805B ILE* 1.3 60.7 + - - +
807B MET* 3.3 11.0 + - - +
808B TRP 3.1 16.3 + - - -
850B MET* 3.6 3.6 - - - +
853B CYS* 3.8 18.8 - - - -
854B TRP* 3.3 25.4 - - - -
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Residues in contact with ILE 805 (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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782B ARG 3.8 15.3 - - - +
783B TRP* 3.6 27.1 - - + +
801B TRP* 3.2 21.4 + - + +
802B SER 2.9 7.4 + - - +
804B GLY* 1.3 75.0 - - - +
806B VAL* 1.3 54.3 + - - +
808B TRP* 2.9 5.4 + - + +
809B GLU* 2.8 30.9 + - - +
817B PRO* 3.4 35.0 - - + -
818B TYR* 3.8 22.0 - - - +
836B LEU* 3.9 9.0 - - + -
854B TRP* 3.5 26.9 - - + +
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Residues in contact with VAL 806 (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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700B LEU* 5.0 0.2 - - + -
720B LEU* 4.4 2.7 - - + -
723B ILE* 3.9 33.4 - - + -
740B LEU* 3.7 25.6 - - + +
741B ALA* 3.7 24.0 - - - -
742B ALA* 4.5 12.3 - - - +
745B ILE* 4.7 1.8 - - + -
783B TRP* 4.9 0.2 - - + -
802B SER 2.9 18.1 + - - +
803B PHE* 3.5 9.6 - - + +
805B ILE* 1.3 71.1 - - - +
807B MET* 1.3 69.2 + - - +
808B TRP 3.1 0.2 + - - -
809B GLU* 3.1 10.4 + - - +
810B VAL* 2.9 28.1 + - + +
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Residues in contact with MET 807 (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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720B LEU* 3.6 20.8 - - + +
803B PHE* 2.7 54.8 + - + +
804B GLY* 3.4 7.6 - - - +
806B VAL* 1.3 74.7 - - - +
808B TRP* 1.3 57.0 + - - +
810B VAL* 3.7 1.2 - - - +
811B MET* 3.0 32.9 + - - +
846B ILE* 3.5 44.4 - - + +
849B LEU* 3.6 27.6 - - + -
850B MET* 3.8 26.5 - - + +
853B CYS* 4.4 3.8 - - - -
871B LEU* 5.0 1.8 - - + -
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Residues in contact with TRP 808 (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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804B GLY 3.1 11.6 + - - +
805B ILE* 2.9 10.2 + - - +
807B MET* 1.3 73.6 - - - +
809B GLU* 1.3 66.2 + - - +
811B MET* 3.2 1.7 + - - +
812B THR* 2.8 41.9 + - + -
815B GLU* 3.6 38.4 - - + -
816B ARG 3.7 4.0 - - - -
817B PRO* 3.4 29.4 - - + -
818B TYR 4.2 1.8 - - - -
819B TRP* 3.8 30.3 - + - -
836B LEU* 3.6 30.0 - - + +
837B PRO* 2.8 29.8 + - + -
838B THR 4.7 0.2 - - - -
839B PRO* 3.7 18.6 - - + +
850B MET* 3.8 20.2 - - - +
854B TRP* 4.2 6.3 - + + -
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Residues in contact with GLU 809 (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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701B ASP* 4.4 8.5 - - - +
704B LEU* 4.1 1.8 - - - +
742B ALA* 2.9 44.5 + - + +
743B ARG 4.8 1.0 + - - -
783B TRP* 3.0 35.8 + - - -
805B ILE 2.8 15.6 + - - +
806B VAL* 3.5 15.0 - - - +
808B TRP* 1.3 75.2 - - + +
810B VAL* 1.3 57.9 + - - +
812B THR* 3.4 8.2 - - - +
813B TYR 3.2 2.3 + - - -
814B GLY* 2.6 35.0 + - - +
815B GLU 3.8 9.1 - - - +
817B PRO* 3.6 22.3 - - + +
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Residues in contact with VAL 810 (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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700B LEU* 3.6 31.9 - - + -
704B LEU* 3.6 9.9 - - + +
716B LEU* 3.7 46.3 - - + +
719B MET* 3.9 11.9 - - + -
720B LEU* 3.7 23.3 - - + -
723B ILE* 4.7 0.7 - - + -
742B ALA* 5.4 0.4 - - + -
806B VAL* 2.9 22.4 + - + +
807B MET 3.7 2.9 - - - +
809B GLU* 1.3 75.0 - - + +
811B MET* 1.3 60.1 + - - +
812B THR 3.0 8.9 + - - -
813B TYR* 3.2 11.1 + - - -
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Residues in contact with MET 811 (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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713B VAL* 4.5 12.6 - - + +
716B LEU* 3.7 35.7 - - + +
717B VAL* 4.9 3.4 - - + -
720B LEU* 3.9 20.6 - - + -
807B MET 3.0 21.1 + - - +
810B VAL* 1.3 74.9 - - - +
812B THR* 1.3 57.7 + - - +
813B TYR* 3.5 9.8 - - - -
839B PRO* 3.7 28.1 - - + +
840B MET 4.5 7.1 - - - +
841B ASP 5.3 0.9 - - - +
842B CYS* 4.0 7.1 - - + +
843B PRO* 4.2 24.7 - - + -
846B ILE* 3.6 26.5 - - + -
850B MET* 4.1 1.1 - - + -
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Residues in contact with THR 812 (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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708B ASP* 4.8 1.4 - - - +
808B TRP* 2.8 35.4 - - + +
809B GLU* 3.4 8.7 - - - +
810B VAL 3.0 0.2 - - - -
811B MET* 1.3 76.5 - - - +
813B TYR* 1.3 68.6 + - - +
815B GLU* 3.0 48.1 + - + +
839B PRO* 3.7 19.7 - - - +
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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