Contacts of the helix formed by residues 870 - 884 (chain B) in PDB entry 5MJA
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 ARG 870 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807B VAL* 4.6 3.1 - - - -
868B ARG 5.0 2.9 - - - +
869B PRO* 1.3 77.4 - - - +
871B PHE* 1.3 64.6 + - - +
872B ALA* 3.2 9.0 - - + +
873B GLU* 3.1 33.8 + - + +
874B ILE* 3.1 11.8 + - - +
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Residues in contact with PHE 871 (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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729B ALA* 4.1 9.9 - - - +
732B MET* 3.5 47.1 - - + -
733B LYS* 3.6 24.5 - - + +
736B SER* 3.7 23.5 + - - +
745B LEU* 4.4 0.2 - - + -
803B SER* 3.9 5.4 - - - -
806B ASP* 3.7 17.5 - - + -
807B VAL* 3.6 33.8 - - + +
810B TYR* 3.5 29.4 - + + -
870B ARG* 1.3 72.6 - - - +
872B ALA* 1.4 56.0 + - - +
874B ILE* 3.2 14.9 + - + +
875B VAL* 3.0 32.7 + - - +
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Residues in contact with ALA 872 (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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733B LYS* 3.7 32.9 - - - +
737B GLU* 4.0 11.5 + - - +
870B ARG* 3.2 7.8 - - + +
871B PHE* 1.4 76.3 - - - +
873B GLU* 1.3 58.8 + - + +
875B VAL* 3.5 3.1 + - - +
876B ASN* 3.1 36.8 + - - +
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Residues in contact with GLU 873 (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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868B ARG 4.7 0.9 - - - +
869B PRO* 3.7 18.7 - - + +
870B ARG* 3.1 39.3 + - + +
872B ALA* 1.3 77.9 - - + +
874B ILE* 1.3 59.9 + - - +
876B ASN* 3.2 10.4 + - - +
877B THR* 2.9 36.3 + - - +
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Residues in contact with ILE 874 (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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729B ALA* 3.7 14.6 - - + -
807B VAL* 3.9 26.2 - - + -
810B TYR* 3.5 29.4 - - + +
856B LEU* 4.3 16.2 - - + -
860B CYS* 3.9 10.8 - - - -
869B PRO* 3.9 17.9 - - + +
870B ARG 3.1 13.4 + - - +
871B PHE* 3.5 29.8 - - + +
873B GLU* 1.3 75.8 - - - +
875B VAL* 1.3 63.6 + - - +
877B THR* 3.3 7.0 + - - -
878B LEU* 3.0 27.4 + - + +
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Residues in contact with VAL 875 (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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676A ASP* 5.3 0.7 - - - +
726B ARG* 3.5 35.8 - - - +
729B ALA* 3.6 34.8 - - + +
730B ALA* 3.7 10.5 - - + +
733B LYS* 4.2 15.9 - - + -
871B PHE 3.0 18.5 + - - +
872B ALA* 3.7 8.5 - - - +
874B ILE* 1.3 75.4 - - - +
876B ASN* 1.3 60.7 + - - +
878B LEU* 3.3 6.0 + - - +
879B ASP* 2.8 34.0 + - - +
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Residues in contact with ASN 876 (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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611A ALA* 3.7 25.3 - - + +
673A GLY 5.3 4.5 - - - +
872B ALA* 3.1 21.1 + - - +
873B GLU* 3.2 12.9 + - - +
875B VAL* 1.3 79.1 - - - +
877B THR* 1.3 57.3 + - - +
879B ASP* 3.4 6.6 + - - +
880B LYS* 3.0 43.2 + - - +
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Residues in contact with THR 877 (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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856B LEU* 4.1 21.9 - - + +
873B GLU* 2.9 20.2 + - - +
874B ILE* 3.3 7.1 + - - -
876B ASN* 1.3 76.7 - - - +
878B LEU* 1.4 55.6 + - - +
880B LYS* 3.3 14.2 + - - +
881B MET* 3.1 50.0 + - + +
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Residues in contact with LEU 878 (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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722B VAL* 4.2 13.2 - - + +
725B LEU* 3.7 5.4 - - + +
726B ARG* 3.5 36.6 - - + +
729B ALA* 4.1 2.9 - - + -
810B TYR* 3.3 27.1 - - - +
814B MET* 5.0 0.9 - - + -
853B LEU* 3.9 21.3 - - + -
856B LEU* 3.8 20.9 - - + -
874B ILE* 3.0 27.1 + - + +
875B VAL* 3.7 4.0 - - - +
877B THR* 1.4 72.6 - - - +
879B ASP* 1.4 58.4 + - - +
881B MET* 3.3 11.1 + - - +
882B ILE* 3.0 35.3 + - - +
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Residues in contact with ASP 879 (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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611A ALA* 3.7 12.6 - - + +
612A LYS* 3.4 22.7 - - + +
726B ARG* 2.8 46.6 + - - +
875B VAL* 2.8 23.8 + - - +
876B ASN* 3.6 11.1 - - - +
878B LEU* 1.4 74.2 - - - +
880B LYS* 1.3 62.5 + - - +
882B ILE* 3.6 3.4 + - - +
883B ARG* 3.0 44.8 + - - +
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Residues in contact with LYS 880 (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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609A GLU* 5.6 10.4 - - - +
610A PHE 4.7 4.0 - - - +
611A ALA* 3.4 38.4 - - - +
876B ASN* 3.0 25.2 + - - +
877B THR* 3.3 12.2 + - - +
879B ASP* 1.3 74.8 - - - +
881B MET* 1.4 53.1 + - + +
883B ARG* 3.2 5.0 + - - +
884B ASN* 2.8 40.2 + - + +
887B SER* 4.8 0.7 - - - -
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Residues in contact with MET 881 (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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719B ILE* 5.0 0.2 - - - +
722B VAL* 4.8 3.1 - - + -
852B ALA* 3.5 41.5 - - + +
853B LEU* 3.9 20.0 - - + +
856B LEU* 4.6 3.8 - - + -
877B THR* 3.1 36.3 + - + +
878B LEU* 3.3 17.5 + - - +
880B LYS* 1.4 75.7 - - - +
882B ILE* 1.3 61.2 + - - +
884B ASN 3.3 18.9 + - - +
885B PRO* 4.9 0.5 - - - +
887B SER* 3.4 22.2 - - - +
888B LEU* 3.4 38.8 - - + +
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Residues in contact with ILE 882 (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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640A LEU* 4.0 20.9 - - + +
641A PRO* 3.6 23.0 - - - +
643A LYS* 4.3 15.9 - - - +
719B ILE* 3.9 22.5 - - + +
722B VAL* 3.7 21.1 - - + -
723B GLY* 4.5 11.4 - - - +
726B ARG* 4.0 31.2 - - + -
878B LEU 3.0 21.8 + - - +
879B ASP* 3.8 9.2 - - - +
881B MET* 1.3 75.4 - - - +
883B ARG* 1.3 72.0 + - - +
888B LEU* 4.8 0.2 - - - -
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Residues in contact with ARG 883 (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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611A ALA 4.0 0.7 - - - -
612A LYS* 3.6 49.1 + - - +
613A GLU 3.5 20.3 - - - +
614A ILE* 3.5 15.8 - - + +
615A ASP 5.2 0.9 + - - -
618A PHE* 3.3 25.9 - - - -
640A LEU* 4.2 19.5 - - + +
641A PRO* 4.9 1.8 - - - -
683A LEU 4.5 0.2 + - - -
684A GLU* 2.8 38.6 + - - +
879B ASP* 3.0 42.8 + - - +
880B LYS* 3.2 6.5 + - - +
882B ILE* 1.3 92.3 - - - +
884B ASN* 1.3 57.1 + - - +
885B PRO* 3.4 5.1 - - - +
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Residues in contact with ASN 884 (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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880B LYS* 2.8 16.5 + - + +
881B MET 3.3 7.6 + - - +
883B ARG* 1.3 78.6 - - - +
885B PRO* 1.4 66.7 - - - +
886B ALA* 3.6 18.7 + - - +
887B SER* 2.8 51.0 + - - +
888B LEU 3.9 0.5 + - - -
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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