Contacts of the helix formed by residues 877 - 891 (chain B) in PDB entry 5ZCS
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 ASN 877 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837B ARG* 6.1 0.8 - - - +
838B GLN* 6.1 2.4 - - + +
875B GLU* 3.4 25.6 + - + +
876B GLN* 1.3 77.6 - - - +
878B GLN* 1.3 61.2 + - - +
879B GLY* 4.5 2.0 - - - +
880B THR* 3.6 23.2 + - - +
881B ARG* 3.1 29.4 + - - +
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Residues in contact with GLN 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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876B GLN 3.5 7.1 + - - +
877B ASN* 1.3 72.7 - - - +
879B GLY* 1.3 58.9 + - - +
881B ARG* 4.4 8.7 - - - +
882B ARG* 2.9 46.4 + - + +
1572B ASP* 5.8 3.6 - - - +
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Residues in contact with GLY 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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838B GLN* 3.5 30.0 - - - +
877B ASN* 3.3 2.5 - - - +
878B GLN* 1.3 76.9 - - - +
880B THR* 1.3 57.9 + - - +
882B ARG* 4.3 6.3 - - - -
883B GLU* 3.3 28.0 - - - +
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Residues in contact with THR 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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837B ARG* 4.1 7.5 - - + +
838B GLN* 3.8 22.0 + - - +
841B LEU* 4.6 24.9 - - + +
871B PHE* 5.5 8.3 - - + +
872B LEU* 6.2 1.1 - - + -
875B GLU* 4.4 17.4 + - + +
877B ASN* 3.3 28.9 + - - +
878B GLN 3.2 0.6 - - - -
879B GLY* 1.3 76.8 - - - +
881B ARG* 1.3 61.2 + - + +
883B GLU* 3.4 2.3 + - - +
884B ALA* 2.9 32.2 + - + +
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Residues in contact with ARG 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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871B PHE 5.7 0.4 - - - +
872B LEU* 2.4 50.2 + - + +
873B LYS* 4.0 15.0 + - - +
875B GLU 2.8 32.7 + - - +
876B GLN* 3.7 21.3 - - - +
877B ASN 3.1 17.4 + - - +
878B GLN* 4.0 8.7 - - - +
880B THR* 1.3 79.5 - - + +
882B ARG* 1.3 60.6 + - - +
883B GLU 3.4 0.7 + - - -
884B ALA* 4.4 0.5 - - - +
885B ILE* 3.3 29.7 + - + +
1572B ASP* 4.0 22.2 + - - +
1575B LEU* 5.4 3.4 - - - +
1576B THR* 4.7 11.3 + - - -
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Residues in contact with ARG 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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878B GLN* 2.9 30.9 + - - +
879B GLY* 5.0 5.4 - - - +
881B ARG* 1.3 75.3 - - - +
883B GLU* 1.3 70.8 + - + +
885B ILE* 4.5 5.2 - - - +
886B ARG* 4.1 5.5 + - - +
1565B ASP* 3.1 44.9 + - - +
1568B ARG* 3.5 39.5 - - + +
1569B ASP* 3.2 23.3 + - - -
1572B ASP* 3.5 22.9 - - - +
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Residues in contact with GLU 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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838B GLN* 4.9 15.7 - - - +
841B LEU* 5.1 9.9 - - + -
842B TRP* 4.0 29.0 - - + +
879B GLY* 3.3 21.7 + - - +
880B THR* 3.4 3.2 + - - +
881B ARG 3.2 0.2 - - - -
882B ARG* 1.3 92.5 + - + +
884B ALA* 1.3 60.1 + - - +
885B ILE 3.3 1.8 - - - -
886B ARG* 3.2 29.1 + - - +
887B VAL* 2.9 33.3 + - + +
1565B ASP* 5.8 0.2 - - - +
1568B ARG* 6.0 0.7 - - - -
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Residues in contact with ALA 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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841B LEU* 4.8 17.2 - - + +
871B PHE* 6.5 0.7 - - + -
872B LEU* 3.8 27.1 - - + -
880B THR* 2.9 22.1 + - + +
883B GLU* 1.3 73.8 - - - +
885B ILE* 1.3 60.5 + - - +
887B VAL* 3.3 8.0 + - - -
888B LEU* 2.9 41.6 + - + +
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Residues in contact with ILE 885 (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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872B LEU* 5.0 6.5 - - + -
881B ARG* 3.3 13.2 + - + +
882B ARG* 4.6 6.1 - - - +
883B GLU 3.3 0.2 - - - -
884B ALA* 1.3 77.9 - - - +
886B ARG* 1.3 56.9 + - - +
888B LEU* 3.7 4.1 - - - +
889B GLY* 2.9 27.9 + - - -
1568B ARG* 5.0 9.9 - - + +
1571B LEU* 3.8 41.7 - - + +
1572B ASP* 3.4 26.0 - - - +
1575B LEU* 3.8 31.6 - - + -
1593B CYS* 5.2 8.0 - - + +
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Residues in contact with ARG 886 (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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842B TRP* 4.9 1.4 - - - -
845B GLY* 4.5 14.3 + - - -
846B GLN* 2.6 34.8 + - - +
849B ALA* 5.9 4.2 - - - +
882B ARG 4.1 4.3 + - - +
883B GLU* 3.2 35.1 + - - +
885B ILE* 1.3 79.2 - - - +
887B VAL* 1.3 58.0 + - + +
889B GLY* 5.1 0.7 - - - -
890B LEU* 2.9 56.6 + - + +
1561B GLN* 6.0 1.4 - - - +
1568B ARG* 3.6 41.8 - - - +
1600B GLU* 5.9 5.3 - - - +
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Residues in contact with VAL 887 (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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841B LEU* 3.6 36.1 - - + +
842B TRP* 5.6 0.4 - - - -
844B LEU* 5.0 6.5 - - + +
845B GLY* 3.7 20.9 - - - +
883B GLU* 2.9 22.5 + - + +
884B ALA* 3.6 11.0 - - - +
885B ILE 3.3 0.2 - - - -
886B ARG* 1.3 81.5 - - + +
888B LEU* 1.3 71.1 + - + +
889B GLY 3.4 0.5 + - - -
890B LEU* 3.7 8.3 + - - +
891B LEU* 3.9 11.3 + - - +
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Residues in contact with LEU 888 (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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841B LEU* 6.2 1.6 - - + -
865B LEU* 5.9 3.8 - - + -
868B LEU* 3.8 46.9 - - + -
872B LEU* 5.7 5.4 - - + -
884B ALA* 2.9 28.3 + - + +
885B ILE* 3.7 4.7 - - - +
887B VAL* 1.3 87.5 - - + +
889B GLY* 1.3 57.0 + - - +
891B LEU* 4.5 6.6 + - + +
892B GLY 4.1 13.2 + - - +
1593B CYS* 5.1 2.7 - - - -
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Residues in contact with GLY 889 (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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885B ILE 2.9 16.1 + - - -
886B ARG* 5.1 0.2 - - - -
888B LEU* 1.3 77.9 - - - +
890B LEU* 1.3 63.2 + - - +
891B LEU 3.2 2.7 + - - -
892B GLY* 3.6 12.1 + - - -
1593B CYS* 4.0 27.1 - - - +
1594B HIS* 4.5 1.9 - - - -
1597B SER* 3.3 22.3 + - - -
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Residues in contact with LEU 890 (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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845B GLY 6.0 1.6 - - - +
848B VAL* 4.8 16.5 - - + +
849B ALA* 4.5 19.1 - - + -
886B ARG* 2.9 56.0 + - + +
887B VAL* 4.4 4.3 - - - +
888B LEU 3.7 0.2 - - - -
889B GLY* 1.3 74.1 - - - +
891B LEU* 1.3 63.2 + - - +
1568B ARG* 4.5 7.6 - - - +
1596B LEU* 6.3 0.4 - - + -
1597B SER* 3.9 18.0 + - - +
1600B GLU* 3.3 28.3 - - + +
1601B GLU* 3.7 12.8 - - - +
1622B ARG* 4.3 16.7 + - - +
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Residues in contact with LEU 891 (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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848B VAL* 5.1 11.1 - - + +
853B TYR 5.2 3.1 - - - +
854B VAL* 5.4 7.6 - - + -
855B VAL* 5.5 6.1 - - + +
858B TYR* 3.8 48.5 - - + +
887B VAL 3.9 12.2 + - - +
888B LEU* 4.6 5.8 - - + +
889B GLY 3.2 0.8 - - - -
890B LEU* 1.3 79.0 - - - +
892B GLY* 1.3 67.3 + - - +
893B ALA 4.8 6.1 - - - +
894B LEU* 5.5 10.3 - - + -
1622B ARG* 3.4 30.0 - - + +
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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