Contacts of the helix formed by residues 866 - 875 (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 GLU 866 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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862B PRO 4.1 8.1 - - - +
863B THR* 3.7 12.9 + - - +
864B LEU 3.3 0.4 - - - -
865B LEU* 1.3 88.0 + - - +
867B VAL* 1.3 65.0 + - - +
868B LEU 3.3 2.0 - - - -
869B LEU* 3.3 23.3 + - + +
870B ASN* 3.5 10.9 - - - +
899B HIS* 4.1 17.0 + - - -
903B ILE* 5.7 3.5 - - - +
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Residues in contact with VAL 867 (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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829B GLN* 3.7 28.9 - - + +
863B THR* 3.4 19.5 - - - +
864B LEU* 3.7 21.7 + - + +
865B LEU 3.6 0.4 - - - -
866B GLU* 1.3 76.2 - - + +
868B LEU* 1.3 59.6 + - - +
869B LEU 3.2 0.4 - - - -
870B ASN* 3.0 14.4 + - + +
871B PHE* 2.9 53.0 + - + -
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Residues in contact with LEU 868 (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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861B TYR* 6.4 0.2 - - + -
864B LEU 3.8 14.3 + - - +
865B LEU* 3.4 32.5 - - + +
867B VAL* 1.3 76.3 - - - +
869B LEU* 1.3 65.2 + - + +
871B PHE* 3.5 17.9 - - + +
872B LEU* 2.9 45.6 + - + +
888B LEU* 3.8 46.0 - - + -
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Residues in contact with LEU 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B GLU* 3.3 19.2 + - + +
867B VAL 3.2 0.6 - - - -
868B LEU* 1.3 87.3 - - + +
870B ASN* 1.3 68.3 + - - +
872B LEU* 3.8 7.4 + - + -
873B LYS* 3.4 48.4 + - + +
1575B LEU* 5.7 5.8 - - + +
1579B ALA 3.3 25.6 - - - +
1580B GLY 3.4 20.0 - - - +
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Residues in contact with ASN 870 (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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866B GLU 3.5 13.2 - - - +
867B VAL* 3.0 16.1 + - + +
869B LEU* 1.3 85.0 - - - +
871B PHE* 1.3 62.9 + - + +
872B LEU 3.3 0.2 - - - -
873B LYS* 4.5 5.7 - - - +
874B THR* 2.7 44.0 + - - +
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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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828B LEU* 3.3 65.1 - - + -
829B GLN* 4.3 1.3 - - - -
831B SER* 5.5 1.8 - - - -
837B ARG* 4.1 22.2 - - - +
841B LEU* 6.0 6.3 - - + -
864B LEU* 5.2 1.3 - - + -
867B VAL* 2.9 40.3 + - + -
868B LEU* 3.2 19.3 + - + +
870B ASN* 1.3 81.6 - - + +
872B LEU* 1.3 61.1 + - + +
873B LYS 3.2 3.6 + - - -
874B THR* 3.9 6.9 + - - -
875B GLU* 4.0 18.7 + - - +
880B THR* 5.5 7.8 - - + +
881B ARG* 5.7 1.2 - - - +
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Residues in contact with LEU 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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868B LEU* 2.9 33.9 + - + +
869B LEU* 4.3 9.0 - - + +
870B ASN 3.3 0.6 - - - -
871B PHE* 1.3 78.5 - - + +
873B LYS* 1.3 60.6 + - + +
880B THR* 5.6 1.8 - - + -
881B ARG* 2.4 54.1 + - + +
884B ALA* 3.8 32.3 - - + -
885B ILE* 5.0 4.3 - - + -
888B LEU* 5.7 5.2 - - + -
1575B LEU* 3.8 42.1 - - + +
1576B THR* 5.2 1.4 + - - -
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Residues in contact with LYS 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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869B LEU* 3.4 35.8 + - + +
870B ASN* 3.3 7.7 + - - +
871B PHE 3.2 0.4 - - - -
872B LEU* 1.3 84.6 - - + +
874B THR* 1.3 64.0 + - - +
875B GLU 3.9 0.2 - - - -
876B GLN* 4.4 5.0 + - - -
881B ARG* 4.0 9.5 + - - +
1575B LEU* 4.1 5.6 + - + +
1576B THR* 2.7 48.5 + - + +
1580B GLY* 3.8 24.9 - - - -
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Residues in contact with THR 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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837B ARG* 6.3 0.4 - - - +
870B ASN* 2.7 28.4 + - - +
871B PHE* 4.9 3.1 - - - -
873B LYS* 1.3 78.2 - - - +
875B GLU* 1.3 70.3 + - + +
876B GLN* 2.8 26.5 + - - +
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Residues in contact with GLU 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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834B LEU* 4.1 14.1 - - - +
837B ARG* 2.8 54.4 + - - +
871B PHE* 4.0 14.0 + - - +
874B THR* 1.3 87.0 - - + +
876B GLN* 1.3 54.4 + - - +
877B ASN* 3.4 25.8 + - + +
880B THR* 4.4 13.7 + - + +
881B ARG* 2.8 31.7 + - - +
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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