Contacts of the helix formed by residues 900 - 907 (chain A) in PDB entry 4ZYX
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 SER 900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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871A ARG* 4.2 11.3 - - - +
872A VAL* 4.0 30.8 - - - +
875A ASP* 2.6 30.9 + - - +
898A ILE 4.1 0.8 + - - -
899A LEU* 1.3 75.8 - - - +
901A GLY* 1.3 64.9 + - - +
902A PRO* 3.8 5.3 - - - +
903A PHE* 3.3 14.6 + - - +
904A VAL* 3.1 21.2 + - - +
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Residues in contact with GLY 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A LEU 3.9 0.8 + - - -
900A SER* 1.3 70.3 - - - +
902A PRO* 1.3 66.0 - - - +
904A VAL* 3.3 3.9 + - - +
905A GLN* 2.8 30.3 + - - +
948A GLU* 3.5 40.0 + - - +
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Residues in contact with PRO 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A VAL* 5.0 11.7 - - + -
900A SER* 3.7 11.9 - - - +
901A GLY* 1.3 87.9 - - - +
903A PHE* 1.3 55.6 + - - +
905A GLN* 3.3 7.1 + - + +
906A LYS* 2.9 30.1 + - - +
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Residues in contact with PHE 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A LEU* 5.4 3.8 - - + -
875A ASP* 3.7 35.4 - - + +
878A ILE* 4.0 11.4 - - + -
879A ASP* 3.9 18.8 - - + -
882A LEU* 3.8 22.2 - - + -
890A VAL* 5.3 0.7 - - + -
899A LEU* 3.9 30.1 - - + -
900A SER* 3.3 20.3 + - - +
901A GLY 3.3 0.6 - - - -
902A PRO* 1.3 74.8 - - - +
904A VAL* 1.3 68.2 + - - +
906A LYS* 3.2 5.1 + - + +
907A TRP* 3.1 49.7 + + - +
911A MET* 3.8 27.8 - - + -
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Residues in contact with VAL 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A LEU* 3.8 15.7 - - + -
900A SER 3.1 17.9 + - - +
901A GLY 3.6 4.5 - - - +
903A PHE* 1.3 75.3 - - - +
905A GLN* 1.3 59.1 + - - +
907A TRP 3.3 2.8 + - - -
908A ASN* 3.0 28.1 + - - +
911A MET* 4.1 9.9 - - + +
946A VAL* 3.5 23.6 - - + +
947A ALA* 3.5 29.6 - - - -
948A GLU* 3.5 9.2 - - + +
1102A 3YB 3.6 24.7 - - - +
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Residues in contact with GLN 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901A GLY 2.8 17.3 + - - +
902A PRO* 3.6 8.3 - - + +
904A VAL* 1.3 79.0 - - - +
906A LYS* 1.3 63.9 + - - +
908A ASN* 3.2 32.0 + - - +
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Residues in contact with LYS 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879A ASP* 2.7 40.1 + - - +
883A GLU* 3.1 29.0 + - - +
902A PRO 2.9 17.8 + - - +
903A PHE* 3.2 8.0 + - - +
905A GLN* 1.3 75.6 - - - +
907A TRP* 1.3 71.7 + - + +
908A ASN 3.3 3.3 + - - +
910A LYS* 4.9 9.0 + - - +
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Residues in contact with TRP 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879A ASP* 2.9 26.2 + - - -
882A LEU* 3.5 33.2 - - + -
883A GLU* 4.1 13.9 - - - -
887A ILE* 3.3 29.8 - - + -
888A ASP 3.8 14.4 - - - -
890A VAL* 3.8 20.4 - - + -
903A PHE* 3.1 47.8 + + - +
904A VAL 3.5 2.9 - - - -
906A LYS* 1.3 89.7 - - + +
908A ASN* 1.3 58.5 + - - +
909A GLY 3.2 0.3 + - - -
910A LYS* 2.8 48.9 + - + +
911A MET* 3.4 27.5 + - + +
946A VAL 5.6 0.3 - - - +
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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