Contacts of the helix formed by residues 900 - 906 (chain C) in PDB entry 4OQB
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 MET 900 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820C ASN 5.0 1.1 - - - +
821C THR* 3.5 44.0 - - + +
822C HIS 4.4 6.3 - - - +
823C ALA* 4.8 8.1 - - + +
861C TRP* 3.4 7.7 - - - +
898C ALA* 3.3 4.0 - - + +
899C ASP* 1.3 94.4 - - - +
901C VAL* 1.3 65.1 + - - +
902C SER* 3.4 4.8 + - - +
903C LYS* 3.7 13.0 + - + +
904C SER* 3.5 19.4 + - - -
954C THR* 4.8 13.5 - - + +
956C PRO* 5.1 11.2 - - + -
972C GLY 5.3 1.1 - - - +
974C GLY* 5.1 10.5 - - - +
986C TYR* 3.5 40.8 - - + -
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Residues in contact with VAL 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818C VAL* 3.4 37.9 - - + +
821C THR* 3.1 16.6 + - - +
822C HIS* 4.6 3.4 - - - +
831C LEU* 4.9 8.7 - - + -
861C TRP* 3.3 54.1 - - + +
900C MET* 1.3 72.1 - - - +
902C SER* 1.3 59.3 + - - +
904C SER 3.5 0.5 + - - -
905C ALA* 2.8 35.9 + - + +
919C ILE* 3.4 10.1 - - + +
1005C LEU* 4.3 13.5 - - + -
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Residues in contact with SER 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821C THR 3.8 0.8 + - - -
822C HIS* 3.9 16.8 - - - -
823C ALA* 3.5 27.1 - - - -
826C HIS* 3.1 30.2 - - - +
829C TYR* 2.9 16.9 + - - -
831C LEU* 5.0 0.4 - - - -
900C MET* 3.3 1.2 - - - -
901C VAL* 1.3 80.2 - - - +
903C LYS* 1.3 59.8 + - - +
905C ALA* 3.0 11.7 + - - -
906C ASN* 2.6 25.1 + - - -
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Residues in contact with LYS 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823C ALA* 5.2 0.2 - - - +
826C HIS* 3.9 16.2 + - + -
898C ALA* 4.3 12.1 - - + -
900C MET* 3.7 17.2 + - + +
901C VAL 3.5 0.4 - - - -
902C SER* 1.3 79.3 - - - +
904C SER* 1.3 61.8 + - - +
906C ASN* 3.7 12.1 + - - +
907C TYR* 3.4 28.1 - - + -
984C LEU* 4.1 6.1 - - - +
986C TYR* 3.0 51.8 + - + +
987C ASN 3.4 8.5 + - - +
988C GLU* 3.2 35.9 + - - +
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Residues in contact with SER 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861C TRP* 3.2 36.0 + - - +
862C HIS* 3.9 1.0 - - - -
863C GLY* 3.4 28.4 - - - +
897C PHE 5.0 0.2 - - - -
898C ALA* 3.5 14.1 + - - +
900C MET 3.5 2.0 + - - -
901C VAL 3.5 1.9 + - - -
902C SER 3.2 0.2 - - - -
903C LYS* 1.3 77.8 - - - +
905C ALA* 1.3 63.1 - - - +
907C TYR* 3.1 19.1 + - - +
919C ILE* 3.6 19.7 - - - -
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Residues in contact with ALA 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829C TYR* 3.9 11.0 - - + +
831C LEU* 4.5 9.0 - - + -
901C VAL* 2.8 22.3 + - + +
902C SER* 3.0 10.0 + - - +
904C SER* 1.3 72.4 - - - +
906C ASN* 1.3 60.6 + - - +
907C TYR 3.2 0.2 - - - -
908C CYS* 3.2 24.1 + - - +
909C HIS 4.4 0.9 + - - -
910C THR* 4.9 0.9 + - - -
919C ILE* 3.4 13.7 - - + +
1005C LEU* 5.1 0.9 - - + -
1007C PHE* 3.8 27.0 - - + -
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Residues in contact with ASN 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826C HIS* 3.8 21.9 + - - +
829C TYR* 2.6 27.3 + - - -
902C SER 2.6 31.1 + - - -
903C LYS* 3.8 10.5 + - - +
904C SER 3.2 1.0 - - - -
905C ALA* 1.3 77.2 - - - +
907C TYR* 1.3 64.6 + - + +
908C CYS 3.2 1.8 + - - -
909C HIS* 3.5 20.4 + - - -
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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