Contacts of the helix formed by residues 904 - 913 (chain O) in PDB entry 5X0X
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 904 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136I T 3.1 23.6 + - - -
137I A 4.2 12.3 + - - -
898O ARG 3.7 20.3 + - - -
901O ASN* 2.6 37.4 + - - +
902O ALA 3.2 1.2 - - - +
903O GLN* 1.3 72.4 - - - +
905O LYS* 1.3 65.3 + - - +
906O LEU* 4.5 4.3 - - - -
907O SER* 2.5 30.1 + - - -
908O LEU* 3.7 1.9 + - - +
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Residues in contact with LYS 905 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I A 2.7 52.1 + - - +
136I T 2.8 19.3 + - - +
877O ILE* 3.4 30.9 - - + +
880O ARG* 5.6 6.7 - - - +
903O GLN 3.3 4.1 + - - -
904O SER* 1.3 70.1 - - - +
906O LEU* 1.3 64.8 + - + +
908O LEU* 3.0 17.8 - - + +
909O THR* 2.9 39.8 + - + +
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Residues in contact with LEU 906 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I A 4.6 2.7 - - - +
136I T 3.9 13.7 + - - +
822O ILE* 5.4 5.2 - - + -
873O PHE* 3.4 53.6 - - + +
876O ILE* 5.0 11.4 - - + -
877O ILE* 3.7 29.4 - - + -
898O ARG* 5.4 6.7 - - + +
899O MET* 5.1 6.5 - - - -
904O SER* 3.2 3.1 - - - -
905O LYS* 1.3 77.8 - - - +
907O SER* 1.3 65.3 + - - +
909O THR* 2.5 29.5 + - - +
910O LEU* 2.9 21.7 + - + +
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Residues in contact with SER 907 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899O MET* 3.5 35.5 - - - -
901O ASN 4.2 4.0 - - - -
902O ALA* 2.3 47.1 + - - -
904O SER* 2.5 16.4 + - - -
906O LEU* 1.3 78.9 - - - +
908O LEU* 1.3 59.9 + - - +
910O LEU* 3.8 9.9 + - - +
911O ASN* 3.2 16.2 - - - +
940O PHE* 4.1 7.6 - - - -
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Residues in contact with LEU 908 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902O ALA 4.0 9.9 - - - +
903O GLN* 4.0 10.5 - - - +
904O SER 3.8 12.3 - - - +
905O LYS* 3.0 25.8 - - + +
907O SER* 1.3 77.0 + - - +
909O THR* 1.3 83.7 + - + +
910O LEU 3.1 1.8 - - - -
911O ASN* 2.9 23.2 + - + +
912O THR* 2.9 17.7 + - - +
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Residues in contact with THR 909 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876O ILE* 4.6 8.4 - - - +
877O ILE* 5.2 6.8 - - + +
880O ARG* 5.3 15.7 - - - -
905O LYS* 2.9 45.8 + - + +
906O LEU* 2.5 33.4 + - - +
908O LEU* 1.3 79.9 - - + +
910O LEU* 1.3 55.2 + - - +
912O THR* 2.7 13.5 + - - -
913O HIS* 2.2 40.6 + - - +
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Residues in contact with LEU 910 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820O LEU* 6.5 0.7 - - + -
822O ILE* 5.0 10.5 - - + -
876O ILE* 4.0 26.7 - - + -
891O MET* 4.6 19.8 - - + +
893O ILE* 4.1 17.5 - - + -
899O MET* 4.6 6.5 - - - -
906O LEU* 2.9 25.2 + - + +
907O SER 3.9 5.6 - - - +
908O LEU 3.1 0.2 - - - -
909O THR* 1.3 78.3 - - - +
911O ASN* 1.3 56.8 + - - +
913O HIS* 3.3 17.7 - - + +
914O TYR 2.7 27.9 - - - +
915O HIS* 4.4 2.4 + - - -
919O ARG* 5.9 1.5 - - - -
940O PHE* 3.6 33.9 - - + -
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Residues in contact with ASN 911 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907O SER 3.2 18.6 + - - +
908O LEU* 2.9 13.7 + - - +
910O LEU* 1.3 78.9 - - - +
912O THR* 1.3 60.2 + - - +
913O HIS 3.5 0.2 + - - -
914O TYR* 3.5 10.2 + - - -
915O HIS* 4.0 23.5 + - + -
919O ARG* 5.7 3.2 - - - +
940O PHE* 4.7 15.3 - - - -
946O PHE* 5.5 8.8 - - - -
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Residues in contact with THR 912 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880O ARG* 4.5 20.6 - - - +
884O SER* 4.2 6.3 + - - -
908O LEU* 2.9 15.1 + - - +
909O THR* 2.7 19.8 + - - -
911O ASN* 1.3 69.5 - - - +
913O HIS* 1.3 56.4 + - - +
914O TYR* 3.0 11.1 + - - +
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Residues in contact with HIS 913 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820O LEU* 3.6 27.9 - - + +
876O ILE* 4.3 23.1 - - + +
880O ARG* 4.5 8.7 - - + -
883O LEU* 3.3 22.7 - - + +
884O SER* 3.1 53.2 + - - +
886O VAL 5.3 0.2 - - - +
888O TRP* 4.0 7.2 - + - -
891O MET* 5.1 7.1 - - + +
909O THR* 2.2 28.3 + - - +
910O LEU* 3.3 22.9 - - + +
911O ASN 3.1 0.6 - - - -
912O THR* 1.3 69.3 - - - +
914O TYR* 1.3 68.5 + - - +
915O HIS* 3.6 1.7 + - - -
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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