Contacts of the helix formed by residues 873 - 879 (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 PHE 873 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15J T 6.0 0.2 - - - -
822O ILE* 4.5 11.0 - - + -
823O VAL 3.1 27.8 + - - -
824O PRO* 3.3 34.5 - - + -
825O LEU 5.1 0.7 - - - -
872O THR* 1.3 78.0 - - - +
874O GLU* 1.3 73.7 + - + +
876O ILE* 3.2 19.4 - - - +
877O ILE* 3.6 7.7 + - - +
893O ILE* 5.7 2.7 - - + -
894O ASP 4.1 13.0 - - - -
898O ARG* 3.4 57.9 - - + +
906O LEU* 3.4 35.4 - - + +
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Residues in contact with GLU 874 (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 6.1 1.0 - - - +
14J A 5.2 7.9 - - - +
15J T 5.1 3.7 - - - +
16J C 3.0 39.4 + - - +
872O THR* 3.3 7.3 - - - +
873O PHE* 1.3 81.3 - - + +
875O TYR* 1.3 72.6 + - + +
877O ILE* 2.5 42.6 + - - +
878O LYS* 3.0 19.8 + - + +
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Residues in contact with TYR 875 (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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16J C 2.9 31.3 + - - -
17J T 4.0 15.4 + - - -
825O LEU* 5.7 2.7 - - + -
847O PHE* 4.5 17.3 - - + -
848O LYS* 4.3 10.9 - - - -
849O GLY 4.6 2.1 + - - -
854O ARG* 3.3 52.7 + - - -
871O THR* 3.5 16.2 - - - +
872O THR* 3.2 22.3 + - + -
873O PHE 3.5 0.6 - - - -
874O GLU* 1.3 76.0 - - + +
876O ILE* 1.3 62.5 + - - +
878O LYS* 3.9 21.3 - - + +
879O GLU* 2.9 49.8 + - + +
883O LEU* 3.9 2.1 - - - +
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Residues in contact with ILE 876 (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* 4.7 6.1 - - + -
822O ILE* 4.1 22.0 - - + -
871O THR* 3.6 26.5 - - + -
872O THR 3.1 17.5 + - - +
873O PHE* 3.2 11.7 - - - +
874O GLU 3.0 0.2 - - - -
875O TYR* 1.3 77.2 - - - +
877O ILE* 1.3 51.7 + - + +
880O ARG* 2.6 40.2 - - + +
883O LEU* 4.0 16.4 - - + -
906O LEU* 5.0 9.2 - - + -
909O THR* 4.6 9.8 - - - +
910O LEU* 4.0 26.0 - - + -
913O HIS* 4.3 14.8 - - + +
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Residues in contact with ILE 877 (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 3.9 29.2 - - - +
873O PHE 4.1 7.0 - - - +
874O GLU* 2.5 26.7 + - - +
876O ILE* 1.3 71.7 - - + +
878O LYS* 1.3 66.3 + - + +
880O ARG* 3.1 29.4 + - - +
905O LYS* 3.4 37.0 - - + +
906O LEU* 3.7 29.2 - - + -
909O THR* 5.2 6.5 - - + -
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Residues in contact with LYS 878 (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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16J C 2.2 47.3 + - - -
17J T 3.0 23.5 + - - +
854O ARG* 5.2 2.5 - - - +
874O GLU* 3.0 19.6 + - + +
875O TYR* 4.2 24.8 - - + -
877O ILE* 1.3 83.5 - - + +
879O GLU* 1.3 62.1 + - + +
880O ARG* 3.2 1.8 + - - +
881O ALA* 4.4 6.1 + - - +
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Residues in contact with GLU 879 (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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847O PHE* 3.0 49.8 - - - -
854O ARG* 3.2 19.3 - - - +
858O GLN* 3.2 33.1 + - - +
875O TYR* 2.9 30.0 + - + +
878O LYS* 1.3 72.3 - - + +
880O ARG* 1.3 55.5 + - - +
881O ALA* 2.9 4.3 - - - -
882O LEU* 2.6 30.7 + - + +
883O LEU* 2.9 32.0 + - + +
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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