Contacts of the helix formed by residues 933 - 942 (chain O) in PDB entry 5Z3U
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 933 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900O LYS* 4.5 10.5 - - - +
901O ASN* 3.5 34.0 - - - +
927O LEU* 3.3 26.2 - - + +
928O GLN* 5.1 2.8 - - - +
931O LEU 3.4 0.2 - - - -
932O PRO* 1.3 102.5 - - + +
934O LEU* 1.3 58.3 + - - +
935O TRP* 2.9 3.4 - - - -
936O ALA* 2.4 36.8 + - + +
937O LEU 2.9 10.2 + - - -
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Residues in contact with LEU 934 (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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926O PRO* 6.0 3.8 - - + -
927O LEU* 3.2 14.7 - - + +
931O LEU* 3.5 44.6 - - + +
932O PRO 3.3 1.0 - - - -
933O GLU* 1.3 75.4 - - - +
935O TRP* 1.3 64.0 + - + +
937O LEU* 3.6 23.3 - - + -
938O LEU* 2.9 53.1 + - + +
945O ILE* 4.9 0.4 - - - -
956O PHE* 6.3 3.1 - - + -
983O LEU* 5.9 7.0 - - + -
987O LEU* 5.3 16.8 - - + -
991O LEU* 6.4 3.1 - - + -
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Residues in contact with TRP 935 (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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932O PRO* 3.6 18.5 + - + +
933O GLU* 4.7 0.4 - - - -
934O LEU* 1.3 80.0 - - + +
936O ALA* 1.3 58.8 + - - +
938O LEU 3.1 0.2 + - - -
939O ASN* 2.8 33.3 + - - +
945O ILE* 3.4 19.9 - - + +
949O VAL* 3.0 51.4 - - + -
950O LYS* 3.1 23.8 - - - -
952O PHE* 3.3 25.6 - + - +
953O ASP* 3.1 40.8 - - + -
956O PHE* 4.0 15.9 - + - -
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Residues in contact with ALA 936 (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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900O LYS 3.7 22.7 - - - +
902O ALA* 4.3 20.1 - - + +
933O GLU* 2.4 30.6 + - + +
935O TRP* 1.3 75.3 - - - +
937O LEU* 1.3 64.2 + - - +
939O ASN* 3.0 16.8 + - - +
940O PHE* 3.0 18.0 + - - +
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Residues in contact with LEU 937 (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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789O ILE* 4.4 16.4 - - + -
896O GLY 5.2 5.2 - - - +
897O HIS* 6.2 1.6 - - - -
899O MET* 5.2 5.8 - - + -
900O LYS* 5.1 14.6 + - - +
921O ILE* 4.4 20.9 - - + -
926O PRO* 5.4 3.4 - - + -
927O LEU* 3.6 42.4 - - + +
933O GLU 2.9 5.3 + - - -
934O LEU* 3.5 24.9 - - + +
936O ALA* 1.3 74.5 - - + +
938O LEU* 1.3 60.5 + - + +
940O PHE* 2.5 32.9 + - - +
941O VAL* 2.8 14.0 + - - +
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Residues in contact with LEU 938 (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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789O ILE* 5.4 2.9 - - + -
934O LEU* 2.9 41.3 + - + +
935O TRP 3.5 0.2 - - - -
937O LEU* 1.3 82.5 - - + +
939O ASN* 1.3 57.0 + - - +
941O VAL* 3.7 17.8 - - + +
942O LEU* 3.2 22.7 + - - +
944O LYS* 3.2 37.6 + - - +
945O ILE* 3.5 32.7 + - + +
986O VAL* 5.5 0.4 - - + -
987O LEU* 4.6 18.4 - - + -
990O PHE* 5.0 9.0 - - + -
991O LEU* 5.9 5.4 - - + -
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Residues in contact with ASN 939 (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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902O ALA* 5.9 2.1 - - + +
919O ARG* 3.9 7.6 + - - -
935O TRP* 2.8 28.1 + - - +
936O ALA* 3.1 18.2 - - - +
937O LEU 2.9 0.2 + - - -
938O LEU* 1.3 77.5 - - - +
940O PHE* 1.3 59.8 + - - +
942O LEU 3.2 17.3 + - - +
945O ILE* 3.4 11.5 - - - +
946O PHE* 3.2 42.2 - - + +
949O VAL* 3.6 16.2 - - - +
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Residues in contact with PHE 940 (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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891O MET* 4.5 13.5 - - + -
893O ILE* 4.9 7.6 - - + -
899O MET* 4.7 20.2 - - + -
910O LEU* 4.5 23.6 - - + -
911O ASN* 5.1 12.3 - - - -
919O ARG* 2.8 66.2 + - + +
920O LEU 4.1 9.4 - - - -
921O ILE* 3.6 34.8 - - + -
936O ALA 3.0 9.2 + - - +
937O LEU* 2.5 16.8 + - + +
939O ASN* 1.3 72.3 - - - +
941O VAL* 1.3 56.9 + - - -
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Residues in contact with VAL 941 (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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787O ASN* 3.2 28.0 + - - +
788O GLY* 4.1 24.7 - - - +
789O ILE* 3.4 34.5 - - + +
919O ARG* 3.7 1.3 - - - -
921O ILE* 4.8 3.1 - - + -
937O LEU 2.8 23.0 + - - +
938O LEU* 3.7 14.1 - - + +
939O ASN 3.2 0.4 - - - -
940O PHE* 1.3 81.1 - - - +
942O LEU* 1.3 81.2 + - + +
990O PHE* 4.1 20.0 - - + -
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Residues in contact with LEU 942 (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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682O LEU* 6.0 5.8 - - + -
685O GLN* 5.8 4.3 - - + +
786O LEU* 4.0 25.4 - - + -
787O ASN* 3.6 31.4 - - + +
919O ARG* 3.6 9.9 - - - +
938O LEU 3.2 14.5 + - - +
939O ASN* 3.2 12.3 - - - +
941O VAL* 1.3 97.1 - - + +
943O PRO* 1.3 75.7 - - + +
944O LYS* 3.1 15.4 + - + +
946O PHE* 4.4 1.0 - - - -
989O PRO 5.2 2.9 - - - +
990O PHE* 3.4 35.2 - - + -
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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