Contacts of the helix formed by residues 933 - 938 (chain O) in PDB entry 6IY3
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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923O THR* 5.5 3.8 - - - +
925O THR 4.9 0.7 - - - +
926O PRO* 3.7 13.6 - - - +
927O LEU* 3.1 42.7 + - + +
932O PRO* 1.3 70.8 - - - +
934O LEU* 1.3 56.5 + - - +
935O TRP* 3.2 32.2 + - + -
936O ALA 3.9 0.5 + - - -
937O LEU* 3.0 67.6 + - + +
938O LEU* 3.6 5.7 + - - +
987O LEU* 4.9 17.2 - - + +
991O LEU* 5.7 3.4 - - + -
1235O VAL* 5.0 2.1 - - - +
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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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902O ALA* 5.0 10.8 - - + -
931O LEU* 3.7 24.0 - - + -
932O PRO 2.5 16.7 + - - +
933O GLU* 1.3 68.6 - - - +
935O TRP* 1.3 71.7 + - + +
936O ALA 2.8 13.3 + - - -
938O LEU* 2.8 42.7 + - + +
939O ASN* 3.0 31.6 + - - +
950O LYS* 6.0 1.3 - - - -
953O ASP* 3.8 36.6 - - + +
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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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896O GLY 4.9 4.2 + - - -
899O MET* 4.2 7.5 - - - +
900O LYS* 3.3 51.6 - - + +
901O ASN* 4.2 4.3 - - - +
902O ALA* 4.8 12.4 - - - +
921O ILE* 6.4 0.2 - - + -
926O PRO 4.8 1.3 - - - -
927O LEU* 3.5 33.7 - - + -
928O GLN 4.8 0.4 - - - -
930O ASN* 3.2 33.9 - - + -
931O LEU* 3.2 8.1 - - + -
932O PRO 3.1 19.5 - - - -
933O GLU* 3.2 39.9 + - - +
934O LEU* 1.3 86.4 - - + +
936O ALA* 1.3 82.3 + - + +
937O LEU* 4.7 1.6 - - - +
939O ASN* 4.3 4.1 - - - +
940O PHE* 3.4 19.4 + - - +
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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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899O MET* 5.2 3.8 - - + -
921O ILE* 4.8 15.3 - - + -
934O LEU 2.8 2.8 + - - -
935O TRP* 1.3 92.7 - - + +
937O LEU* 1.3 72.3 + - + +
938O LEU 3.0 7.0 + - - -
939O ASN 3.4 0.3 + - - -
940O PHE* 2.8 20.6 + - + -
941O VAL* 2.8 38.5 + - + +
942O LEU 4.4 0.2 + - - -
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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* 3.7 35.9 - - + -
921O ILE* 4.3 9.6 - - + -
923O THR* 6.0 2.5 - - + -
933O GLU* 3.0 45.9 + - + +
935O TRP* 4.7 2.9 - - - +
936O ALA* 1.3 92.2 - - + +
938O LEU* 1.3 58.7 + - - +
941O VAL* 4.5 6.1 - - - -
942O LEU* 5.6 4.8 - - - +
945O ILE* 4.6 6.9 - - - +
987O LEU* 5.0 9.9 - - + +
990O PHE* 5.0 12.9 - - + -
991O LEU* 3.7 41.5 - - + -
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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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932O PRO* 6.0 4.0 - - + -
933O GLU 4.3 3.6 - - - +
934O LEU* 2.8 43.7 + - + +
937O LEU* 1.3 81.0 - - - +
939O ASN* 1.3 67.6 + - - +
942O LEU 4.8 0.2 - - - -
945O ILE* 3.1 43.3 - - + +
949O VAL* 3.6 53.2 - - + +
950O LYS* 5.0 0.7 - - - -
953O ASP* 4.7 7.4 - - + -
983O LEU* 6.5 0.9 - - + -
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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