Contacts of the helix formed by residues 883 - 888 (chain A) in PDB entry 3IAY
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 ASP 883 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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881A ARG 3.9 3.8 + - - -
882A VAL* 1.3 77.0 - - - +
884A ILE* 1.3 72.9 + - - +
885A SER* 2.6 42.0 + - - +
886A LYS* 2.9 28.3 + - + +
887A LEU* 3.9 1.4 + - - +
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Residues in contact with ILE 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882A VAL 3.4 2.2 + - - -
883A ASP* 1.3 77.6 + - - +
885A SER* 1.3 66.7 + - - +
887A LEU* 3.0 23.3 + - + -
888A ILE* 3.4 12.9 + - + +
927A VAL* 3.9 18.6 - - + -
942A PRO* 3.8 36.8 - - + +
945A VAL* 3.9 22.2 - - + -
946A LEU* 4.0 33.0 - - + -
952A VAL* 4.8 8.7 - - + -
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Residues in contact with SER 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844A SER* 3.9 5.7 + - - -
883A ASP* 2.6 28.1 + - - +
884A ILE* 1.3 81.5 - - - +
886A LYS* 1.3 67.1 + - - +
887A LEU 3.4 0.3 + - - -
888A ILE* 3.7 28.6 + - - +
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Residues in contact with LYS 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A CYS* 3.3 9.0 - - - +
844A SER* 3.2 20.9 - - - +
845A LEU* 3.0 40.7 + - + +
848A ILE* 4.0 24.6 - - + +
882A VAL* 3.9 23.1 - - + -
883A ASP* 2.9 19.6 + - + +
885A SER* 1.3 82.4 + - - +
887A LEU* 1.3 59.5 + - - +
888A ILE 3.5 0.4 - - - -
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Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A CYS* 3.8 2.2 - - - -
845A LEU* 3.7 30.1 - - + -
877A ILE* 5.8 1.6 - - + -
880A ASN* 5.9 2.9 - - - +
882A VAL* 3.8 30.5 - - + +
883A ASP 4.0 7.2 - - - +
884A ILE* 3.0 15.7 + - - +
886A LYS* 1.3 78.9 - - - +
888A ILE* 1.3 63.2 + - - +
889A ILE* 3.3 4.3 + - - +
927A VAL* 3.8 8.4 - - + +
952A VAL* 4.0 28.5 - - + -
954A SER* 6.1 1.1 - - - +
957A TYR* 2.7 56.5 + - + +
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Residues in contact with ILE 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A ARG* 5.8 1.2 + - - -
842A SER 4.3 1.4 - - - +
843A CYS* 3.4 18.4 - - - -
844A SER 4.4 2.1 + - - -
884A ILE* 3.4 13.4 + - + +
885A SER* 3.9 25.0 - - - +
886A LYS 3.5 1.6 - - - -
887A LEU* 1.3 75.2 - - - +
889A ILE* 1.3 65.8 + - - +
890A SER* 4.2 4.2 + - - +
925A ASP* 3.7 35.9 - - + +
926A TYR 3.3 7.6 - - - +
927A VAL* 3.9 5.4 - - + -
942A PRO* 3.9 27.6 - - + -
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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