Contacts of the helix formed by residues 925 - 933 (chain A) in PDB entry 3S51
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 LYS 925 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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866A PRO 4.5 3.0 + - - -
867A ASP* 3.5 24.3 + - - +
870A PHE* 3.4 52.6 - - + +
918A VAL* 5.3 0.4 - - - -
922A TYR* 2.5 25.3 + - + +
924A PRO* 1.3 73.9 - - + +
926A VAL* 1.3 62.6 + - - -
927A GLN 3.2 3.1 - - - -
928A GLN* 3.0 26.2 + - + +
929A PHE* 2.8 20.4 + - - +
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Residues in contact with VAL 926 (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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918A VAL* 4.4 14.6 - - + +
919A LEU* 4.6 7.0 - - + -
922A TYR 3.6 0.6 + - - -
923A GLN* 2.8 42.0 + - + +
924A PRO 3.2 1.2 - - - -
925A LYS* 1.3 77.9 - - - +
927A GLN* 1.3 64.6 + - + +
929A PHE* 3.3 9.2 + - + +
930A LEU* 3.1 40.2 + - + +
947A VAL* 3.9 15.0 - - + -
991A LEU* 3.7 35.4 - - + -
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Residues in contact with GLN 927 (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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924A PRO 4.7 9.4 + - - +
925A LYS 3.2 0.6 - - - -
926A VAL* 1.3 79.2 - - + +
928A GLN* 1.3 76.8 + - - +
930A LEU* 3.6 4.9 + - - +
931A GLN* 3.2 32.9 + - - +
947A VAL* 3.3 38.6 - - + +
950A ARG* 5.4 2.6 - - - +
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Residues in contact with GLN 928 (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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870A PHE* 3.7 16.4 - - + -
874A CYS* 4.9 0.4 - - - -
924A PRO 4.5 7.5 + - - -
925A LYS* 3.3 34.5 - - + +
927A GLN* 1.3 87.4 + - - +
929A PHE* 1.3 65.5 + - - +
931A GLN* 3.1 23.6 + - - +
932A ALA* 3.3 10.9 + - - +
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Residues in contact with PHE 929 (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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870A PHE* 3.4 16.8 - + + -
873A LEU 4.3 5.6 - - - -
874A CYS* 3.8 21.8 - - - -
877A THR* 3.4 42.0 - - + -
914A THR* 3.8 4.0 - - + -
915A PHE* 3.8 23.1 - + - -
918A VAL* 3.4 44.6 - - + -
925A LYS 2.8 12.6 + - - +
926A VAL* 3.5 8.1 - - + +
927A GLN 3.3 0.2 - - - -
928A GLN* 1.3 76.9 - - - +
930A LEU* 1.3 72.7 + - + +
932A ALA* 3.1 18.5 + - - +
933A LEU* 3.5 26.1 - - + +
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Residues in contact with LEU 930 (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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915A PHE* 4.5 11.7 - - + -
926A VAL* 3.1 33.8 + - + +
927A GLN* 4.1 2.5 - - - +
929A PHE* 1.3 87.5 - - + +
931A GLN* 1.3 62.0 + - - +
933A LEU* 3.2 35.6 + - + +
934A ASP* 3.5 11.8 - - - +
947A VAL* 4.0 14.6 - - + +
950A ARG* 3.4 47.0 - - + +
951A ALA 4.4 1.3 - - - +
954A GLN* 4.5 7.2 - - + +
988A LEU* 4.5 10.8 - - + -
991A LEU* 4.0 11.9 - - + -
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Residues in contact with GLN 931 (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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927A GLN* 3.2 24.6 + - - +
928A GLN* 3.1 13.9 + - - +
930A LEU* 1.3 72.9 - - - +
932A ALA* 1.3 62.2 + - - +
933A LEU 3.0 5.8 + - - -
934A ASP* 3.1 17.9 + - - +
950A ARG* 3.0 41.0 - - - +
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Residues in contact with ALA 932 (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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874A CYS* 3.7 33.4 - - + +
878A ARG* 3.0 38.0 + - - +
928A GLN 3.3 4.1 + - - +
929A PHE 3.1 11.7 + - - +
931A GLN* 1.3 78.6 - - - +
933A LEU* 1.3 59.6 + - + +
934A ASP 3.3 2.9 + - - -
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Residues in contact with LEU 933 (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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874A CYS 4.7 2.7 - - - +
877A THR* 3.6 29.4 - - + -
878A ARG* 3.6 29.0 - - + +
881A LEU* 3.9 13.9 - - + +
915A PHE* 4.2 13.2 - - + -
929A PHE* 3.5 35.0 - - + +
930A LEU* 3.4 30.3 - - + +
931A GLN 3.0 1.2 - - - -
932A ALA* 1.3 80.0 - - + +
934A ASP* 1.3 61.5 + - - +
954A GLN* 4.4 20.5 + - - +
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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