Contacts of the helix formed by residues 926 - 935 (chain C) in PDB entry 3P23
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 PRO 926 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835C LEU 4.6 1.6 - - - +
836C GLU* 3.9 36.8 - - + +
839C LEU* 3.5 24.0 - - + +
908C LYS* 5.3 4.3 - - - -
924C THR 4.1 0.4 - - - -
925C LEU* 1.3 89.8 - - + +
927C ASP* 1.3 73.0 + - + +
929C PHE 4.2 2.0 - - - -
930C VAL* 3.4 23.6 + - - +
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Residues in contact with ASP 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835C LEU* 3.2 38.4 - - + +
836C GLU* 4.0 11.5 + - - +
924C THR 3.7 0.4 + - - -
925C LEU 3.4 3.2 - - - -
926C PRO* 1.3 84.5 - - - +
928C ASP* 1.3 70.0 + - - +
929C PHE 3.0 4.9 + - - -
930C VAL* 3.2 3.6 + - - +
931C CYS* 3.1 28.8 + - - -
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Residues in contact with ASP 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835C LEU* 6.0 0.2 - - - +
922C LEU 3.3 9.6 - - - +
923C GLY 3.6 19.5 - - - +
924C THR* 3.3 16.6 + - - +
927C ASP* 1.3 84.2 - - - +
929C PHE* 1.3 56.5 + - - +
931C CYS* 3.9 9.1 - - - +
932C TYR* 3.1 22.9 + - - +
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Residues in contact with PHE 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839C LEU* 3.6 27.6 - - + -
904C MET* 3.7 24.7 - - + -
907C LYS* 4.5 4.3 - - + -
908C LYS* 4.0 13.5 - - + -
911C TYR* 4.1 14.6 - + - -
922C LEU* 3.7 44.2 - - + -
923C GLY* 4.1 1.8 - - - -
924C THR 3.0 16.3 + - - +
925C LEU* 3.3 33.4 - - + -
926C PRO 4.3 2.0 - - - +
927C ASP 3.0 0.4 - - - -
928C ASP* 1.3 78.2 - - - +
930C VAL* 1.3 63.7 + - - +
932C TYR* 3.3 16.1 - - - +
933C PHE* 3.4 28.5 - + - -
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Residues in contact with VAL 930 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835C LEU* 3.7 33.0 - - + +
838C GLN* 4.3 7.6 - - + +
839C LEU* 3.7 39.9 - - + +
842C PHE* 4.2 19.8 - - + -
904C MET* 5.8 1.6 - - + -
926C PRO 3.4 14.5 + - - +
927C ASP 3.2 10.5 + - - +
929C PHE* 1.3 79.6 - - - +
931C CYS* 1.3 64.1 + - - +
932C TYR 3.2 0.7 - - - -
933C PHE* 3.5 7.4 + - + +
934C THR* 3.1 29.9 + - - +
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Residues in contact with CYS 931 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835C LEU* 3.6 35.2 - - - -
927C ASP 3.1 17.3 + - - +
928C ASP* 4.0 9.4 - - - +
929C PHE 3.3 0.2 - - - -
930C VAL* 1.3 79.2 - - - +
932C TYR* 1.3 59.3 + - - +
934C THR* 3.5 15.9 - - + -
935C SER* 2.9 35.2 + - - -
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Residues in contact with TYR 932 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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878C ILE* 3.6 2.7 - - + +
879C THR* 2.6 44.7 + - + -
882C LEU* 3.0 23.8 - - + +
921C THR 2.8 30.5 - - - -
922C LEU* 3.5 19.5 - - + +
928C ASP 3.1 15.0 + - - +
929C PHE* 3.3 13.2 - - - +
931C CYS* 1.3 79.8 - - - +
933C PHE* 1.3 86.1 + + - +
935C SER* 3.8 4.5 + - - -
936C ARG* 2.9 66.8 + - - +
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Residues in contact with PHE 933 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C PHE* 6.1 2.0 - - + -
874C TRP* 6.0 1.6 - + - -
878C ILE* 4.8 3.1 - - + -
882C LEU* 4.2 13.2 - - + -
900C LEU* 4.3 17.0 - - + -
903C ALA* 5.8 1.8 - - + -
904C MET* 3.2 52.3 - - + -
907C LYS* 5.8 2.2 - - + -
922C LEU* 3.9 15.7 - - + -
929C PHE* 3.4 33.7 - + - -
930C VAL* 3.5 7.1 + - + +
931C CYS 3.2 0.2 - - - -
932C TYR* 1.3 107.2 - + - +
934C THR* 1.3 59.0 + - - +
935C SER 3.5 0.2 - - - -
936C ARG* 3.8 2.5 - - - -
937C PHE* 3.0 46.1 + + + +
940C LEU* 4.6 6.5 - - + +
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Residues in contact with THR 934 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C HIS* 3.3 54.0 + - + +
801C GLU* 6.4 0.2 - - + -
835C LEU* 6.0 1.2 - - + +
838C GLN* 4.4 5.9 + - - -
842C PHE* 5.2 6.4 - - - -
930C VAL* 3.1 22.1 + - - +
931C CYS* 3.1 19.2 + - + +
933C PHE* 1.3 75.7 - - - +
935C SER* 1.3 65.6 + - - +
936C ARG 3.1 4.8 + - - -
937C PHE 3.5 20.1 - - - -
938C PRO* 3.5 4.2 - - - +
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Residues in contact with SER 935 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798C GLU 5.2 2.3 - - - +
800C HIS* 5.3 2.2 - - - +
871C LYS* 5.6 0.7 + - - -
931C CYS* 2.9 19.6 + - - -
932C TYR* 3.8 6.4 + - - -
934C THR* 1.3 80.6 - - - +
936C ARG* 1.3 68.1 + - - +
937C PHE 3.6 0.2 - - - -
938C PRO* 4.6 8.6 - - - +
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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