Contacts of the helix formed by residues 56 - 66 (chain C) in PDB entry 5YWB
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 LEU 56 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG 2.6 10.7 + - - -
55C PHE* 1.3 72.2 - - - +
57C GLN* 1.3 57.3 + - - -
58C ASP 3.6 0.9 - - - -
59C VAL* 3.1 24.5 - - + +
60C PHE* 2.9 25.5 + - - +
132D PHE* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PHE 3.0 7.4 + - - +
56C LEU* 1.3 74.6 - - - +
58C ASP* 1.3 62.1 + - - +
59C VAL 3.1 1.1 - - - -
60C PHE* 2.9 23.3 + - - +
61C THR* 3.0 17.3 + - - +
68E TRP* 6.4 2.0 - - + -
174E ALA* 6.3 3.4 - - + -
176E ARG* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 3.3 35.1 - - + +
57C GLN* 1.3 77.3 - - - +
59C VAL* 1.3 57.5 + - - +
61C THR* 3.1 11.1 + - - +
62C THR* 2.7 35.2 + - - +
176E ARG* 4.9 6.0 - - + +
177E ARG* 4.3 22.7 - - + +
206E ARG* 4.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 3.4 25.4 - - + +
56C LEU* 3.1 24.5 - - + +
57C GLN 3.1 0.8 - - - -
58C ASP* 1.3 74.1 - - - +
60C PHE* 1.3 63.7 + - - +
61C THR 3.1 1.6 - - - -
62C THR* 3.9 6.9 - - - -
63C LEU* 2.9 30.9 + - + +
49D ILE* 4.6 27.1 - - + +
132D PHE* 5.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU 2.9 14.0 + - - +
57C GLN* 2.9 15.3 + - - +
59C VAL* 1.3 78.5 - - + +
61C THR* 1.3 58.9 + - + +
63C LEU* 3.2 32.9 - - + +
64C VAL* 3.6 9.4 - - - +
162C ILE* 5.8 7.4 - - + -
166C CYS* 5.7 0.3 - - - +
171E THR* 5.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN 3.0 10.6 + - - +
58C ASP* 3.1 20.7 + - - +
60C PHE* 1.3 79.0 - - + +
62C THR* 1.3 63.0 + - - +
63C LEU 3.1 1.6 - - - -
64C VAL* 3.1 19.1 + - - +
65C ASP* 3.1 11.6 + - - +
169C MET* 5.6 9.2 - - - -
171E THR 5.0 7.0 - - - +
172E ALA 5.6 2.0 - - - +
173E GLN 5.0 6.1 - - - +
174E ALA* 4.9 17.9 - - + -
177E ARG* 5.0 9.2 + - + -
293E THR* 5.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASP* 2.7 30.6 + - - +
59C VAL* 3.9 7.9 - - - -
61C THR* 1.3 73.9 + - - +
63C LEU* 1.3 62.4 + - - +
65C ASP* 3.3 25.4 + - + +
66C LEU* 3.5 18.0 + - + +
49D ILE* 5.1 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL 2.9 11.6 + - - +
60C PHE* 3.2 30.1 - - + +
61C THR 3.1 0.2 - - - -
62C THR* 1.3 77.3 - - - +
64C VAL* 1.3 69.5 + - + +
66C LEU* 3.2 28.6 + - + +
71C THR* 3.8 8.6 + - - +
74C ILE* 4.8 12.1 - - + +
75C PHE* 3.5 37.0 - - + -
162C ILE* 5.7 8.3 - - + -
166C CYS* 4.6 11.7 - - + -
49D ILE* 4.9 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE 3.6 16.6 - - - +
61C THR* 3.1 12.0 + - - +
63C LEU* 1.3 81.3 - - + +
65C ASP* 1.3 63.0 + - - +
66C LEU 3.4 8.5 + - - +
71C THR* 5.0 3.9 + - - -
75C PHE* 6.2 0.4 - - - -
166C CYS* 4.2 24.2 - - + +
169C MET* 4.6 18.2 - - + +
170C LYS* 3.3 42.0 - - + +
173C GLN* 4.3 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR 3.1 11.5 + - - +
62C THR* 3.3 20.4 - - + +
63C LEU 3.2 0.4 - - - -
64C VAL* 1.3 75.8 - - - +
66C LEU* 1.3 65.4 + - + +
67C LYS* 3.6 3.1 + - - +
173C GLN* 5.8 2.0 - - - -
175C HIS* 5.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C THR* 3.6 20.6 - - + +
63C LEU* 3.2 18.2 + - + +
64C VAL 3.5 8.5 - - - +
65C ASP* 1.3 82.5 - - + +
67C LYS* 1.3 67.6 + - - +
68C TRP* 3.6 1.2 + - - -
70C HIS* 4.2 23.3 - - + -
71C THR* 4.0 11.9 - - - +
74C ILE* 5.6 9.9 - - + -
48D PHE 4.8 7.4 - - - +
49D ILE* 4.9 14.4 - - + +
52D GLY* 3.9 36.8 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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