Contacts of the helix formed by residues 54 - 67 (chain C) in PDB entry 2WP9
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 SER 54 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER 4.5 0.7 - - - +
52C LEU 3.3 1.8 - - - -
53C SER* 1.3 85.9 + - - +
55C PRO* 1.3 77.3 - - - +
56C GLU* 3.8 7.9 + - - +
57C GLY 3.1 22.5 + - - -
58C PHE 3.2 8.8 + - - -
45D TYR* 3.7 17.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 1.3 92.5 - - - +
56C GLU* 1.3 62.0 + - + +
58C PHE* 3.4 4.0 + - - +
59C GLU* 3.4 25.5 + - - +
45D TYR* 3.8 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 3.9 8.5 - - - +
55C PRO* 1.3 81.3 - - + +
57C GLY* 1.3 64.4 + - - +
58C PHE 3.2 0.2 - - - -
59C GLU* 3.4 8.9 + - - +
60C GLN* 3.2 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 3.4 35.7 - - - +
53C SER* 4.3 3.4 - - - -
54C SER* 3.1 16.0 + - - -
56C GLU* 1.3 80.6 - - - +
58C PHE* 1.3 59.9 + - - +
60C GLN* 3.4 11.2 - - - +
61C ALA* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 3.7 17.6 + - - +
54C SER 3.2 5.3 + - - -
55C PRO 3.6 5.2 - - - +
56C GLU 3.2 0.6 - - - -
57C GLY* 1.3 78.5 - - - +
59C GLU* 1.3 69.0 + - + +
61C ALA* 3.2 5.4 + - + +
62C SER* 3.0 41.2 + - - -
43D LEU* 3.3 30.3 - - + -
44D THR* 4.9 0.2 - - - -
45D TYR* 3.3 48.7 - + + -
48D TRP* 3.7 43.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO 3.4 12.0 + - - +
56C GLU* 3.4 9.4 + - - +
58C PHE* 1.3 83.3 - - + +
60C GLN* 1.3 56.8 + - - +
62C SER* 3.2 10.4 + - - +
63C ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C TRP* 6.0 3.0 - - - -
50C THR* 3.9 19.8 + - + +
56C GLU* 3.2 24.4 + - + +
57C GLY* 3.4 13.8 - - - +
59C GLU* 1.3 77.6 - - - +
61C ALA* 1.3 55.8 + - - +
63C ALA* 3.3 7.1 + - - +
64C ILE* 3.1 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.5 17.0 - - + +
50C THR* 4.5 4.0 - - + +
51C SER* 3.7 28.0 - - - +
57C GLY 3.0 13.4 + - - +
58C PHE* 3.2 9.8 + - + +
60C GLN* 1.3 73.4 - - - +
62C SER* 1.3 58.5 + - - +
64C ILE* 3.4 10.1 + - - +
65C MET* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.0 36.7 + - - -
59C GLU* 3.2 10.3 + - - +
61C ALA* 1.3 76.0 - - - +
63C ALA* 1.3 58.0 + - - +
65C MET* 3.3 9.7 + - - +
66C GLY* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU 2.9 15.5 + - - +
60C GLN* 3.6 8.7 - - - +
61C ALA 3.2 0.2 - - - -
62C SER* 1.3 76.2 - - - +
64C ILE* 1.3 62.3 + - + +
66C GLY* 3.0 19.0 + - - +
67C SER* 3.6 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C TRP* 3.7 33.2 - - + -
47C LEU* 4.3 15.7 - - + -
50C THR* 5.6 2.9 - - + -
60C GLN* 3.1 30.4 + - + +
61C ALA* 3.6 10.3 - - - +
62C SER 3.3 0.2 - - - -
63C ALA* 1.3 72.0 - - + +
65C MET* 1.3 62.1 + - + +
66C GLY 3.0 5.7 + - - -
67C SER* 3.2 14.6 + - - +
70C VAL* 3.3 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.3 18.6 - - + -
61C ALA* 2.9 21.8 + - + +
62C SER* 3.3 9.6 + - - +
64C ILE* 1.3 75.3 - - - +
66C GLY* 1.3 61.9 + - - +
67C SER 3.3 0.9 - - - -
70C VAL* 4.2 10.5 - - + -
71C LYS* 3.4 27.5 + - + +
74C MET* 4.1 42.8 - - + +
128C VAL* 4.5 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C SER 2.9 13.6 + - - -
63C ALA* 3.0 9.6 + - - -
65C MET* 1.3 76.5 - - - +
67C SER* 1.3 65.5 + - - +
68C PHE* 3.4 8.7 + - - -
71C LYS* 3.2 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA 3.6 5.4 + - - -
64C ILE* 3.2 15.4 + - - -
65C MET 3.9 0.2 - - - +
66C GLY* 1.3 77.6 - - - +
68C PHE* 1.3 58.9 + - - +
69C PHE* 3.4 10.0 + - - +
70C VAL* 3.4 22.7 + - - +
71C LYS* 2.9 27.4 + - - +
----------------------------------------------------------
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