Contacts of the helix formed by residues 53 - 63 (chain C) in PDB entry 2YVX
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 53 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU 3.4 12.3 - - - +
26C GLU* 4.4 13.5 - - - +
51C LEU 3.5 2.4 - - - +
52C LEU* 1.3 104.3 - - + +
54C LYS* 1.3 67.1 + - - +
55C ALA* 3.0 6.6 + - + +
56C LYS* 3.3 25.0 + - + +
57C ALA* 3.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU 3.8 0.4 + - - -
53C PRO* 1.3 71.6 - - - +
55C ALA* 1.3 64.7 + - - +
57C ALA* 4.1 4.0 - - - +
58C ALA* 3.2 22.3 + - - +
80C ARG* 4.9 17.3 - - - +
83C GLU* 4.0 43.4 + - - +
84C ILE* 4.9 3.7 - - - +
86C GLU* 5.3 4.8 - - - +
87C GLU* 3.4 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PRO* 3.0 5.3 + - + +
54C LYS* 1.3 75.2 - - - +
56C LYS* 1.3 70.5 + - + +
58C ALA* 3.0 14.4 + - - +
59C GLU* 3.0 15.0 + - - +
87C GLU* 3.9 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU 4.5 0.9 - - - +
26C GLU* 3.9 26.7 + - - +
27C GLU 5.5 0.2 - - - -
28C ILE 3.3 26.6 + - - +
29C HIS* 4.3 1.2 - - - +
30C PRO* 3.8 29.5 - - + +
52C LEU* 3.4 37.9 - - + -
53C PRO* 3.3 20.2 + - + -
55C ALA* 1.3 80.5 - - + +
57C ALA* 1.3 63.4 + - - +
59C GLU* 3.3 2.8 + - - +
60C VAL* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 3.9 25.7 - - + +
52C LEU* 3.9 25.0 - - + +
53C PRO 3.1 15.7 + - - +
54C LYS* 4.1 2.7 - - - +
56C LYS* 1.3 80.0 - - - +
58C ALA* 1.3 62.6 + - - +
60C VAL* 3.7 0.6 + - - -
61C LEU* 3.4 19.8 + - - +
80C ARG* 5.4 2.9 - - - +
84C ILE* 4.0 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LYS 3.2 12.6 + - - +
55C ALA 3.0 3.8 + - - +
57C ALA* 1.3 76.0 - - - +
59C GLU* 1.3 68.4 + - - +
61C LEU* 3.2 11.1 + - - +
62C SER 3.3 4.5 + - - -
84C ILE* 3.6 19.7 - - + +
87C GLU 3.3 26.9 - - - +
88C LEU* 3.0 35.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
29C HIS* 6.4 0.4 - - + -
30C PRO* 4.1 20.4 - - + -
34C LEU* 6.3 0.4 - - + -
55C ALA 3.0 12.2 + - - +
56C LYS* 3.5 11.0 - - - +
58C ALA* 1.3 72.1 - - - +
60C VAL* 1.3 55.2 + - - +
61C LEU 2.8 15.1 + - - -
62C SER* 2.9 18.1 + - - -
63C HIS* 3.2 43.5 + - + +
88C LEU* 4.2 5.1 - - - +
89C SER* 6.1 1.0 - - - -
92C ASP* 6.2 0.2 - - - -
226D ASP* 5.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PRO* 3.6 30.3 - - + +
33C LEU* 3.9 30.7 - - + -
34C LEU* 3.1 46.7 - - + +
37C TRP* 5.1 8.3 - - + -
49C LEU* 4.9 9.4 - - + -
52C LEU* 4.3 4.3 - - + -
56C LYS 3.0 20.5 + - - +
57C ALA 4.1 4.0 - - - +
59C GLU* 1.3 74.0 - - - +
61C LEU* 1.3 60.0 + - - +
63C HIS 3.9 1.9 + - - -
64C LEU* 3.7 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.3 18.4 - - + -
57C ALA 3.4 10.3 + - - +
58C ALA* 3.2 10.0 + - - +
59C GLU 2.8 3.0 + - - -
60C VAL* 1.3 76.4 - - - +
62C SER* 1.3 56.7 + - - +
63C HIS 3.0 9.8 + - - -
64C LEU* 3.1 44.7 + - + +
69C GLN* 3.5 34.2 - - + +
72C TYR* 4.8 9.4 - - + +
73C LEU* 5.0 18.6 - - + -
76C LEU* 6.4 0.9 - - + -
84C ILE* 4.7 20.4 - - + -
85C LEU* 6.3 2.5 - - + -
88C LEU* 5.3 8.5 - - + -
----------------------------------------------------------
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 ALA 3.3 8.2 + - - -
59C GLU* 2.9 13.2 + - - -
61C LEU* 1.3 77.7 - - - +
63C HIS* 1.3 66.8 + - - +
64C LEU 3.3 4.0 + - - +
69C GLN* 4.0 17.5 + - - -
88C LEU* 4.2 9.1 - - - +
92C ASP* 2.4 50.3 + - - +
96C ALA* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 3.9 9.9 + - + +
34C LEU* 3.3 44.1 - - + +
59C GLU* 3.2 39.6 + - + +
60C VAL 4.0 1.3 - - - -
61C LEU 3.0 1.4 - - - -
62C SER* 1.3 98.3 + - - +
64C LEU* 1.3 58.4 + - - +
92C ASP* 4.8 4.3 + - - -
224D ASP* 4.1 8.4 + - - -
226D ASP* 3.8 24.7 + - - -
----------------------------------------------------------
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