Contacts of the helix formed by residues 62 - 74 (chain C) in PDB entry 4BPU
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 ASN 62 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TYR* 4.0 19.7 - - + +
40C PHE* 4.0 9.0 - - - -
41C GLN* 4.8 0.4 - - - +
60C PHE* 3.5 1.1 - - - +
61C ASN* 1.3 85.8 - - - +
63C GLN* 1.3 66.0 + - - +
64C SER* 3.2 27.8 + - - +
65C ASP* 3.3 16.5 + - - +
66C LEU* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 3.8 12.5 - - + +
24C SER* 3.6 35.2 + - - +
27C TYR* 3.6 43.0 - - + +
62C ASN* 1.3 77.4 - - - +
64C SER* 1.3 60.2 + - - +
66C LEU* 3.2 9.8 + - + +
67C GLU* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASN* 3.2 19.0 + - - +
63C GLN* 1.3 77.5 - - - +
65C ASP* 1.3 57.2 + - - +
67C GLU* 3.1 12.5 + - - +
68C LYS* 2.9 32.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
59C SER 5.1 0.2 - - - +
60C PHE* 4.1 10.7 - - + -
61C ASN* 3.1 37.6 + - + +
62C ASN* 3.3 25.6 + - - +
64C SER* 1.3 77.9 - - - +
66C LEU* 1.3 57.0 + - - +
68C LYS* 3.5 14.3 + - - +
69C GLU* 2.9 41.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
23C TYR* 4.1 16.8 - - + +
26C TYR* 3.8 34.1 - - + -
27C TYR* 5.6 2.2 - - + -
40C PHE* 4.1 17.0 - - + -
45C PHE* 5.1 4.3 - - + -
47C PHE* 5.3 0.2 - - + -
60C PHE* 3.3 44.4 - - + +
62C ASN 3.2 11.6 + - - +
63C GLN* 3.3 12.1 - - - +
64C SER 3.0 0.4 - - - -
65C ASP* 1.3 75.7 - - - +
67C GLU* 1.3 66.9 + - - +
70C MET* 2.9 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 4.9 5.6 + - - +
23C TYR* 3.6 39.6 - - + +
63C GLN* 2.9 45.7 + - - +
64C SER* 3.5 9.9 - - - +
66C LEU* 1.3 74.9 - - - +
68C LYS* 1.3 56.4 + - - +
70C MET* 4.0 0.5 - - - +
71C GLN* 2.9 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER 2.9 16.8 + - - +
65C ASP* 3.6 15.2 + - - +
67C GLU* 1.3 76.8 - - - +
69C GLU* 1.3 79.6 + - - +
71C GLN* 3.1 11.5 + - - +
72C ALA* 2.8 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.9 4.5 - - + -
58C GLN* 5.7 2.9 + - - +
60C PHE* 3.6 26.7 - - + -
65C ASP* 2.9 34.1 + - - +
68C LYS* 1.3 96.7 + - + +
70C MET* 1.3 56.9 + - - +
72C ALA* 3.6 10.2 - - - +
73C ALA* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.8 17.7 - - + -
21C PHE* 3.9 17.9 - - + -
23C TYR* 3.6 34.5 - - + +
26C TYR* 5.3 2.5 - - - -
45C PHE* 6.4 0.4 - - - -
47C PHE* 3.7 26.7 - - + -
60C PHE* 5.2 0.2 - - + -
66C LEU* 2.9 42.8 + - + +
69C GLU* 1.3 75.8 - - - +
71C GLN* 1.3 61.0 + - - +
74C ASN* 2.8 32.1 + - - +
75C PRO* 3.6 7.5 - - + +
78C ILE* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS 5.6 0.7 - - - +
17C TYR* 3.2 33.2 + - - +
18C ARG* 2.8 54.4 + - + +
23C TYR* 3.9 4.0 + - - +
67C GLU* 2.9 45.9 + - - +
68C LYS* 3.6 6.7 - - - +
70C MET* 1.3 75.6 - - - +
72C ALA* 1.3 60.1 + - - +
74C ASN* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 2.8 26.9 + - + +
69C GLU* 3.6 17.5 - - - +
71C GLN* 1.3 76.4 - - - +
73C ALA* 1.3 60.9 + - - +
74C ASN* 4.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.6 13.7 - - + -
49C LEU* 3.9 28.2 - - + +
55C ILE* 6.2 1.1 - - + -
69C GLU* 2.9 18.7 + - - +
70C MET 4.2 1.1 - - - +
72C ALA* 1.3 76.4 - - - +
74C ASN* 1.3 73.7 + - - +
75C PRO* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO 5.5 1.3 - - - +
13C LEU* 4.1 13.6 - - + +
14C LYS* 3.4 44.8 - - + +
17C TYR* 3.4 22.9 - - + +
49C LEU* 4.8 1.4 - - - +
50C LYS 5.7 0.3 + - - -
70C MET 2.8 15.1 + - - -
71C GLN* 3.0 27.5 + - - +
72C ALA 4.4 4.4 + - - -
73C ALA* 1.3 74.2 - - - +
75C PRO* 1.3 68.7 - - - +
76C TYR* 4.0 7.8 + - - -
----------------------------------------------------------
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