Contacts of the helix formed by residues 18 - 34 (chain C) in PDB entry 5V6Y
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 GLY 18 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.8 4.2 - - - +
17C LYS* 1.3 73.0 - - - +
19C TYR* 1.3 58.9 + - - -
20C ASN 3.2 3.4 - - - -
21C GLY* 3.5 6.1 + - - -
22C LEU* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 3.7 16.6 - - + -
14C ASN 4.4 1.1 - - - -
15C GLY* 3.2 27.1 - - - -
17C LYS* 3.0 18.6 + - - +
18C GLY* 1.3 73.4 - - - +
20C ASN* 1.3 98.3 + - - +
22C LEU* 3.5 3.8 + - - -
23C ALA* 3.0 23.9 + - - +
39C VAL* 3.5 32.4 - - + +
41C HIS* 3.6 42.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY* 3.2 1.0 - - - -
19C TYR* 1.3 108.1 + - - +
21C GLY* 1.3 64.8 + - - +
23C ALA* 3.0 18.9 + - - +
24C GLU* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY* 3.5 8.0 + - - -
20C ASN* 1.3 77.8 - - - +
22C LEU* 1.3 61.2 + - - +
24C GLU* 3.3 25.3 + - - +
25C VAL* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.8 37.6 - - + +
13C ILE* 4.2 19.5 - - + -
18C GLY 3.0 17.4 + - - +
19C TYR 3.6 5.6 - - - +
20C ASN 3.2 0.2 - - - -
21C GLY* 1.3 75.4 - - - +
23C ALA* 1.3 63.5 + - - +
25C VAL* 3.2 20.7 + - + +
26C GLY* 3.1 17.2 + - - -
37C VAL* 5.5 0.5 - - - +
39C VAL* 4.0 17.8 - - + +
63C PHE* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR 3.0 13.8 + - - +
20C ASN* 3.0 14.1 + - - +
22C LEU* 1.3 74.1 - - - +
24C GLU* 1.3 61.6 + - + +
26C GLY* 3.1 3.8 + - - +
27C LYS* 2.8 27.4 + - - +
37C VAL 5.4 4.5 - - - +
39C VAL* 3.7 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASN 3.1 13.4 + - - +
21C GLY* 3.5 15.8 - - - +
22C LEU 3.2 0.4 - - - -
23C ALA* 1.3 74.1 - - + +
25C VAL* 1.3 60.6 + - + +
27C LYS* 3.2 14.0 + - + +
28C LYS* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 3.4 15.5 - - - +
22C LEU* 3.2 21.9 + - + +
24C GLU* 1.3 75.7 - - + +
26C GLY* 1.3 59.1 + - - +
28C LYS* 3.2 10.0 + - + +
29C PHE* 2.9 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 3.1 12.0 + - - -
23C ALA 3.1 4.7 + - - -
25C VAL* 1.3 74.6 - - - +
27C LYS* 1.3 58.9 + - - +
29C PHE* 3.3 4.8 + - - +
30C GLU* 2.8 29.9 + - - +
37C VAL* 3.6 41.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA 2.8 16.9 + - - +
24C GLU* 3.2 17.5 + - + +
26C GLY* 1.3 71.2 - - - +
28C LYS* 1.3 62.7 + - - +
30C GLU* 3.4 12.8 + - + +
31C LYS* 3.1 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU 2.9 12.9 + - - +
25C VAL* 3.2 13.0 + - + +
27C LYS* 1.3 77.7 - - - +
29C PHE* 1.3 61.0 + - - +
31C LYS* 3.4 10.8 + - + +
32C ASP* 3.1 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.3 15.3 - - + -
25C VAL* 2.9 16.9 + - + +
26C GLY* 3.6 8.7 - - - +
28C LYS* 1.3 77.1 - - - +
30C GLU* 1.3 57.1 + - - +
32C ASP* 3.6 2.6 + - + -
33C THR* 2.6 64.8 + - + +
35C ILE* 3.6 26.2 - - + -
37C VAL* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY 2.8 15.8 + - - +
27C LYS* 3.8 11.8 - - - +
28C LYS 3.3 0.2 - - - -
29C PHE* 1.3 78.3 - - - +
31C LYS* 1.3 57.9 + - - +
34C GLY* 3.0 28.5 + - - +
35C ILE 3.3 22.4 + - - +
36C LYS* 3.2 48.1 + - - +
37C VAL 4.3 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 3.1 17.6 + - + +
28C LYS* 3.9 10.5 - - + +
29C PHE 3.4 0.4 - - - -
30C GLU* 1.3 78.0 - - - +
32C ASP* 1.3 68.0 + - - +
34C GLY 4.7 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LYS* 3.1 49.8 + - - +
29C PHE* 4.3 1.8 - - - +
30C GLU 3.3 0.2 - - - -
31C LYS* 1.3 89.3 - - - +
33C THR* 1.3 68.6 + - + +
34C GLY 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 2.6 53.0 + - + +
32C ASP* 1.3 86.1 - - + +
34C GLY* 1.3 59.1 + - - +
35C ILE* 3.1 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLU* 3.0 22.6 + - - +
31C LYS 4.7 0.8 - - - -
32C ASP 3.8 0.8 - - - -
33C THR* 1.3 75.4 - - - +
35C ILE* 1.3 64.5 + - - +
36C LYS* 3.6 3.3 + - - +
----------------------------------------------------------
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