Contacts of the helix formed by residues 24 - 37 (chain X) in PDB entry 1YKX
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 24 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18X ASP* 4.6 0.7 - - - -
19X ASN* 3.4 20.6 - - - +
22X GLY 3.7 4.9 + - - -
23X TYR* 1.3 76.5 - - - +
25X LEU* 1.3 66.5 + - - +
26X GLY 4.0 3.5 + - - -
27X ASN* 2.9 37.7 + - - +
28X TRP* 3.5 3.1 - - - -
120X VAL* 3.9 12.5 - - - +
121X GLN* 5.5 5.0 - - - +
124X ILE* 6.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X ALA* 3.6 31.0 - - + +
12X MET* 3.8 22.2 - - + -
13X LYS* 3.9 16.6 - - + +
18X ASP* 3.0 36.6 + - + +
23X TYR 3.8 0.4 + - - -
24X SER* 1.3 72.3 - - - +
26X GLY* 1.3 63.9 + - - +
28X TRP* 3.0 20.7 + - + -
29X VAL* 3.2 21.7 + - + +
124X ILE* 4.2 15.7 - - + +
129X LEU* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24X SER* 3.1 4.8 + - - -
25X LEU* 1.3 78.8 - - - +
27X ASN* 1.3 56.8 + - - +
29X VAL* 4.6 0.7 - - - -
30X CYS* 3.0 31.4 + - - +
120X VAL* 3.3 32.7 - - - +
121X GLN* 4.8 0.9 - - - -
123X TRP* 4.0 4.4 - - - +
124X ILE* 4.1 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X TYR* 4.2 12.9 - - + +
24X SER* 2.9 43.3 + - - +
26X GLY* 1.3 77.9 - - - +
28X TRP* 1.3 58.0 + - - +
30X CYS* 3.5 2.5 + - - +
31X ALA* 3.0 28.6 + - - +
105X MET* 3.8 14.6 - - - -
111X TRP* 3.0 37.5 + - - +
115X CYS 5.1 0.3 - - - +
116X LYS* 5.4 0.3 - - - -
120X VAL* 3.7 24.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 28 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X MET* 3.7 23.8 - - + +
17X LEU* 3.1 57.9 + - + -
20X TYR* 4.3 8.9 + - + -
23X TYR* 3.3 20.7 + - + +
24X SER 3.5 15.3 - - - -
25X LEU* 3.0 10.6 + - + +
27X ASN* 1.3 73.6 - - - +
29X VAL* 1.3 60.9 + - - +
31X ALA* 3.8 1.7 - - - +
32X ALA* 3.1 28.1 + - - +
56X LEU* 4.4 13.6 - - + +
95X ALA* 4.2 12.6 - - + -
99X VAL* 3.8 37.9 - - + -
105X MET* 3.8 30.1 - - + -
108X TRP* 3.9 24.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X ARG* 4.3 9.9 - - + +
8X LEU* 4.8 2.2 - - + -
9X ALA* 3.9 33.7 - - + +
12X MET* 4.2 8.3 - - - -
25X LEU* 3.2 17.3 + - + +
26X GLY* 4.0 6.3 - - - +
28X TRP* 1.3 73.7 - - - +
30X CYS* 1.3 65.1 + - - +
32X ALA* 3.4 3.2 + - - -
33X LYS* 3.0 20.4 + - - +
38X PHE* 3.4 26.6 - - + -
123X TRP* 4.0 29.4 - - + +
124X ILE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 30 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26X GLY 3.0 18.7 + - - +
27X ASN* 3.7 4.5 - - - +
28X TRP 3.3 0.2 - - - -
29X VAL* 1.3 78.4 - - - +
31X ALA* 1.3 61.3 + - - +
33X LYS* 3.3 2.6 + - - +
34X PHE* 3.2 42.6 + - - -
114X ARG 4.1 1.1 - - - -
115X CYS* 2.0 50.7 - - + -
118X THR* 5.0 0.7 - - - -
120X VAL* 4.7 3.8 - - + -
123X TRP* 3.4 37.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27X ASN 3.0 17.9 + - - +
28X TRP 3.8 4.7 - - - +
29X VAL 3.3 0.2 - - - -
30X CYS* 1.3 78.4 - - - +
32X ALA* 1.3 55.7 + - - +
34X PHE* 3.5 2.0 + - - +
35X GLU* 2.9 41.3 + - + +
56X LEU* 4.3 11.4 - - + -
105X MET* 3.8 19.7 - - + -
108X TRP* 5.1 3.8 - - + -
111X TRP* 4.2 15.5 - - + +
115X CYS* 3.7 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X LEU* 3.6 29.2 - - + -
12X MET* 4.4 2.2 - - + -
28X TRP 3.1 17.9 + - - +
29X VAL 3.7 1.6 - - - +
31X ALA* 1.3 73.2 - - - +
33X LYS* 1.3 68.3 + - - +
36X SER* 3.0 28.1 + - - -
37X ASN 3.3 1.7 + - - -
38X PHE* 3.5 3.2 + - + -
55X ILE* 3.7 26.5 - - + +
56X LEU* 4.1 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29X VAL 3.0 17.7 + - - +
30X CYS 3.5 5.6 - - - +
31X ALA 3.3 0.2 - - - -
32X ALA* 1.3 75.8 - - - +
34X PHE* 1.3 73.4 + - + +
37X ASN* 2.8 54.8 + - - +
38X PHE* 3.5 36.2 - - + -
123X TRP* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X CYS* 3.2 38.0 + - - +
33X LYS* 1.3 91.6 - - + +
35X GLU* 1.3 64.0 + - - +
110X ALA* 4.0 21.8 - - + +
114X ARG* 3.3 66.3 + - + +
115X CYS* 3.8 11.4 - - - -
123X TRP* 3.8 24.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31X ALA* 2.9 28.5 + - - +
34X PHE* 1.3 79.9 - - - +
36X SER* 1.3 59.3 + - - +
44X ASN* 4.6 4.9 + - - -
55X ILE 4.0 10.5 - - - +
56X LEU* 4.4 2.7 - - - +
57X GLN* 3.3 44.7 - - + +
108X TRP* 3.8 33.4 - - + +
109X VAL* 3.9 8.3 + - - +
110X ALA* 3.1 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32X ALA 3.0 8.4 + - - -
35X GLU* 1.3 77.6 - - - +
37X ASN* 1.3 70.9 + - - +
38X PHE 3.4 6.8 + - - -
39X ASN* 3.1 32.4 + - - +
42X ALA* 3.8 12.2 - - - +
54X GLY 3.5 11.9 - - - -
55X ILE* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X VAL* 4.2 11.4 - - - +
32X ALA 3.3 0.2 + - - -
33X LYS* 2.8 59.0 + - - +
35X GLU 3.9 0.4 - - - -
36X SER* 1.3 74.3 - - - +
38X PHE* 1.3 72.2 + - - +
39X ASN* 3.2 3.4 + - + +
----------------------------------------------------------
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