Contacts of the helix formed by residues 32 - 49 (chain A) in PDB entry 2KK0
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 ASP 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.1 26.7 - - + +
31A GLY* 1.3 77.9 - - - +
33A PRO* 1.4 80.1 - - - +
34A LYS* 2.8 56.9 + - - +
35A ARG* 2.9 20.7 + - + +
36A LYS* 3.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 4.2 3.1 - - - +
32A ASP* 1.4 94.7 - - - +
34A LYS* 1.3 67.2 + - + +
36A LYS* 3.2 21.3 - - + +
37A GLU* 3.1 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 2.8 40.5 + - - +
33A PRO* 1.3 75.7 - - + +
35A ARG* 1.3 61.3 + - - +
37A GLU* 4.0 8.7 - - - +
38A PHE* 3.2 20.3 + - - +
67A PHE* 3.3 23.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 3.6 20.6 - - - +
27A TYR* 4.0 10.5 - - - +
29A LEU* 3.3 32.7 - - - +
30A ASP* 2.8 49.2 + - + +
32A ASP* 2.9 17.7 + - + +
34A LYS* 1.3 82.3 - - - +
36A LYS* 1.3 63.0 + - - +
39A LEU* 3.1 31.7 + - + +
67A PHE* 3.3 46.6 - - - +
68A MET* 2.9 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.7 34.3 - - + -
31A GLY* 4.7 11.4 - - - -
32A ASP 3.3 21.1 - - - +
33A PRO* 3.2 27.8 - - + +
35A ARG* 1.3 77.8 - - - +
37A GLU* 1.3 72.4 + - + +
39A LEU* 3.9 0.3 - - - +
40A ASP* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.1 36.5 + - + +
34A LYS* 4.0 7.9 + - - +
36A LYS* 1.3 82.8 - - + +
38A PHE* 1.3 64.8 + - - +
40A ASP* 4.0 2.4 - - - +
41A ASP* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS 3.2 16.0 + - - +
37A GLU* 1.3 78.6 - - - +
39A LEU* 1.3 63.8 + - + +
41A ASP* 3.8 3.8 - - - +
42A LEU* 2.8 58.7 + - + +
67A PHE* 3.4 44.6 - + + -
70A TYR* 3.5 42.0 - + + -
116A LEU* 4.4 2.2 - - + -
119A TYR* 3.5 40.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.5 58.3 - - + +
27A TYR* 3.9 22.2 - - + +
29A LEU* 5.8 0.2 - - + -
35A ARG* 3.1 25.7 + - + +
38A PHE* 1.3 85.3 - - + +
40A ASP* 1.3 57.9 + - - +
42A LEU* 3.3 5.3 + - + +
43A PHE* 2.9 45.3 + - + -
66A LEU* 4.6 4.7 - - + -
67A PHE* 3.9 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 4.2 13.0 + - + +
36A LYS 3.0 19.0 + - - +
37A GLU* 4.1 1.8 - - - +
39A LEU* 1.3 76.2 - - - +
41A ASP* 1.3 64.8 + - - +
43A PHE* 3.3 10.9 + - - +
44A SER* 3.1 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU 2.9 19.4 + - - +
38A PHE* 3.8 3.1 - - - +
40A ASP* 1.3 78.7 + - - +
42A LEU* 1.3 57.4 + - - +
44A SER* 3.9 5.0 - - - -
45A PHE* 3.0 30.9 + - - +
119A TYR* 2.9 30.3 + - - +
123A LYS* 4.7 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 2.8 35.2 + - + +
39A LEU* 3.4 5.4 - - + +
41A ASP* 1.3 74.4 + - - +
43A PHE* 1.3 78.4 + - + +
45A PHE* 3.0 8.1 + - + +
46A MET* 2.8 45.4 + - + +
66A LEU* 5.1 7.4 - - + -
115A TYR* 4.5 11.4 - - + +
116A LEU* 3.4 34.8 - - + -
118A PRO* 6.2 1.3 - - + -
119A TYR* 4.0 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 5.7 7.4 - - - -
23A PHE* 5.7 1.6 - - + -
26A LEU* 3.7 24.5 - - + -
27A TYR* 3.2 33.9 - + - -
39A LEU* 2.9 31.9 + - + +
40A ASP* 3.8 7.6 - - - +
42A LEU* 1.3 83.8 - - + +
44A SER* 1.3 63.1 + - - +
46A MET* 3.2 12.4 - - - +
47A GLN* 3.1 26.6 + - - +
52A PRO* 5.0 1.4 - - - +
53A VAL* 3.6 35.2 - - + +
56A ILE* 5.6 0.4 - - + -
66A LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.1 24.6 + - - -
41A ASP* 3.9 6.0 - - - -
43A PHE* 1.3 75.7 - - - +
45A PHE* 1.3 62.8 + - - +
47A GLN* 3.3 11.4 + - - +
48A LYS* 3.0 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.0 20.0 + - - +
42A LEU* 3.0 9.2 + - + +
44A SER* 1.3 75.9 - - - +
46A MET* 1.3 67.3 + - + +
48A LYS* 3.2 30.2 + - + +
49A ARG* 3.6 38.1 + - - +
118A PRO* 3.7 25.4 - - + -
119A TYR* 3.9 26.0 - + + -
122A GLU* 3.7 38.6 - - + -
123A LYS* 5.0 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 2.8 28.1 + - + +
43A PHE* 3.2 25.4 - - - +
45A PHE* 1.3 78.2 - - + +
47A GLN* 1.3 62.8 + - - +
49A ARG* 3.3 18.9 - - - +
51A THR* 2.9 57.7 + - + +
52A PRO* 3.8 7.0 - - + -
53A VAL* 3.5 33.7 - - + -
114A LYS 4.8 1.1 - - - +
115A TYR* 3.7 43.1 - - + +
118A PRO* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE 3.1 21.4 + - - +
44A SER* 3.5 9.3 - - - +
45A PHE 3.2 0.2 - - - -
46A MET* 1.3 76.2 - - - +
48A LYS* 1.3 65.7 + - + +
50A GLY* 3.0 14.4 + - - -
51A THR 4.4 0.2 - - - +
52A PRO* 4.0 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.0 33.8 + - - +
45A PHE* 3.2 19.0 + - + +
47A GLN* 1.3 77.2 - - + +
49A ARG* 1.3 58.6 + - + +
50A GLY 3.4 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.6 27.0 + - - +
46A MET* 3.3 14.8 - - - +
48A LYS* 1.3 76.4 - - + +
50A GLY* 1.3 63.2 + - - +
51A THR* 3.9 11.3 - - + +
118A PRO* 3.6 38.1 + - - +
122A GLU* 3.5 24.2 + - - -
----------------------------------------------------------
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