Contacts of the helix formed by residues 36 - 67 (chain X) in PDB entry 5KHU
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 36 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X VAL* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36X ASN* 3.8 24.7 - - - +
38X ILE* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X VAL* 3.8 25.4 - - - +
39X ASP* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X ILE* 3.8 28.9 - - - +
40X HIS* 3.8 27.1 - - - +
42X ARG* 4.5 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 40 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X ASP* 3.8 25.1 - - - +
41X VAL* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X HIS* 3.8 29.2 - - - +
42X ARG* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X ASP* 4.5 15.0 - - - +
41X VAL* 3.8 25.6 - - - +
43X ASP* 3.8 28.9 - - - +
45X ALA* 4.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X ARG* 3.8 26.0 - - - +
44X MET* 3.8 29.2 - - - +
46X ALA* 4.3 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 44 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X ASP* 3.8 24.5 - - - +
45X ALA* 3.8 28.9 - - - +
47X ALA* 4.3 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X ARG* 4.4 16.6 - - - +
44X MET* 3.8 29.6 - - - +
46X ALA* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X ASP* 4.3 16.4 - - - +
45X ALA* 3.8 24.5 - - - +
47X ALA* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X MET* 4.3 18.2 - - - +
46X ALA* 3.8 29.4 - - - +
48X GLY* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X ALA* 3.8 29.2 - - - +
49X LEU* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X GLY* 3.8 28.5 - - - +
50X HIS* 3.7 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 50 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X LEU* 3.7 30.3 - - - +
51X SER* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X HIS* 3.8 29.6 - - - +
52X ASN* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X SER* 3.8 27.8 - - - +
53X VAL* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X ASN* 3.8 29.6 - - - +
54X ARG* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X VAL* 3.8 26.5 - - - +
55X LEU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X ARG* 3.8 29.8 - - - +
56X LEU* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X LEU* 3.8 25.4 - - - +
57X SER* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X LEU* 3.8 29.2 - - - +
58X SER* 3.8 27.1 - - - +
60X LEU* 4.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X SER* 3.8 25.8 - - - +
59X LEU* 3.8 28.9 - - - +
61X LEU* 4.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58X SER* 3.8 29.4 - - - +
60X LEU* 3.8 26.0 - - - +
62X THR* 4.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X SER* 4.6 13.7 - - - +
59X LEU* 3.8 24.5 - - - +
61X LEU* 3.8 28.9 - - - +
63X MET* 4.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58X SER* 4.5 16.4 - - - +
60X LEU* 3.8 26.0 - - - +
62X THR* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X LEU* 4.6 14.6 - - - +
61X LEU* 3.8 28.9 - - - +
63X MET* 3.8 24.5 - - - +
65X ASN* 4.5 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X LEU* 4.5 16.8 - - - +
62X THR* 3.8 25.8 - - - +
64X SER* 3.8 28.9 - - - +
66X ASN* 4.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X MET* 3.8 25.6 - - - +
65X ASN* 3.8 29.2 - - - +
67X ASN* 4.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62X THR* 4.5 15.0 - - - +
64X SER* 3.8 29.4 - - - +
66X ASN* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X MET* 4.5 13.9 - - - +
65X ASN* 3.8 28.9 - - - +
67X ASN* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64X SER* 4.6 12.3 - - - +
66X ASN* 3.8 29.2 - - - +
68X PRO* 3.8 29.2 - - - -
----------------------------------------------------------
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