Contacts of the helix formed by residues 55 - 67 (chain H) in PDB entry 1XK4
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 55 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H LYS 4.3 1.8 + - - +
52H GLU* 3.1 15.2 + - - +
53H ASN 3.2 2.2 - - - -
54H LYS* 1.3 80.4 - - - +
56H GLU* 1.3 59.7 + - - +
57H LYS* 3.0 25.9 + - - +
58H VAL* 2.8 46.4 + - + +
59H ILE* 3.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LYS* 2.6 42.7 + - + +
53H ASN 4.8 1.9 + - - -
54H LYS 4.2 1.2 - - - -
55H ASN* 1.3 72.9 + - - +
57H LYS* 1.3 59.6 + - + +
59H ILE* 3.3 10.5 + - - +
60H GLU* 3.0 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ASN* 3.0 16.5 + - - +
56H GLU* 1.3 77.4 - - + +
58H VAL* 1.3 61.0 + - + +
60H GLU* 3.4 19.5 + - - +
61H HIS* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLU* 3.7 38.4 - - + +
55H ASN* 2.8 34.7 + - + +
57H LYS* 1.3 76.2 - - - +
59H ILE* 1.3 65.4 + - - +
61H HIS* 3.1 9.4 + - + +
62H ILE* 3.0 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.8 26.8 - - + -
38H LYS* 4.1 26.5 - - + +
41H VAL* 3.9 24.7 - - + -
49H LEU* 5.1 0.2 - - + -
52H GLU* 3.5 41.3 - - + +
53H ASN* 3.9 13.2 - - - +
55H ASN 3.9 4.3 - - - +
56H GLU* 3.3 12.5 + - - +
58H VAL* 1.3 77.3 - - - +
60H GLU* 1.3 61.7 + - - +
62H ILE* 3.2 14.6 + - + +
63H MET* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H GLN* 3.6 21.8 + - - +
37H PHE* 6.1 0.2 - - - -
38H LYS* 2.7 36.3 + - - +
56H GLU* 3.0 24.9 + - - +
57H LYS* 3.6 20.8 - - - +
59H ILE* 1.3 76.5 - - - +
61H HIS* 1.3 56.7 + - - +
63H MET* 3.3 7.2 + - - +
64H GLU* 3.0 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E HIS* 4.1 11.8 + + - -
95G HIS* 5.6 5.9 + - - +
57H LYS 3.0 13.3 + - - +
58H VAL* 3.1 12.1 + - + +
60H GLU* 1.3 73.5 - - - +
62H ILE* 1.3 63.3 + - + +
64H GLU* 3.2 17.3 + - - +
65H ASP* 2.8 73.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 4.0 20.0 - - + -
49H LEU* 4.5 15.9 - - + -
52H GLU* 4.3 13.0 - - + -
58H VAL* 3.0 29.9 + - + +
59H ILE* 3.5 26.5 - - + +
61H HIS* 1.3 76.9 - - + +
63H MET* 1.3 63.5 + - - +
65H ASP* 3.4 8.4 + - - +
66H LEU* 3.1 33.0 + - + +
82H LEU* 4.4 15.3 - - + -
85H ARG* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU 3.6 20.6 - - - +
33H ASN 3.8 0.7 - - - +
34H GLN* 3.6 39.0 - - + +
37H PHE* 3.7 32.9 - - + -
59H ILE 3.0 8.8 + - - +
60H GLU* 3.6 10.5 - - - +
62H ILE* 1.3 79.3 - - - +
64H GLU* 1.3 57.7 + - + +
66H LEU* 3.1 5.5 + - - +
67H ASP* 2.9 29.7 + - + +
72H LYS* 3.5 28.5 - - - +
73H GLN* 3.8 8.3 - - - +
74H LEU* 3.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASN* 2.8 23.1 + - - -
27E HIS* 5.6 0.2 - - - -
34H GLN* 5.3 6.0 + - - +
60H GLU* 3.0 37.9 + - - +
61H HIS* 3.6 16.4 + - - +
63H MET* 1.3 75.6 - - + +
65H ASP* 1.3 62.9 + - - +
67H ASP* 3.3 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASN* 3.4 17.4 + - - +
27E HIS* 2.9 47.5 + - + +
95G HIS* 5.3 2.3 + - - -
61H HIS* 2.8 52.1 + - - +
62H ILE* 3.7 7.7 - - - +
63H MET 3.3 0.2 - - - -
64H GLU* 1.3 77.4 - - - +
66H LEU* 1.3 59.4 + - - +
68H THR* 4.2 6.9 - - - +
85H ARG* 5.2 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ASP* 4.7 0.2 - - - +
37H PHE* 4.2 2.7 - - + -
62H ILE* 3.1 32.9 + - + +
63H MET 3.1 7.8 + - - +
65H ASP* 1.3 74.6 - - - +
67H ASP* 1.3 59.8 + - - +
68H THR* 2.9 17.5 + - - +
74H LEU* 3.7 29.6 - - + -
78H GLU* 3.3 39.2 - - - +
79H PHE* 5.1 0.4 - - - -
81H MET* 4.2 7.0 - - + -
82H LEU* 3.8 39.9 - - + +
85H ARG* 3.9 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASN* 3.1 14.0 + - - +
63H MET* 2.9 18.7 + - + +
64H GLU* 3.7 8.5 - - - +
65H ASP 3.3 1.2 - - - -
66H LEU* 1.3 73.6 - - - +
68H THR* 1.3 62.7 + - - +
69H ASN* 3.1 5.9 - - - +
70H ALA* 3.1 12.5 + - - -
71H ASP* 3.1 5.9 + - - +
72H LYS* 2.7 33.1 + - - +
73H GLN 3.8 7.2 - - - +
74H LEU* 3.8 8.7 - - + -
78H GLU* 3.7 2.7 - - - -
4511H CA 2.3 31.7 - - - -
----------------------------------------------------------
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