Contacts of the helix formed by residues 52 - 65 (chain H) in PDB entry 1XFB
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 THR 52 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H GLU* 2.9 13.9 + - - +
51H ASN* 1.3 73.6 - - - +
53H GLU* 1.3 77.2 + - + +
54H GLU* 3.2 19.7 - - + +
55H ASN* 3.3 27.7 + - - +
56H ARG* 3.2 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H THR* 1.3 79.5 - - + +
54H GLU* 1.3 58.5 + - - +
56H ARG* 3.1 31.7 + - - +
57H ARG 2.9 22.9 + - - -
82H GLU* 3.6 11.4 - - - +
86H GLN* 3.5 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H THR* 3.1 14.1 - - + +
53H GLU* 1.3 77.8 - - - +
55H ASN* 1.3 63.1 + - - +
57H ARG* 2.9 35.4 + - - +
58H LEU* 2.7 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 4.4 4.7 - - + +
49H VAL* 3.7 17.6 - - + +
50H GLU* 2.5 45.4 + - - +
52H THR* 3.3 21.4 + - - +
53H GLU 3.5 0.4 - - - -
54H GLU* 1.3 80.7 - - - +
56H ARG* 1.3 56.6 + - - +
58H LEU* 3.6 18.3 - - - +
59H TYR* 3.0 22.0 + - - +
314H TRP* 3.5 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H VAL* 3.2 34.0 - - - +
40H MET* 3.5 37.2 - - + -
44H LEU* 4.1 5.8 - - + -
51H ASN* 2.8 35.0 + - - +
52H THR 3.2 16.6 + - - +
53H GLU* 3.1 28.8 - - - +
54H GLU 3.0 0.6 - - - -
55H ASN* 1.3 74.5 - - - +
57H ARG* 1.3 66.1 + - - +
59H TYR* 3.1 6.9 + - - +
60H ARG* 2.8 39.3 + - - +
80H PHE* 6.2 0.4 - - - -
82H GLU* 2.8 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLU 2.9 8.4 + - - +
54H GLU* 2.9 37.5 + - - +
56H ARG* 1.3 75.6 - - - +
58H LEU* 1.3 86.9 + - - +
60H ARG* 3.4 1.5 + - - +
61H GLN* 2.9 32.6 + - - +
86H GLN* 3.4 34.2 + - + +
87H LYS 3.0 31.6 + - - +
88H ASP 3.6 9.1 + - - -
89H ASP* 2.9 30.7 + - - +
94H PHE* 3.4 14.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLU* 2.7 37.4 + - + +
55H ASN* 3.6 24.2 - - - +
57H ARG* 1.3 98.2 - - - +
59H TYR* 1.3 63.5 + - - +
61H GLN* 3.0 31.7 - - - +
62H VAL* 3.1 12.1 + - - +
89H ASP* 4.4 4.0 - - - +
314H TRP* 4.0 15.5 - - + +
316H GLY 5.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H MET* 4.6 20.2 - - + -
44H LEU* 4.9 3.4 - - + -
55H ASN 3.0 15.3 + - - +
56H ARG* 3.1 4.9 + - - +
58H LEU* 1.3 76.8 - - - +
60H ARG* 1.3 79.9 + - - +
62H VAL* 2.9 32.7 + - + +
63H LEU* 3.4 23.0 + - + +
307H GLN* 2.7 55.8 + - - +
310H ALA 4.9 1.8 - - - -
311H LEU* 3.3 46.5 - - + +
314H TRP* 3.6 24.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ALA* 3.1 23.0 + - - +
35H GLU* 2.6 62.8 + - - +
40H MET* 3.5 23.9 - - - +
56H ARG* 2.8 38.2 + - - +
57H ARG 3.8 3.1 - - - +
59H TYR* 1.3 81.9 - - - +
61H GLN* 1.3 57.7 + - - +
63H LEU* 3.1 9.9 + - - +
64H PHE* 2.9 50.2 + - + -
80H PHE* 4.2 5.7 - - - +
82H GLU* 5.1 0.4 + - - -
83H THR* 3.3 30.1 + - + +
86H GLN* 4.2 3.4 - - - +
94H PHE* 4.1 6.3 - - + -
307H GLN* 4.8 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ARG* 2.9 16.8 + - - +
58H LEU* 3.0 24.8 - - - +
59H TYR 3.0 0.2 - - - -
60H ARG* 1.3 75.5 - - - +
62H VAL* 1.3 55.6 + - - +
64H PHE* 4.4 0.9 - - + +
65H SER* 2.6 46.8 + - - +
88H ASP* 3.0 16.2 - - + +
89H ASP* 2.7 60.5 + - - +
94H PHE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H LEU 3.1 15.0 + - - +
59H TYR* 2.9 20.2 + - + +
61H GLN* 1.3 74.9 - - - +
63H LEU* 1.3 66.2 + - + +
65H SER* 3.2 11.0 + - - -
310H ALA* 5.7 0.7 - - + -
314H TRP* 3.9 29.6 - - + +
321H ALA* 3.6 12.6 - - + +
324H ALA* 3.3 31.4 - - + -
325H THR* 2.8 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.2 18.2 - - + -
33H ALA* 4.4 11.0 - - + -
59H TYR* 3.9 34.5 - - + +
60H ARG* 3.1 10.9 + - - +
61H GLN 3.0 0.6 - - - -
62H VAL* 1.3 78.5 - - + +
64H PHE* 1.3 69.4 + - + +
65H SER 3.1 4.0 - - - -
66H ALA* 3.1 24.1 + - - +
307H GLN* 3.6 38.1 - - + +
310H ALA* 4.6 3.8 - - + -
328H PHE* 3.4 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.3 12.6 - - + -
33H ALA* 4.4 13.2 - - + -
60H ARG* 2.9 32.3 + - + +
61H GLN 4.2 1.6 - - - +
63H LEU* 1.3 76.5 - - + +
65H SER* 1.3 58.7 + - - +
66H ALA* 3.1 6.8 + - - +
77H VAL* 3.6 25.8 - - + -
79H PHE* 3.7 22.0 - + - -
83H THR* 3.6 27.6 - - + -
94H PHE* 3.3 35.7 - + + -
97H THR* 3.6 23.1 - - + +
98H ILE* 3.5 27.1 - - + +
101H LYS* 4.4 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H GLN* 2.6 31.0 + - - +
62H VAL* 3.2 13.0 + - - -
63H LEU 3.1 0.2 - - - -
64H PHE* 1.3 75.2 - - - +
66H ALA* 1.3 67.4 + - - +
67H ASP* 3.5 2.4 + - - +
97H THR* 5.6 1.1 - - - -
325H THR* 3.8 10.1 + - - +
----------------------------------------------------------
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