Contacts of the helix formed by residues 52 - 65 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E GLU* 2.9 14.6 + - - +
51E ASN* 1.3 73.3 - - - +
53E GLU* 1.3 78.0 + - + +
54E GLU* 3.2 19.5 - - + +
55E ASN* 3.3 26.5 + - - +
56E ARG* 3.2 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E THR* 1.3 79.3 - - + +
54E GLU* 1.3 58.9 + - - +
56E ARG* 3.1 30.6 + - - +
57E ARG* 2.9 23.4 + - - -
82E GLU* 3.6 11.8 - - - +
86E GLN* 3.5 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E THR* 3.1 14.3 - - + +
53E GLU* 1.3 77.4 - - - +
55E ASN* 1.3 62.1 + - - +
57E ARG* 2.9 35.9 + - - +
58E LEU* 2.7 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E LEU* 4.4 4.5 - - + +
49E VAL* 3.7 18.2 - - + +
50E GLU* 2.5 43.9 + - - +
52E THR* 3.3 21.7 + - - +
53E GLU 3.5 0.4 - - - -
54E GLU* 1.3 80.0 - - - +
56E ARG* 1.3 56.4 + - - +
58E LEU* 3.6 18.7 - - - +
59E TYR* 3.0 22.7 + - - +
314E TRP* 3.5 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E VAL* 3.2 34.9 - - - +
40E MET* 3.5 36.1 - - + -
44E LEU* 4.1 5.2 - - + -
51E ASN* 2.8 35.6 + - - +
52E THR 3.2 17.8 + - - +
53E GLU* 3.1 29.0 - - - +
54E GLU 3.0 0.8 - - - -
55E ASN* 1.3 74.9 - - - +
57E ARG* 1.3 67.2 + - - +
59E TYR* 3.1 6.9 + - - +
60E ARG* 2.8 39.6 + - - +
80E PHE* 6.2 0.4 - - - -
82E GLU* 2.8 41.2 + - - +
86E GLN* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLU 2.9 9.7 + - - +
54E GLU* 2.9 37.6 + - - +
56E ARG* 1.3 75.2 - - - +
58E LEU* 1.3 87.4 + - - +
60E ARG* 3.4 1.3 + - - -
61E GLN* 2.9 33.0 + - - +
86E GLN* 3.4 34.9 + - + +
87E LYS 3.0 31.2 + - - +
88E ASP* 3.6 9.9 + - - +
89E ASP* 2.9 30.9 + - - +
94E PHE* 3.4 14.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLU* 2.7 36.3 + - + +
55E ASN* 3.6 24.5 - - - +
57E ARG* 1.3 98.5 - - - +
59E TYR* 1.3 63.0 + - - +
61E GLN* 3.0 30.5 - - - +
62E VAL* 3.1 12.5 + - - +
89E ASP* 4.4 3.6 - - - +
314E TRP* 4.0 14.8 - - + +
316E GLY 5.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E MET* 4.6 20.6 - - + -
44E LEU* 4.9 3.6 - - + -
55E ASN 3.0 14.8 + - - +
56E ARG* 3.7 4.5 - - - +
58E LEU* 1.3 77.6 - - - +
60E ARG* 1.3 80.3 + - - +
62E VAL* 2.9 32.7 + - + +
63E LEU* 3.4 24.3 + - + +
307E GLN* 2.7 55.5 + - - +
310E ALA 4.9 2.2 - - - -
311E LEU* 3.3 44.0 + - + +
314E TRP* 3.6 24.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 3.1 24.3 + - - +
35E GLU* 2.6 63.2 + - - +
40E MET* 3.5 23.0 - - - +
56E ARG* 2.8 36.9 + - - +
57E ARG 3.8 3.6 - - - +
59E TYR* 1.3 81.9 - - - +
61E GLN* 1.3 57.2 + - - +
63E LEU* 3.1 9.8 + - - +
64E PHE* 2.9 49.8 + - + -
80E PHE* 4.2 4.9 - - - +
82E GLU* 5.1 0.4 + - - -
83E THR* 3.3 29.6 + - + +
86E GLN* 4.2 3.4 - - - +
94E PHE* 4.1 6.7 - - + -
307E GLN* 4.8 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ARG* 2.9 16.6 + - - +
58E LEU* 3.0 24.4 - - - +
59E TYR 3.0 0.2 - - - -
60E ARG* 1.3 75.5 - - - +
62E VAL* 1.3 55.1 + - - +
64E PHE* 4.4 0.9 - - - +
65E SER* 2.6 47.0 + - - +
88E ASP* 3.0 16.4 - - + +
89E ASP* 2.7 59.8 + - - +
90E ASN* 6.0 0.2 - - - +
94E PHE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LEU 3.1 15.0 + - - +
59E TYR* 2.9 21.5 + - + +
61E GLN* 1.3 74.1 - - - +
63E LEU* 1.3 66.1 + - + +
65E SER* 3.2 10.6 + - - -
310E ALA* 5.7 0.7 - - + -
314E TRP* 3.9 29.6 - - + +
321E ALA* 3.6 13.0 - - + +
324E ALA* 3.3 31.0 - - + -
325E THR* 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 4.2 19.7 - - + -
33E ALA* 4.4 11.2 - - + -
59E TYR* 3.9 34.1 - - + +
60E ARG* 3.1 10.3 + - - +
61E GLN 3.0 0.4 - - - -
62E VAL* 1.3 78.1 - - + +
64E PHE* 1.3 70.1 + - + +
65E SER 3.1 4.3 - - - -
66E ALA* 3.1 24.4 + - - +
307E GLN* 3.6 37.9 - - + +
310E ALA* 4.6 4.0 - - + -
328E PHE* 3.4 39.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 4.3 11.9 - - + -
33E ALA* 4.4 12.6 - - + -
60E ARG* 2.9 32.5 + - + +
61E GLN 4.2 1.3 - - - +
63E LEU* 1.3 76.4 - - + +
65E SER* 1.3 58.7 + - - +
66E ALA* 3.1 7.1 + - - +
77E VAL* 3.6 26.2 - - + -
79E PHE* 3.7 20.6 - + - -
83E THR* 3.6 28.0 - - + -
94E PHE* 3.3 36.6 - + + -
97E THR* 3.6 23.7 - - + +
98E ILE* 3.5 24.7 - - + +
101E LYS* 4.4 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLN* 2.6 30.5 + - - +
62E VAL* 3.2 13.0 + - - -
63E LEU 3.1 0.2 - - - -
64E PHE* 1.3 74.7 - - - +
66E ALA* 1.3 67.8 + - - +
67E ASP* 3.5 2.1 + - - +
97E THR* 5.6 0.9 - - - -
101E LYS* 5.4 0.2 - - - -
325E THR* 3.8 9.7 + - - +
----------------------------------------------------------
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