Contacts of the strand formed by residues 46 - 53 (chain E) in PDB entry 1AXC
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 SER 46 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 3.4 25.2 - - - +
40E MET* 3.5 9.4 - - - +
41E ASP* 2.7 42.6 + - - +
44E HIS 4.2 0.9 - - - -
45E VAL* 1.3 78.1 - - - +
47E LEU* 1.3 61.6 + - - +
211E TYR* 3.9 11.3 - - - -
215E PHE* 3.8 21.5 - - - -
250E TYR 3.1 13.5 - - - -
251E LEU* 4.5 1.6 - - - -
147F MET* 3.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLN* 3.9 21.5 - - + +
39E SER 3.4 13.0 - - - +
40E MET* 3.6 23.3 - - + -
41E ASP 5.2 0.2 - - - +
46E SER* 1.3 76.6 - - - +
48E VAL* 1.3 75.9 + - - +
49E GLN* 4.7 1.1 - - + -
126E LEU* 3.7 31.2 - - + -
128E ILE* 3.7 15.7 - - + -
249E TYR* 3.3 3.8 - - - +
250E TYR* 2.7 59.3 + - + +
147F MET* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 3.4 17.7 - - + -
22E LEU* 3.6 32.8 - - + -
23E ILE* 4.4 19.7 - - + -
37E LEU* 4.2 7.4 - - + -
38E GLN* 3.2 8.3 - - - +
39E SER 2.9 35.1 + - - +
47E LEU* 1.3 77.6 - - - +
49E GLN* 1.3 65.6 + - - +
247E LEU* 3.4 28.9 - - + -
248E LYS 3.2 6.3 - - - +
249E TYR* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ASN* 4.4 5.1 + - - +
37E LEU 3.1 9.8 + - - +
38E GLN* 4.2 19.7 - - + +
47E LEU* 4.7 0.7 - - + -
48E VAL* 1.3 76.4 - - - +
50E LEU* 1.3 76.7 + - - +
51E THR* 2.8 24.1 + - - -
128E ILE* 6.3 0.7 - - + -
246E HIS* 2.9 27.5 + - - -
247E LEU* 3.6 3.4 - - - -
248E LYS* 2.8 46.8 + - + +
250E TYR* 4.4 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.5 31.2 - - + -
19E LEU* 4.2 6.3 - - + -
28E TRP* 3.9 28.3 - - + -
35E VAL* 5.0 3.1 - - + +
36E ASN* 3.2 3.3 - - - -
37E LEU* 2.7 49.7 + - + +
49E GLN* 1.3 81.2 + - - +
51E THR* 1.3 68.6 + - - +
52E LEU* 4.1 17.5 - - + +
241E ILE* 3.6 21.8 - - + -
246E HIS 3.6 12.3 - - - +
247E LEU* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E VAL 3.6 3.6 - - - -
36E ASN* 2.9 17.1 + - - +
49E GLN* 2.8 26.7 + - - -
50E LEU* 1.3 71.4 - - - +
52E LEU* 1.3 64.8 + - - +
53E ARG* 4.3 22.9 - - + +
245E GLY* 3.1 7.1 + - - -
246E HIS* 2.9 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 6.1 1.1 - - + -
11E ILE* 4.6 4.3 - - + -
12E LEU* 4.3 24.5 - - + -
15E VAL* 4.5 6.5 - - + -
28E TRP* 4.9 1.6 - - + -
34E GLY* 3.3 1.4 - - - -
35E VAL* 2.9 47.5 + - + +
50E LEU* 4.1 20.9 - - + -
51E THR* 1.3 74.5 - - - +
53E ARG* 1.3 63.8 + - - +
57E PHE* 3.8 15.8 - - + -
241E ILE* 3.7 31.4 - - + -
244E MET* 3.4 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E SER 3.5 7.6 - - - +
51E THR* 3.9 17.0 - - + +
52E LEU* 1.3 73.9 - - - +
54E SER* 1.3 60.6 + - - +
55E GLU* 3.3 23.9 + - + +
56E GLY* 2.8 23.3 + - - +
57E PHE* 3.4 8.9 - - - -
240E LYS* 5.9 2.4 - - - +
243E ASP* 3.9 19.2 + - - +
244E MET* 2.8 29.2 + - - +
245E GLY* 3.2 27.9 + - - +
246E HIS* 5.6 2.4 + - - -
----------------------------------------------------------
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