Contacts of the helix formed by residues 32 - 45 (chain E) in PDB entry 5XS0
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 32 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C CYS* 4.0 3.1 - - - -
203D ALA 4.6 0.2 + - - -
207D SER* 3.2 36.0 + - - +
30E GLN 3.3 6.0 + - - +
31E TYR* 1.3 73.6 - - - +
33E ALA* 1.3 57.8 + - - +
34E GLU* 3.9 16.5 + - - +
35E GLU* 3.1 18.4 + - - +
36E TYR* 2.7 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TYR* 3.5 31.8 - - + +
208C CYS* 3.5 36.6 - - + +
32E THR* 1.3 73.8 - - - +
34E GLU* 1.3 66.5 + - + +
36E TYR* 3.9 0.7 - - - +
37E GLN* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TYR* 5.1 7.2 - - - +
203D ALA* 3.6 21.5 - - + +
206D ASN* 5.4 8.8 - - - +
207D SER* 5.7 0.5 - - - -
32E THR* 3.9 15.2 + - - +
33E ALA* 1.3 88.9 + - + +
35E GLU* 1.3 56.7 + - - +
37E GLN* 3.4 4.6 + - - +
38E ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D VAL* 5.0 2.5 - - + +
203D ALA* 3.6 17.2 - - + +
204D ARG* 3.3 33.8 + - + +
207D SER* 3.2 19.1 + - - -
31E TYR* 3.5 26.4 - - + -
32E THR* 3.1 17.7 + - - +
34E GLU* 1.3 76.2 - - - +
36E TYR* 1.3 66.6 + - - +
38E ALA* 3.4 1.6 + - - +
39E ILE* 2.9 35.0 + - + +
79E PHE* 4.9 0.5 - - - +
116E LYS* 2.9 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 3.2 27.0 + - - -
204C ARG* 2.8 53.7 + - + -
205C TYR* 4.3 12.3 - - - -
208C CYS* 4.0 25.1 - - - -
80D GLY* 4.5 2.5 - - - -
81D TYR* 3.3 36.1 + + - -
82D ASN* 3.9 15.7 - - - -
31E TYR* 4.1 11.3 - - + +
32E THR 2.7 22.2 + - - +
33E ALA 3.9 4.3 - - - +
35E GLU* 1.3 73.7 - - - +
37E GLN* 1.3 65.1 + - + +
40E GLN* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 4.5 14.6 + - - +
205C TYR* 3.7 47.2 + - + +
33E ALA 2.9 18.3 + - - +
34E GLU* 4.0 3.3 - - - +
36E TYR* 1.3 84.0 - - + +
38E ALA* 1.3 63.6 + - - +
40E GLN* 3.4 3.5 + - + +
41E LYS* 2.9 61.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D SER* 3.9 18.4 - - - +
200D VAL* 3.4 32.8 - - + +
203D ALA* 4.5 1.3 - - + -
34E GLU 2.9 19.0 + - - +
35E GLU* 3.7 5.6 - - - +
37E GLN* 1.3 78.4 - - - +
39E ILE* 1.3 57.5 + - - +
41E LYS* 3.3 8.1 + - - +
42E ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D TYR* 3.4 30.1 - - + +
200D VAL* 3.5 21.1 - - + -
31E TYR* 3.5 36.8 - - + +
35E GLU* 2.9 29.3 + - + +
38E ALA* 1.3 72.4 - - - +
40E GLN* 1.3 60.7 + - - +
42E ALA* 3.2 0.5 + - - -
43E LEU* 2.9 39.6 + - + +
78E MET* 3.5 34.3 - - + +
79E PHE* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 3.6 20.5 + - - +
204C ARG* 3.4 18.2 - - - +
76D ASN* 3.4 24.0 + - - +
77D GLU* 3.9 17.3 + - - +
80D GLY* 4.3 2.2 - - - -
81D TYR* 3.5 26.1 + - + +
36E TYR* 2.9 34.5 + - + +
37E GLN* 3.8 5.2 - - + +
39E ILE* 1.3 79.5 - - - +
41E LYS* 1.3 61.9 + - - +
43E LEU* 3.7 9.6 + - - +
44E ARG* 3.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D SER* 6.0 2.0 - - - +
37E GLN* 2.9 56.1 + - + +
38E ALA* 3.6 6.7 - - - +
40E GLN* 1.3 76.6 - - + +
42E ALA* 1.3 64.2 + - - +
44E ARG* 3.2 37.8 + - - +
45E GLN* 4.1 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D GLU* 3.6 23.6 - - - +
200D VAL* 3.8 7.2 - - + -
38E ALA 2.9 17.4 + - - +
41E LYS* 1.3 77.1 - - - +
43E LEU* 1.3 62.6 + - - +
45E GLN* 3.0 35.2 + - - +
78E MET* 3.7 22.2 - - + -
161E ALA* 3.5 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D TYR* 3.5 26.5 - - + -
39E ILE* 2.9 32.9 + - + +
40E GLN* 4.1 7.0 - - - +
41E LYS 3.2 0.4 - - - -
42E ALA* 1.3 75.9 - - - +
44E ARG* 1.3 57.0 + - - +
78E MET* 3.7 17.9 - - + -
79E PHE* 4.6 3.1 - - + -
158E PHE* 3.3 34.3 - - + +
159E GLY* 4.0 1.5 - - - -
160E ASN 3.1 10.6 + - - -
161E ALA* 2.9 39.0 + - + -
162E LEU* 4.1 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 3.5 23.7 - - - +
201C GLU* 4.6 9.9 + - - +
77D GLU* 2.7 50.4 + - - +
40E GLN* 3.8 37.9 + - - +
41E LYS* 3.2 31.2 + - - +
42E ALA 3.2 1.2 - - - -
43E LEU* 1.3 76.0 - - - +
45E GLN* 1.3 65.7 + - - +
46E ARG* 3.3 6.4 + - - +
160E ASN* 3.4 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D LYS 4.8 10.0 - - - +
191D ALA 5.0 0.2 - - - -
192D LYS* 3.6 36.6 + - + +
197D GLU* 2.6 36.1 + - - +
41E LYS 4.3 3.1 - - - +
42E ALA* 3.0 30.8 + - - +
44E ARG* 1.3 77.4 - - - +
46E ARG* 1.3 60.8 + - - +
78E MET* 5.6 0.2 - - - -
160E ASN* 3.5 0.7 - - - -
161E ALA* 3.1 31.2 + - + -
----------------------------------------------------------
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