Contacts of the helix formed by residues 23 - 44 (chain U) in PDB entry 4B2Q
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 GLN 23 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121T ARG* 5.8 1.9 + - - -
124T LEU* 6.2 0.2 - - - +
19U ILE* 3.4 15.5 - - + +
20U PRO* 3.4 23.9 - - + +
21U ARG 2.8 0.6 - - - -
22U ASN* 1.3 102.8 + - - +
24U LYS* 1.3 68.5 + - - +
25U ALA* 3.1 4.4 + - - +
26U VAL* 3.2 22.1 + - + +
27U ALA 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLU* 4.5 14.6 + - - -
19U ILE* 4.0 10.8 - - + +
20U PRO 3.2 5.2 + - - +
21U ARG* 3.0 20.7 + - + +
23U GLN* 1.3 76.6 - - - +
25U ALA* 1.3 52.9 + - - +
27U ALA* 3.1 4.0 + - + +
28U ASN* 2.8 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U ARG 4.6 0.6 + - - -
22U ASN 5.3 1.8 - - - +
23U GLN* 4.8 2.7 - - - +
24U LYS* 1.3 81.4 - - - +
26U VAL* 1.3 71.4 + - + +
28U ASN* 3.0 16.9 + - - +
29U SER* 3.1 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124T LEU* 5.9 2.0 - - + -
23U GLN* 3.2 22.2 + - + +
25U ALA* 1.3 78.6 - - + +
27U ALA* 1.3 66.2 + - - +
29U SER* 2.8 19.7 + - - -
30U LEU* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124T LEU* 5.9 0.2 - - - -
15U PHE* 3.7 23.1 - - + -
19U ILE* 3.6 40.8 - - + -
23U GLN 3.1 3.4 + - - -
24U LYS* 3.5 8.5 - - + +
26U VAL* 1.3 78.9 - - - +
28U ASN* 1.3 65.3 + - - +
30U LEU* 3.1 9.0 + - - +
31U LYS* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U LYS* 2.8 57.7 + - - +
25U ALA* 3.3 10.2 - - - +
27U ALA* 1.3 71.5 - - - +
29U SER* 1.3 64.3 + - - +
31U LYS* 2.8 20.8 + - - +
32U SER* 3.0 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U ALA 3.1 5.8 + - - -
26U VAL* 2.8 14.8 + - - -
28U ASN* 1.3 75.3 - - - +
30U LEU* 1.3 58.5 + - - +
32U SER* 3.1 10.1 + - - -
33U TRP* 3.0 30.9 + - - +
70V GLU 4.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124T LEU* 3.8 28.7 - - + -
127T VAL* 3.9 20.2 - - + +
128T GLN* 4.3 26.9 - - + +
131T ASN* 3.3 25.2 + - - +
15U PHE* 4.3 5.4 - - + -
26U VAL* 2.9 30.5 + - + +
27U ALA* 3.2 14.8 - - - +
29U SER* 1.3 78.8 - - - +
31U LYS* 1.3 61.1 + - - +
33U TRP* 4.7 1.8 - - + -
34U ASN* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER 5.2 0.4 - - - -
469A SER* 5.3 2.0 - - - +
472A SER* 2.5 47.3 + - - -
473A TYR* 5.9 0.2 - - - +
12U TRP* 3.2 58.3 + - + +
15U PHE* 3.9 16.5 - - + -
16U GLY* 5.2 2.8 - - - +
27U ALA 2.9 7.5 + - - +
28U ASN* 2.8 13.6 + - - +
30U LEU* 1.3 74.3 - - - +
32U SER* 1.3 61.0 + - - +
34U ASN* 3.2 5.9 + - - +
35U GLU* 3.0 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28U ASN 3.2 9.2 + - - -
29U SER* 3.1 19.8 + - - -
31U LYS* 1.3 75.0 - - - +
33U TRP* 1.3 54.6 + - - +
35U GLU* 3.1 13.7 + - - +
36U THR* 2.6 41.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 33 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131T ASN* 3.8 19.0 - - + +
135T ALA* 4.9 3.2 - - + +
29U SER 3.0 19.0 + - - +
30U LEU* 3.9 5.8 - - + +
32U SER* 1.3 75.5 - - - +
34U ASN* 1.3 54.9 + - - +
36U THR* 3.2 25.3 - - + -
37U LEU* 2.6 75.6 + - + +
68V LYS 3.4 24.0 - - - -
69V PHE* 4.3 14.6 - + + +
70V GLU* 3.2 67.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127T VAL* 4.8 5.0 + - + +
130T ASN* 4.6 15.8 - - - +
131T ASN* 3.2 24.0 + - - +
134T MET* 3.5 13.4 - - - +
10U ILE* 5.3 1.0 - - - +
12U TRP* 3.8 32.2 - - + -
30U LEU 3.2 9.1 + - - +
31U LYS 3.2 11.7 + - - +
33U TRP* 1.3 79.1 - - - +
35U GLU* 1.3 56.4 + - - +
37U LEU* 3.4 1.4 - - - +
38U THR* 2.6 48.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER 5.4 0.8 - - - +
472A SER* 3.6 16.8 - - - -
475A LYS* 4.2 23.8 + - - +
12U TRP* 5.8 2.6 - - + -
31U LYS* 3.0 41.5 + - - +
32U SER* 3.1 14.4 + - - +
34U ASN* 1.3 77.1 - - - +
36U THR* 1.3 61.6 + - - +
38U THR* 3.1 7.0 + - - -
39U SER* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32U SER* 2.6 21.2 + - - -
33U TRP* 3.2 35.4 - - + +
35U GLU* 1.3 70.5 - - - +
37U LEU* 1.3 69.8 + - + +
39U SER* 2.9 10.1 + - - -
40U ARG* 2.8 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131T ASN* 3.6 34.8 - - - +
134T MET* 3.5 15.3 - - + -
135T ALA* 4.1 24.9 - - + +
138T VAL* 4.4 13.7 - - + -
33U TRP* 2.6 64.5 + - + +
34U ASN 3.4 4.0 - - - +
36U THR* 1.3 76.3 - - + +
38U THR* 1.3 63.2 + - - +
40U ARG* 3.1 8.8 - - + +
41U LEU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A LYS* 5.7 7.4 - - - +
134T MET* 3.5 13.5 - - + +
34U ASN* 2.6 38.7 + - - -
35U GLU* 3.4 10.0 - - - -
37U LEU* 1.3 70.1 - - - +
39U SER* 1.3 68.4 + - - +
40U ARG 3.1 0.7 + - - -
41U LEU* 3.1 17.8 + - + +
42U ALA* 3.2 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35U GLU* 2.8 31.2 + - - +
36U THR* 3.4 7.2 + - - -
38U THR* 1.3 71.5 - - - +
40U ARG* 1.3 68.5 + - - +
42U ALA* 3.0 21.9 + - - +
43U THR* 3.3 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLN 5.4 4.7 + - - -
225A HIS 5.2 2.4 - - - -
226A ASP* 4.2 15.6 - - - +
138T VAL* 3.8 23.5 - - + +
142T GLU* 3.5 20.4 + - - +
36U THR* 2.8 16.2 + - + +
37U LEU* 3.1 15.7 - - + +
38U THR 3.0 0.2 - - - -
39U SER* 1.3 78.6 - - - +
41U LEU* 1.3 58.2 + - - +
43U THR* 2.8 39.3 + - - -
44U LEU* 2.9 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134T MET* 2.6 45.8 - - + -
137T GLU* 3.8 23.6 - - + -
138T VAL* 3.9 14.6 - - + +
141T ARG* 3.0 54.8 + - - +
5U LEU* 4.9 7.6 - - + -
37U LEU 3.1 18.2 + - - +
38U THR* 3.1 6.7 + - + +
40U ARG* 1.3 75.4 - - - +
42U ALA* 1.3 61.9 + - - +
43U THR 3.3 0.3 + - - -
44U LEU* 3.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS 5.0 2.5 - - - +
193A ASN* 4.5 12.0 + - - +
38U THR* 3.2 11.0 + - + +
39U SER* 3.0 17.3 + - - +
41U LEU* 1.3 77.9 - - - +
43U THR* 1.3 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 3.6 45.2 - - + +
193A ASN* 4.1 16.5 - - - +
225A HIS 4.8 0.7 + - - -
226A ASP* 3.2 20.2 + - - +
39U SER* 3.3 17.7 - - - +
40U ARG* 2.8 26.1 + - - -
42U ALA* 1.3 85.4 - - + +
44U LEU* 1.3 61.8 + - - +
45U PRO* 2.9 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 5.1 8.3 - - - +
138T VAL* 4.1 16.6 - - + +
141T ARG* 2.6 47.6 + - + +
142T GLU* 3.7 22.9 - - + +
145T HIS* 3.7 27.6 - - + +
40U ARG* 2.9 60.6 + - + +
41U LEU* 3.5 3.0 + - - +
43U THR* 1.3 76.4 + - - +
45U PRO* 1.3 66.4 - - + +
----------------------------------------------------------
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