Contacts of the helix formed by residues 16 - 35 (chain A) in PDB entry 4BKR
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 HIS 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.5 36.1 + - + +
15A ALA* 1.3 72.7 - - - +
17A PRO* 1.3 66.4 - - + +
18A THR* 3.3 32.4 + - - -
19A GLY 3.2 6.6 + - - -
20A CYS* 2.8 32.6 + - - -
89A TYR* 4.2 0.2 - - - -
374A PHE 2.9 9.6 + - - +
375A GLY* 3.6 16.6 - - - +
376A PHE* 3.8 10.9 - + + -
381A VAL* 4.2 9.6 - - + -
382A ASP 4.8 4.8 + - - -
383A TYR* 3.6 28.4 + + - -
385A ALA 4.8 5.8 + - - -
387A VAL* 4.5 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.6 21.3 - - + -
15A ALA 3.6 4.0 - - - +
16A HIS* 1.3 86.8 - - - +
18A THR* 1.3 58.2 + - - +
20A CYS* 3.9 1.6 - - - +
21A GLU* 3.0 28.9 + - - +
89A TYR* 3.7 44.1 - - + +
387A VAL* 3.7 27.6 - - + -
388A ASN 4.3 7.9 - - - +
389A PRO* 4.8 0.2 - - + -
391A VAL* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 3.3 20.9 + - - -
17A PRO* 1.3 77.6 - - - +
19A GLY* 1.3 59.0 + - - +
21A GLU* 3.3 10.9 + - + +
22A ALA* 3.0 27.8 + - + +
381A VAL* 4.1 20.0 - - + -
382A ASP 5.7 0.9 - - - +
387A VAL* 3.9 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 3.2 8.6 + - - -
18A THR* 1.3 78.6 - - - +
20A CYS* 1.3 58.4 + - - +
22A ALA* 3.2 0.9 + - - +
23A ASN* 2.9 29.3 + - - +
375A GLY* 3.2 28.9 - - - -
378A ILE* 3.7 6.8 - - - +
381A VAL* 3.9 16.8 - - - +
383A TYR* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS 2.8 22.5 + - - +
17A PRO 3.9 0.2 - - - +
19A GLY* 1.3 75.7 - - - +
21A GLU* 1.3 63.9 + - - +
23A ASN* 3.2 5.7 + - - +
24A VAL* 2.9 29.0 + - - +
86A SER* 4.0 17.9 - - - -
89A TYR* 3.6 25.8 - - + -
90A ASN* 3.3 23.3 - - - +
93A ALA* 4.9 0.7 - - - -
373A LEU 4.4 1.8 - - - -
374A PHE 3.6 26.2 - - - -
375A GLY* 3.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO 3.0 15.4 + - - +
18A THR* 3.5 14.0 - - - +
19A GLY 3.2 0.4 - - - -
20A CYS* 1.3 76.3 - - - +
22A ALA* 1.3 57.2 + - - +
24A VAL* 3.3 2.1 + - - +
25A LYS* 2.9 26.2 + - - +
89A TYR 4.9 0.6 + - - +
93A ALA* 3.6 21.5 - - + +
96A LYS* 2.7 43.9 + - - +
97A PHE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.0 16.6 + - + +
19A GLY 3.2 1.3 + - - +
21A GLU* 1.3 79.5 - - - +
23A ASN* 1.3 56.4 + - - +
25A LYS* 3.7 10.4 - - + +
26A LYS* 2.9 27.7 + - - +
378A ILE* 3.6 26.5 - - + +
379A ASP 4.7 4.3 - - - +
381A VAL* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 2.9 17.1 + - - +
20A CYS* 3.5 9.4 - - - +
22A ALA* 1.3 75.1 - - - +
24A VAL* 1.3 63.3 + - + +
26A LYS* 3.3 15.6 + - - +
27A GLN* 3.2 46.1 + - - +
90A ASN* 5.2 6.3 + - - +
372A ASN* 3.4 32.0 + - - +
373A LEU* 4.6 8.5 + - - +
378A ILE* 4.0 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS 2.9 19.1 + - - +
21A GLU 3.7 4.0 - - - +
23A ASN* 1.3 75.9 - - + +
25A LYS* 1.3 63.7 + - - +
27A GLN* 3.2 9.5 + - - +
28A ILE* 3.0 39.9 + - + +
55A LEU* 4.2 14.1 - - + -
59A ILE* 4.1 11.9 - - + -
90A ASN* 3.6 39.3 - - + +
93A ALA* 4.0 8.5 - - + -
94A PHE* 4.2 12.8 - - + +
97A PHE* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 2.9 16.9 + - + +
22A ALA* 3.7 9.2 - - - +
23A ASN 3.2 0.2 - - - -
24A VAL* 1.3 78.1 - - - +
26A LYS* 1.3 57.0 + - - +
28A ILE* 3.2 7.4 + - + +
29A ASP* 2.8 69.0 + - - +
97A PHE* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.9 17.2 + - - +
23A ASN* 3.5 17.7 - - - +
24A VAL 3.3 0.2 - - - -
25A LYS* 1.3 76.7 - - - +
27A GLN* 1.3 58.9 + - + +
29A ASP* 3.4 8.0 + - - +
30A TYR* 2.9 27.1 + - + +
307A GLU* 6.0 2.0 - - - -
378A ILE* 6.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 3.2 39.7 + - - +
24A VAL* 3.2 6.9 + - - +
26A LYS* 1.3 75.0 - - + +
28A ILE* 1.3 66.1 + - - +
30A TYR* 3.3 5.0 + - - +
31A VAL* 3.2 26.0 + - - +
52A GLY 5.0 0.7 - - - +
55A LEU* 3.9 22.2 - - - +
56A ALA* 4.3 13.7 + - - +
59A ILE* 3.8 22.6 - - + +
305A CYS* 4.9 4.9 - - - +
306A ILE* 3.6 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.0 24.7 + - + +
25A LYS* 3.5 8.5 - - + +
27A GLN* 1.3 75.8 - - - +
29A ASP* 1.3 64.9 + - - +
31A VAL* 3.1 5.2 + - - +
32A THR* 2.9 32.8 + - + +
59A ILE* 3.8 16.6 - - + +
63A PHE* 3.6 48.2 - - + -
94A PHE* 5.3 1.6 - - + -
97A PHE* 3.6 44.6 - - + -
101A LYS* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 2.8 57.6 + - - +
26A LYS* 3.8 7.2 + - - +
28A ILE* 1.3 76.0 - - - +
30A TYR* 1.3 65.6 + - - +
32A THR* 3.5 10.2 + - - +
33A THR* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.9 14.8 + - + +
27A GLN 3.4 8.7 - - - +
28A ILE 3.2 0.2 - - - -
29A ASP* 1.3 76.5 - - - +
31A VAL* 1.3 61.2 + - + +
33A THR* 3.7 4.2 - - - -
34A GLU* 2.9 68.6 + - + +
303A GLU* 5.5 0.3 + - - -
306A ILE* 4.0 25.4 - - + -
307A GLU* 3.5 49.9 + - + +
310A TYR* 4.0 17.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 3.2 11.8 + - - +
28A ILE 3.1 8.9 + - - +
30A TYR* 1.3 80.8 - - + +
32A THR* 1.3 58.8 + - - +
34A GLU* 3.3 2.4 + - - +
35A GLY 2.9 28.6 + - - +
59A ILE* 4.1 8.5 - - + +
60A THR* 4.1 7.9 - - - +
63A PHE* 3.6 9.6 - - + +
64A GLY* 3.4 38.4 - - - +
306A ILE* 3.7 25.8 - - + -
310A TYR* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 2.9 24.4 + - + +
29A ASP* 3.5 16.5 + - - -
31A VAL* 1.3 75.4 - - - +
33A THR* 1.3 64.8 + - - +
35A GLY* 3.4 13.6 + - - +
36A PRO* 5.4 0.3 - - - +
63A PHE* 4.1 24.0 - - + +
101A LYS* 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 2.9 25.6 + - - +
30A TYR* 3.7 6.1 - - + +
32A THR* 1.3 76.4 + - - +
34A GLU* 1.3 73.0 + - - +
35A GLY* 4.3 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 2.9 62.2 + - + +
31A VAL 3.7 1.1 - - - +
33A THR* 1.3 83.4 - - - +
35A GLY* 1.3 59.2 + - - +
310A TYR* 3.4 32.0 + - + -
314A LYS* 5.6 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 2.9 10.9 + - - +
32A THR* 3.7 13.5 - - - -
33A THR 3.2 1.8 - - - -
34A GLU* 1.3 79.8 - - - +
36A PRO* 1.3 75.6 - - - +
37A ILE 3.8 0.2 + - - -
63A PHE 5.8 0.4 - - - -
64A GLY* 4.7 2.5 - - - -
310A TYR* 2.6 28.6 + - - -
----------------------------------------------------------
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