Contacts of the helix formed by residues 30 - 46 (chain D) in PDB entry 1EJI
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 ASP 30 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ARG* 2.5 41.6 + - - -
314C VAL* 4.0 12.5 - - + -
317C LYS* 3.5 17.7 + - + +
26D LEU* 3.0 34.0 + - + +
29D SER* 1.3 80.2 - - - +
31D ALA* 1.3 56.7 + - - +
32D GLU* 3.2 6.8 + - - +
33D VAL* 3.1 25.8 + - - +
34D TYR* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LYS* 4.4 4.0 - - - +
27D LYS 4.1 12.8 - - - +
28D ASP 4.0 7.5 + - - +
30D ASP* 1.3 71.5 + - - +
32D GLU* 1.3 59.6 + - - +
34D TYR* 3.5 8.9 - - + +
35D SER* 2.8 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.7 26.1 - - + +
98C LYS* 5.0 5.8 + - - -
99C ARG* 3.1 19.1 + - - +
317C LYS* 5.5 0.9 - - - +
30D ASP* 3.2 9.1 + - - +
31D ALA* 1.3 74.8 - - - +
33D VAL* 1.3 66.7 + - - +
35D SER* 3.2 7.6 + - - -
36D ILE* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 5.1 0.7 - - + -
92C LEU* 4.6 7.9 - - + -
95C LEU* 3.9 15.5 - - + -
99C ARG* 3.9 11.7 - - - +
310C ALA* 4.7 11.7 - - + +
313C ALA* 4.2 13.5 - - + -
314C VAL* 4.0 18.4 - - + -
26D LEU* 4.2 8.3 - - + -
30D ASP* 3.1 29.2 + - + +
32D GLU* 1.3 78.1 - - - +
34D TYR* 1.3 64.0 + - - +
36D ILE* 3.3 9.2 + - - +
37D ILE* 3.0 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 4.0 16.2 - - + +
27D LYS* 3.2 62.2 + - + -
30D ASP 3.0 19.3 + - - +
31D ALA* 3.5 9.2 - - + +
32D GLU 3.2 0.2 - - - -
33D VAL* 1.3 77.5 - - - +
35D SER* 1.3 64.2 + - - +
37D ILE* 3.4 5.3 + - - +
38D LYS* 2.7 62.1 + - + +
484D PHE* 3.4 35.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ALA 2.8 18.6 + - - -
32D GLU* 3.2 8.0 + - - -
34D TYR* 1.3 78.9 - - - +
36D ILE* 1.3 64.1 + - - +
38D LYS* 3.1 8.1 + - - +
39D LYS* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 6.0 3.4 - - + -
88C PHE* 3.7 31.6 - - + +
91C GLU* 3.8 28.5 - - + +
92C LEU* 4.1 28.5 - - + +
95C LEU* 4.1 24.9 - - + -
32D GLU* 3.1 19.5 + - + +
33D VAL* 3.3 8.5 + - - +
35D SER* 1.3 75.5 - - - +
37D ILE* 1.3 63.6 + - + +
39D LYS* 3.1 13.0 + - - +
40D GLU* 2.9 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 4.3 8.5 - - + -
67C SER* 3.8 28.7 - - - +
68C SER* 3.9 3.8 + - - +
69C LEU* 3.8 23.3 - - + -
92C LEU* 6.1 1.1 - - + -
26D LEU* 4.0 26.9 - - + -
33D VAL* 3.0 28.8 + - + +
34D TYR* 3.7 5.4 - - - +
36D ILE* 1.3 77.0 - - + +
38D LYS* 1.3 58.3 + - + +
40D GLU* 3.4 7.0 + - - +
41D SER 2.9 18.5 + - - -
484D PHE* 2.7 59.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 2.7 55.4 + - + +
35D SER* 3.1 9.6 + - - +
37D ILE* 1.3 77.5 - - + +
39D LYS* 1.3 60.8 + - + +
41D SER* 3.2 2.3 + - - -
42D ASN* 2.9 30.8 + - - +
483D ASP* 2.7 55.5 + - - +
484D PHE* 3.9 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PHE* 3.4 37.6 - - + -
91C GLU* 3.3 29.8 + - - +
35D SER* 2.9 33.0 + - - +
36D ILE* 3.1 22.4 + - - +
38D LYS* 1.3 76.4 - - - +
40D GLU* 1.3 57.9 + - - +
42D ASN* 3.4 9.1 + - - +
43D ARG 3.1 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER* 4.2 2.9 - - - +
69C LEU* 4.2 24.2 - - + -
72C LYS* 4.6 4.6 - - + +
85C GLY 4.1 4.1 - - - +
88C PHE* 3.3 30.3 - - + +
89C ILE* 4.5 12.2 + - + -
36D ILE* 2.9 16.0 + - + +
37D ILE* 3.6 7.0 - - - +
39D LYS* 1.3 75.5 - - - +
41D SER* 1.3 64.9 + - - +
42D ASN 3.1 1.6 - - - -
43D ARG* 3.0 42.0 + - - -
44D GLN* 3.2 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER* 3.8 10.1 - - - -
37D ILE 2.9 8.5 + - - -
38D LYS* 3.2 7.4 + - - -
40D GLU* 1.3 77.1 - - - +
42D ASN* 1.3 64.5 + - - +
44D GLN* 3.4 9.1 + - - +
45D ARG* 3.3 13.0 + - - +
478D LEU* 3.8 13.6 - - - +
483D ASP* 4.4 9.8 + - - -
484D PHE* 3.0 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS 2.9 17.5 + - - +
39D LYS* 3.4 9.2 + - - +
41D SER* 1.3 74.4 - - - +
43D ARG* 1.3 59.2 + - - +
45D ARG* 2.7 58.3 + - - +
46D VAL* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LYS* 3.6 24.0 - - - +
84C GLY 5.0 0.2 + - - -
85C GLY* 3.1 36.8 + - - -
87C GLU* 5.7 2.0 - - - +
88C PHE* 3.9 18.8 - - + -
39D LYS 3.1 11.5 + - - +
40D GLU* 3.0 39.1 + - - +
42D ASN* 1.3 81.2 - - - +
44D GLN* 1.3 71.8 + - - +
45D ARG 3.2 0.7 + - - -
46D VAL* 3.5 24.4 + - - +
47D GLY* 3.7 4.9 + - - -
49D GLU* 3.0 27.9 + - - -
54D GLU* 4.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER* 3.4 37.2 + - - +
71C ASN* 3.9 15.2 - - - +
72C LYS* 5.5 2.7 - - - +
40D GLU* 3.2 38.4 + - - +
41D SER* 3.6 7.2 - - - +
42D ASN 3.2 0.6 - - - -
43D ARG* 1.3 89.7 - - - +
45D ARG* 1.3 57.4 + - - +
47D GLY 3.8 6.3 - - - +
49D GLU* 5.0 7.5 - - - +
54D GLU* 6.2 0.4 - - - +
56D PHE* 3.3 41.2 - - + -
411D ARG* 2.9 20.8 + - - -
478D LEU* 4.1 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D SER 3.3 4.7 + - - +
42D ASN* 2.7 44.6 + - - +
44D GLN* 1.3 73.7 - - - +
46D VAL* 1.3 87.0 + - - +
47D GLY 3.2 1.9 + - - -
411D ARG* 2.8 36.1 + - - +
473D ALA* 3.9 5.5 - - - +
474D SER* 3.5 27.3 + - - +
476D PHE 5.0 3.8 - - - +
478D LEU* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ASN* 3.1 27.1 + - - +
43D ARG* 3.6 9.2 - - - +
45D ARG* 1.3 107.6 - - - +
47D GLY* 1.3 56.1 + - - +
381D SER* 4.0 3.6 + - - -
470D GLU* 3.2 42.4 - - + +
473D ALA* 3.8 10.8 - - - -
474D SER* 3.6 13.7 - - - -
----------------------------------------------------------
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