Contacts of the helix formed by residues 21 - 40 (chain A) in PDB entry 5IJO
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 GLU 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 1.3 81.4 + - - +
22A ALA* 1.3 66.1 + - - +
23A LEU* 4.3 7.9 - - + +
24A GLU* 3.5 14.8 + - + +
25A ASN* 3.0 21.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
20A GLN 3.3 5.0 + - - +
21A GLU* 1.3 69.6 - - - +
23A LEU* 1.3 55.6 + - - +
25A ASN* 3.0 5.3 + - - +
26A ALA* 2.7 33.4 + - - +
776A ILE 5.2 1.1 - - - +
779A GLN* 4.9 2.9 - - + -
780A ALA* 3.2 38.6 - - + +
783A GLN* 5.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.3 5.2 - - + +
22A ALA* 1.3 79.8 - - - +
24A GLU* 1.3 63.4 + - - +
26A ALA* 3.3 6.4 + - - +
27A GLY* 3.1 18.4 + - - -
780A ALA 5.2 2.0 - - - -
783A GLN* 5.8 4.7 - - + +
784A LEU* 5.5 6.3 - - - +
827A VAL 5.9 0.7 - - - +
828A ILE* 5.0 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN 5.9 1.3 - - - +
21A GLU* 3.5 17.7 + - + +
22A ALA 3.3 0.2 - - - -
23A LEU* 1.3 78.1 - - - +
25A ASN* 1.3 63.2 + - - +
27A GLY* 3.1 2.7 + - - -
28A ARG* 2.9 22.7 + - - +
828A ILE* 5.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN 5.2 6.3 - - - +
21A GLU 3.0 15.4 + - - +
22A ALA* 3.0 14.8 + - - +
24A GLU* 1.3 76.9 - - - +
26A ALA* 1.3 62.4 + - - +
28A ARG* 3.0 9.3 + - - +
29A LEU* 3.0 21.4 + - - +
780A ALA* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.7 18.5 + - - +
23A LEU 3.8 3.4 - - - +
25A ASN* 1.3 72.2 - - - +
27A GLY* 1.3 63.7 + - - +
29A LEU* 3.1 8.1 + - - +
30A ILE* 3.0 22.5 + - - +
780A ALA* 3.7 17.5 - - - +
781A ILE* 4.2 6.1 - - + -
784A LEU* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.1 13.6 + - - -
24A GLU 3.1 4.0 + - - -
26A ALA* 1.3 76.4 - - - +
28A ARG* 1.3 62.0 + - - +
30A ILE* 3.2 6.1 + - - +
31A ASP* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 2.9 13.5 + - - +
25A ASN* 3.0 10.7 + - - +
27A GLY* 1.3 76.0 - - - +
29A LEU* 1.3 62.7 + - - +
31A ASP* 3.2 5.9 + - - +
32A ARG* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN 3.0 11.2 + - - +
26A ALA* 3.1 11.0 + - - +
28A ARG* 1.3 77.5 - - - +
30A ILE* 1.3 64.0 + - - +
32A ARG* 3.2 6.8 + - - +
33A GLN* 3.0 22.6 + - - +
667A CYS* 5.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.0 12.4 + - - +
27A GLY* 3.2 6.9 + - - +
29A LEU* 1.3 76.5 - - - +
31A ASP* 1.3 58.9 + - - +
33A GLN* 3.1 8.9 + - - +
34A LEU* 2.8 29.7 + - - +
667A CYS* 5.1 8.3 - - + +
670A PHE* 6.1 1.8 - - + -
671A SER* 4.1 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.0 16.1 + - - +
28A ARG* 3.7 6.3 - - - +
30A ILE* 1.3 76.0 - - - +
32A ARG* 1.3 63.8 + - - +
34A LEU* 3.1 7.7 + - - +
35A GLN* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 2.9 16.7 + - - +
29A LEU* 3.6 6.7 - - - +
30A ILE 3.2 0.2 - - - -
31A ASP* 1.3 75.8 - - - +
33A GLN* 1.3 62.6 + - - +
35A GLN* 3.1 10.4 + - - +
36A GLU* 3.0 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 3.0 13.8 + - - +
30A ILE* 3.5 10.3 - - - +
32A ARG* 1.3 73.5 - - - +
34A LEU* 1.3 66.3 + - - +
36A GLU* 3.0 9.8 + - - +
37A ASP* 2.9 22.7 + - - +
667A CYS* 5.6 4.3 - - + +
668A ILE* 5.3 11.7 - - + +
671A SER* 4.8 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE 2.8 14.0 + - - +
31A ASP* 3.1 12.5 + - - +
33A GLN* 1.3 75.0 - - - +
35A GLN* 1.3 64.2 + - - +
37A ASP* 3.0 18.0 + - - +
38A ARG* 3.0 14.3 + - - +
671A SER* 5.0 10.0 - - - +
675A GLY* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP 2.9 12.0 + - - +
32A ARG* 3.3 12.3 - - - +
34A LEU* 1.3 76.5 - - - +
36A GLU* 1.3 63.1 + - - +
38A ARG* 3.1 8.8 + - - +
39A MET* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG 3.0 10.6 + - - +
33A GLN* 3.0 13.0 + - - +
35A GLN* 1.3 77.6 - - - +
37A ASP* 1.3 63.1 + - - +
39A MET* 3.2 14.9 + - - +
40A TYR* 3.5 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 2.9 11.5 + - - +
34A LEU* 3.0 12.1 + - - +
36A GLU* 1.3 80.6 - - - +
38A ARG* 1.3 58.1 + - - +
40A TYR* 3.4 12.3 - - - +
484A THR* 3.0 17.5 - - - -
487A PRO* 4.3 5.2 - - + +
490A VAL* 4.2 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 3.0 11.2 + - - +
35A GLN* 3.1 10.5 + - - +
37A ASP* 1.3 77.9 - - - +
39A MET* 1.3 56.0 + - - +
483A ILE* 3.1 11.2 - - - +
484A THR* 2.7 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN 3.0 15.8 + - - +
36A GLU* 3.2 7.5 + - - +
38A ARG* 1.3 75.4 - - - +
40A TYR* 1.4 68.0 + - - +
41A PRO* 4.2 1.4 - - - +
483A ILE* 4.1 9.7 - - - +
484A THR 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU 3.5 7.3 + - - +
37A ASP 3.4 17.7 - - - +
38A ARG 3.4 0.4 - - - -
39A MET* 1.4 82.9 - - - +
41A PRO* 1.3 67.9 - - - +
442A GLN* 5.9 8.5 - - + +
483A ILE* 3.7 3.6 - - - -
484A THR* 3.0 26.1 + - - -
487A PRO* 4.4 13.5 - - + -
----------------------------------------------------------
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