Contacts of the helix formed by residues 34 - 48 (chain D) in PDB entry 5M64
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 34 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D SER* 4.2 4.5 + - - +
33D THR* 1.3 77.6 - - - +
35D GLU* 1.3 61.3 + - - +
36D VAL 3.3 0.2 - - - -
37D LEU* 3.4 35.4 + - - +
38D GLN* 4.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 5.6 2.5 - - + -
32D SER* 4.0 20.5 + - - +
33D THR 3.1 1.6 - - - -
34D ASP* 1.3 74.6 - - - +
36D VAL* 1.3 63.5 + - - +
37D LEU 3.1 2.2 - - - -
38D GLN* 3.0 35.0 + - - +
39D PHE* 3.1 50.7 + - + -
40G ARG* 4.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D SER 5.9 0.2 - - - +
33D THR* 3.2 18.5 + - + +
35D GLU* 1.3 78.3 - - - +
37D LEU* 1.3 71.2 + - + +
39D PHE* 3.8 4.5 - - + -
40D LEU* 3.0 53.9 + - + +
92D ILE 6.1 0.2 - - - +
93D GLN* 3.5 2.7 - - - +
96D PHE* 4.3 22.2 - - + -
38G ILE* 5.5 8.7 - - + -
40G ARG* 3.7 23.2 - - - +
82G LEU 6.1 0.7 - - - +
123G TYR* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D THR 4.0 0.4 - - - +
34D ASP* 3.4 40.2 - - - +
35D GLU 3.1 0.4 - - - -
36D VAL* 1.3 85.5 - - + +
38D GLN* 1.3 61.4 + - - +
41D GLU* 3.1 27.6 + - - +
93D GLN* 3.7 27.8 + - - +
96D PHE* 3.7 49.6 - - + +
97D LYS* 4.4 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ASP 4.1 1.7 + - - +
35D GLU* 3.0 37.7 + - - +
37D LEU* 1.3 78.4 - - - +
39D PHE* 1.3 71.0 + - + +
41D GLU* 3.5 13.2 - - - +
42D SER* 3.5 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 3.1 41.5 + - + +
36D VAL* 4.1 4.7 - - + +
37D LEU 3.3 0.2 - - - -
38D GLN* 1.3 85.5 - - + +
40D LEU* 1.3 61.8 + - + +
42D SER* 3.4 4.5 + - - -
43D PHE* 2.9 28.8 + - - +
40G ARG* 3.3 48.2 - - - +
85G GLU* 5.7 6.3 - - + -
123G TYR* 3.3 33.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 3.0 33.8 + - + +
39D PHE* 1.3 81.2 - - + +
41D GLU* 1.3 57.8 + - - +
43D PHE* 3.6 11.3 - - + +
44D ILE* 3.0 35.9 + - + +
89D LEU* 4.5 18.8 - - + +
92D ILE* 3.8 35.4 - - + +
93D GLN* 3.3 34.8 - - + +
82G LEU 4.5 16.2 - - - +
83G GLY* 5.8 2.0 - - - -
123G TYR* 5.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU 3.1 24.6 + - - +
38D GLN* 3.5 17.8 - - - +
40D LEU* 1.3 78.8 - - - +
42D SER* 1.3 68.5 + - - +
44D ILE* 3.6 5.0 + - - +
45D ASP* 2.9 54.1 + - - +
93D GLN* 4.1 11.8 - - - +
97D LYS* 4.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLN* 3.5 15.5 + - - -
39D PHE* 3.4 4.1 + - - -
40D LEU 3.3 0.2 - - - -
41D GLU* 1.3 89.1 - - - +
43D PHE* 1.3 61.0 + - - +
45D ASP* 3.7 6.4 - - - +
46D GLU* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PHE 2.9 18.8 + - - +
40D LEU* 3.6 14.8 - - + +
41D GLU 3.3 0.2 - - - -
42D SER* 1.3 77.4 - - - +
44D ILE* 1.3 60.0 + - + +
46D GLU* 3.3 22.7 - - - +
47D LYS* 3.0 43.3 + - + +
89D LEU* 3.6 32.5 - - + -
67G ASN* 5.8 0.9 - - - -
70G VAL* 5.7 3.1 - - + -
83G GLY* 5.5 5.8 - - - -
84G TYR* 3.4 66.0 - + - -
123G TYR* 6.4 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 3.0 23.2 + - + +
41D GLU* 4.0 5.6 - - - +
43D PHE* 1.3 76.4 - - + +
45D ASP* 1.3 70.2 + - - +
47D LYS* 3.6 7.7 - - + +
48D GLU* 3.0 36.8 + - + +
86D ILE* 4.5 23.8 - - + +
89D LEU* 3.8 42.6 - - + -
90D LYS* 5.3 4.3 - - + +
93D GLN* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU* 2.9 40.6 + - - +
42D SER* 3.7 6.9 - - - +
44D ILE* 1.3 80.5 - - - +
46D GLU* 1.3 58.4 + - - +
48D GLU* 3.4 27.2 - - - +
49D ASN* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D SER* 3.0 23.1 + - - +
43D PHE* 3.3 38.1 - - - +
45D ASP* 1.3 76.5 - - - +
47D LYS* 1.3 67.2 + - - +
49D ASN* 3.4 25.4 + - - +
62G MET* 5.5 6.9 - - - +
84G TYR* 4.4 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.0 37.1 + - + +
44D ILE* 3.1 11.4 + - + +
46D GLU* 1.3 81.6 - - - +
48D GLU* 1.3 59.8 + - - +
49D ASN 3.1 15.0 + - - +
82D LEU* 3.4 39.2 - - - +
86D ILE* 3.3 38.6 - - + +
67G ASN* 5.6 2.2 - - - +
84G TYR* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 3.0 29.3 + - + +
45D ASP* 3.4 28.1 - - - +
47D LYS* 1.3 76.4 - - - +
49D ASN* 1.3 62.9 + - - +
86D ILE* 6.4 1.1 - - + -
----------------------------------------------------------
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