Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 2J2M
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 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.4 7.6 - - - -
23A ARG* 2.7 39.6 + - + +
31A THR* 5.0 0.4 - - + -
32A LEU* 3.2 16.7 + - - +
33A LEU 3.2 1.0 - - - -
34A GLU* 1.3 75.6 - - - +
36A TYR* 1.3 60.9 + - - +
37A GLN 3.4 0.5 + - - -
38A LEU* 3.0 30.9 + - + +
39A ILE* 3.1 24.9 + - + +
412B ARG* 2.7 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 4.4 11.0 - - + -
12A GLN* 2.9 35.9 + - + -
34A GLU 2.7 13.7 + - - +
35A ASP* 1.3 70.2 - - - +
37A GLN* 1.3 61.3 + - + +
39A ILE* 4.7 6.7 - - + +
40A GLU* 2.7 73.5 + - + +
412B ARG* 5.3 0.4 - - - +
316C ASN* 4.4 9.2 - - - -
318C GLY 4.3 20.6 - - - +
319C VAL* 3.9 10.1 - - + -
336C LEU* 4.9 6.7 - - + -
340C SER* 3.7 24.7 + - - -
344C ARG* 5.0 2.9 + - - -
351C TYR* 4.5 4.7 + - - -
352C GLN* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 4.4 11.8 - - + +
16A ILE* 3.5 44.7 - - + +
17A GLY 4.8 1.0 + - - -
18A ASP 2.8 27.7 + - - +
19A ASN* 4.0 4.2 + - - +
35A ASP* 3.2 6.2 + - - +
36A TYR* 1.3 86.4 - - + +
38A LEU* 1.3 61.0 + - - +
40A GLU* 4.0 3.8 - - - +
41A LYS* 3.2 24.8 + - + +
140B MET* 3.4 25.3 - - + +
412B ARG* 3.8 19.3 + - - +
400C GLU* 4.2 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.8 10.3 - - - +
31A THR* 3.9 28.0 - - + -
32A LEU 5.5 0.2 - - - +
35A ASP* 3.0 30.2 + - + +
37A GLN* 1.3 75.3 - - - +
39A ILE* 1.3 61.5 + - + +
41A LYS* 3.1 3.8 + - + +
42A ILE* 2.7 60.5 + - + +
139B ALA* 3.9 5.2 - - + -
140B MET* 3.7 46.6 - - + +
334B GLY* 5.0 6.5 - - - -
337B PHE* 6.5 0.9 - - + -
33D LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 4.6 2.0 - - - +
33A LEU* 3.1 37.0 - - + +
35A ASP 3.1 17.0 + - - +
36A TYR* 4.1 5.8 - - + +
38A LEU* 1.3 83.6 - - + +
40A GLU* 1.3 54.8 + - - +
42A ILE* 4.5 4.3 - - - +
43A ALA* 2.6 39.3 + - - +
337B PHE* 4.0 26.7 - - + -
336C LEU 6.4 0.2 - - - -
337C PHE* 4.5 17.5 - - + +
340C SER* 6.5 0.2 - - - -
344C ARG* 4.2 15.5 - - - +
33D LEU* 4.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.4 9.0 - - - +
11A ASN* 2.8 53.4 + - + +
12A GLN* 3.9 1.2 - - - +
36A TYR* 2.7 65.6 + - + +
37A GLN* 4.0 3.7 - - - +
39A ILE* 1.3 72.6 - - - +
41A LYS* 1.3 58.1 + - - +
43A ALA* 4.0 0.7 - - - +
44A HIS* 3.1 28.8 + - + +
344C ARG* 3.7 17.0 + - - +
352C GLN* 5.2 0.2 - - - +
367C GLN* 3.0 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 6.3 2.2 - - + -
19A ASN* 2.9 31.3 + - - +
37A GLN* 3.2 17.6 + - + +
38A LEU* 3.1 5.2 + - - +
40A GLU* 1.3 78.2 - - - +
42A ILE* 1.3 65.9 - - + +
44A HIS* 4.0 2.1 - - - +
45A PHE* 3.1 22.5 + - - +
140B MET* 2.8 34.5 + - - +
143B PRO* 4.3 19.3 - - + +
144B ASP* 2.6 36.6 + - - -
366C TYR* 6.0 3.4 - - - -
367C GLN* 3.9 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 2.7 41.6 + - + +
39A ILE* 4.2 1.3 - - - +
41A LYS* 1.3 71.7 - - + +
43A ALA* 1.3 60.4 + - - +
45A PHE* 3.3 5.0 + - + +
46A ASP* 2.9 50.0 + - - +
139B ALA* 3.6 25.6 - - + +
140B MET* 5.3 0.2 - - - -
143B PRO* 3.7 21.1 - - + -
334B GLY* 4.9 2.2 - - - +
337B PHE* 3.8 16.4 - - + -
338B SER* 3.7 23.6 - - - +
501B HEM 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE 2.6 25.0 + - - +
42A ILE* 1.3 73.2 - - - +
44A HIS* 1.3 60.7 + - - +
46A ASP 3.5 6.1 + - - -
47A ARG* 3.0 27.3 + - - +
337B PHE* 4.1 7.8 - - + -
341B ASP* 3.5 17.9 - - - +
344C ARG* 3.4 39.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 4.7 6.3 - - - +
40A GLU 3.1 14.5 + - - +
41A LYS 4.1 2.2 - - - +
43A ALA* 1.3 73.5 - - - +
45A PHE* 1.3 67.3 + - - +
47A ARG* 2.9 16.9 + - - +
48A GLU* 3.3 10.5 + - - +
344C ARG* 5.1 1.9 - - - +
349C PRO* 3.7 22.7 - - + -
350C ASN* 2.6 28.4 + - - -
353C GLN* 6.1 0.2 - - - -
367C GLN* 3.3 30.4 + - + +
368C ARG* 3.1 40.1 + - - -
369C ASP 3.2 13.9 + - - -
370C GLY* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS 3.1 15.0 + - - +
42A ILE* 3.4 9.4 - - + +
44A HIS* 1.3 76.4 + - - +
46A ASP* 1.3 68.6 + - - +
47A ARG 3.1 5.2 + - - -
48A GLU* 3.3 40.4 + - - +
54B VAL* 3.5 45.0 - - + +
55B VAL* 4.4 2.2 - - + -
142B PHE* 3.5 38.8 - + - -
143B PRO* 3.8 31.0 - - + -
146B VAL* 3.6 31.9 - - + -
147B HIS* 4.2 3.8 - + - -
338B SER* 5.1 0.9 - - - -
501B HEM 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 2.9 27.3 + - - +
43A ALA 3.5 3.8 - - - +
44A HIS 3.2 0.4 - - - -
45A PHE* 1.3 80.1 - - - +
47A ARG* 1.3 58.8 + - - +
48A GLU 3.6 0.4 - - - -
49A ARG 5.3 0.5 + - - -
54B VAL* 5.0 3.7 - - - +
338B SER* 2.7 45.1 + - - +
341B ASP* 2.5 32.4 - - - +
342B THR* 2.6 34.5 + - - -
345B HIS* 3.4 12.3 + - - -
501B HEM 3.5 10.2 - - - +
----------------------------------------------------------
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