Contacts of the helix formed by residues 37 - 50 (chain B) in PDB entry 5IWG
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 PRO 37 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.3 22.1 - - + +
25B GLY* 3.7 8.6 - - - -
27B TYR 3.2 24.0 - - - +
28B TYR* 5.0 2.2 - - + -
29B TYR* 4.1 16.4 - - + +
35B MET* 3.5 13.7 - - + +
36B LYS* 1.4 83.5 - - - +
38B HIS* 1.3 55.9 - - - +
39B ARG* 3.1 2.7 - - + +
40B ILE* 3.0 36.0 + - + +
114B PHE* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY* 3.7 18.0 + - - +
27B TYR 5.1 0.2 + - - -
36B LYS* 4.4 10.1 - - + +
37B PRO* 1.3 76.7 - - - +
39B ARG* 1.3 55.7 + - - +
41B ARG* 3.1 26.0 + - - -
42B MET* 2.9 41.5 + - + +
310B ILE* 4.4 5.8 - - + -
338B TYR* 3.4 37.8 - + - -
341B TYR* 3.1 31.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MET* 3.6 19.6 - - - +
36B LYS* 3.0 25.4 + - - +
37B PRO* 4.9 0.6 - - - +
38B HIS* 1.3 77.0 - - - +
40B ILE* 1.3 71.8 + - + +
42B MET* 3.5 13.5 + - - +
43B THR* 2.8 36.3 + - - -
140B TRP 5.0 1.0 + - - -
305B GLY 2.8 29.7 + - - +
306B GLY* 3.3 13.1 + - - -
307B GLY* 3.1 29.4 + - - +
310B ILE* 3.9 26.4 - - + +
313B VAL* 4.1 16.2 - - + +
314B ALA* 4.6 1.2 - - - +
317B TRP* 3.6 17.9 - - - -
403B IWX 3.5 25.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 5.2 1.2 + - - +
19B TYR 6.1 0.2 - - - +
20B TYR* 4.0 12.1 - - + -
24B ILE* 3.7 26.0 - - + -
37B PRO* 3.0 19.6 + - + +
39B ARG* 1.3 91.3 - - + +
41B ARG* 1.3 60.3 + - - +
43B THR* 3.4 6.6 + - - -
44B HIS* 3.0 27.4 + - - +
114B PHE* 6.4 0.2 - - + -
140B TRP* 3.4 31.6 - - + +
141B ALA* 4.1 24.9 - - + +
317B TRP* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.6 27.3 - - + +
22B GLY 4.1 11.0 + - - -
24B ILE* 4.7 0.4 - - - +
25B GLY* 3.2 31.3 + - - -
26B ASN* 2.7 36.7 + - - +
37B PRO 3.9 1.0 + - - -
38B HIS* 3.1 28.0 + - - +
40B ILE* 1.3 76.0 - - - +
42B MET* 1.3 60.2 + - - +
44B HIS* 3.3 1.9 + - - +
45B ASN* 2.9 30.7 + - + +
338B TYR* 3.4 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 2.9 29.5 + - - +
39B ARG* 3.6 13.9 - - - +
41B ARG* 1.3 75.6 - - - +
43B THR* 1.3 62.7 + - - +
45B ASN* 3.4 1.4 + - - +
46B LEU* 3.0 26.3 + - - +
310B ILE* 3.6 45.5 - - + +
311B ARG* 4.0 15.3 - - - +
314B ALA* 4.0 8.6 - - + +
336B ASN* 5.6 0.7 - - - +
338B TYR* 3.9 23.2 - - + -
341B TYR* 3.4 32.1 - - + -
342B PHE* 4.1 16.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 5.0 0.4 - - - +
39B ARG 2.8 20.1 + - - -
40B ILE* 3.5 10.8 - - - -
41B ARG 3.3 0.2 - - - -
42B MET* 1.3 76.4 - - - +
44B HIS* 1.3 63.1 + - - +
47B LEU* 3.0 34.9 + - + +
140B TRP* 3.9 20.0 - - + -
313B VAL 4.3 0.2 - - - -
314B ALA* 3.4 22.4 + - - +
317B TRP* 3.6 39.0 - - + -
318B THR* 3.4 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 2.9 42.9 + + - +
20B TYR* 3.3 48.0 - + + -
40B ILE 3.0 17.0 + - - +
41B ARG 3.6 4.0 - - - +
43B THR* 1.3 76.1 - - - +
45B ASN* 1.3 60.0 + - - +
47B LEU* 3.4 4.6 + - + +
48B LEU* 2.9 69.5 + - + +
58B ILE* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 2.9 19.6 + - + +
42B MET 3.9 1.8 - - - +
44B HIS* 1.3 79.7 - - + +
46B LEU* 1.3 62.0 + - - +
48B LEU* 3.5 12.5 + - - +
49B ASN* 2.9 47.6 + - - +
336B ASN* 3.3 7.1 - - - +
337B ASP* 2.7 56.5 + - - +
338B TYR* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET 3.0 17.9 + - - +
43B THR* 4.7 0.2 - - - -
45B ASN* 1.3 75.9 + - - +
47B LEU* 1.3 57.6 + - - +
49B ASN* 3.2 3.5 + - - -
50B TYR* 3.0 49.9 + - + -
314B ALA* 4.0 14.8 - - + +
315B ARG* 4.3 4.5 - - - +
318B THR* 3.6 23.3 - - + +
333B LEU* 4.0 23.6 - - + -
334B PRO* 4.2 8.7 - - + -
336B ASN* 3.6 30.9 - - - +
342B PHE* 4.1 23.3 - - + -
348B LEU* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.6 34.8 - - + +
43B THR* 3.0 33.0 + - + +
44B HIS* 3.5 11.2 - - + +
46B LEU* 1.3 73.5 - - - +
48B LEU* 1.3 73.6 + - + +
50B TYR* 3.4 4.6 + - - +
51B GLY 3.3 3.8 + - - -
52B LEU* 3.2 43.1 + - + +
53B TYR 5.1 0.9 - - - +
56B MET* 3.6 26.9 - - + -
58B ILE* 5.2 0.2 - - + -
318B THR* 3.7 15.9 + - + +
321B THR* 3.8 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 2.9 57.4 + - + +
45B ASN* 3.7 14.6 - - - +
47B LEU* 1.3 79.7 - - + +
49B ASN* 1.3 59.7 + - - +
51B GLY* 3.0 15.8 + - - -
53B TYR* 3.4 50.1 - - + -
58B ILE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 2.9 35.7 + - - +
45B ASN* 2.9 50.7 + - - +
46B LEU 3.2 3.8 + - - +
48B LEU* 1.3 78.1 - - - +
50B TYR* 1.3 59.7 + - - +
51B GLY* 3.3 0.6 + - - -
334B PRO* 3.5 21.2 - - + +
335B TYR 3.1 20.0 - - - +
336B ASN* 3.6 10.0 - - + +
337B ASP* 4.5 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.0 32.4 + - + -
47B LEU 3.7 9.0 - - - +
48B LEU 3.3 0.4 - - - -
49B ASN* 1.3 74.7 - - - +
51B GLY* 1.3 58.4 + - - +
52B LEU* 3.4 17.2 + - + +
318B THR* 3.6 26.5 - - + -
329B ILE* 3.7 27.4 - - + +
330B PRO* 2.8 48.4 + - + -
332B GLU 3.6 4.5 + - - -
333B LEU* 3.3 21.3 - - + +
334B PRO* 3.4 27.1 - - + -
348B LEU* 3.5 9.2 - - + +
----------------------------------------------------------
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