Contacts of the helix formed by residues 39 - 50 (chain D) in PDB entry 4HXD
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 ASN 39 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 3.1 10.3 + - - +
38D GLY* 1.3 77.6 + - - +
40D CYS* 1.3 62.8 + - - +
41D PHE* 3.0 4.9 + - - -
42D TYR* 3.0 21.1 + - - +
43D HIS* 3.1 32.7 + - + +
58D PHE* 3.7 31.7 - - + -
62D LYS* 4.5 8.9 - - - +
96D ASP* 3.4 11.1 - - - +
97D ASN* 2.9 42.4 - - - +
98D GLU 4.0 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLY 4.1 0.2 - - - -
101C 4LJ 1.8 62.4 - - + -
34D GLN* 4.0 3.6 - - + +
35D PRO 3.3 19.5 - - - +
37D ASP* 3.6 2.5 + - - -
38D GLY 3.5 0.6 - - - -
39D ASN* 1.3 76.7 - - - +
41D PHE* 1.3 53.1 + - - +
43D HIS* 3.8 9.0 - - - +
44D SER* 2.7 37.2 + - - -
151D HIS* 3.8 10.3 - - + -
152D PHE 3.4 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLY 3.5 19.0 + - - +
38D GLY 6.0 0.2 - - - +
39D ASN 3.0 0.8 + - - -
40D CYS* 1.3 79.6 - - - +
42D TYR* 1.3 96.2 + + + +
44D SER* 2.9 20.1 + - - -
45D ILE* 3.0 39.3 + - + +
100D GLY* 4.0 9.4 - - - +
101D GLY* 3.4 35.2 - - - -
104D GLU* 3.8 14.8 - - + -
105D ALA* 4.0 6.7 - - + -
108D LEU* 4.5 1.3 - - + -
118D LEU* 4.5 9.2 - - + -
144D LEU* 4.0 16.4 - - + -
152D PHE* 3.8 28.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY 5.5 0.2 - - - -
39D ASN* 3.0 14.1 + - - +
41D PHE* 1.3 102.8 - + + +
43D HIS* 1.3 60.3 + - - +
45D ILE* 3.4 3.3 + - - +
46D ALA* 2.9 30.1 + - - +
58D PHE* 3.6 25.6 - - + +
61D VAL* 3.5 22.0 - - + +
62D LYS* 3.6 43.7 - - + -
65D LEU* 3.5 18.2 - - + +
93D ALA* 4.8 4.7 + - - +
98D GLU 4.0 18.6 - - - -
99D TRP 4.4 2.5 + - - -
100D GLY* 3.8 9.8 - - - -
104D GLU* 3.1 25.6 - - + +
108D LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLN* 3.4 17.5 - - - +
35D PRO* 4.3 12.4 - - + +
37D ASP* 3.4 24.0 + - - -
39D ASN* 3.1 38.0 + - + +
40D CYS* 3.8 9.4 - - - +
42D TYR* 1.3 73.4 - - - +
44D SER* 1.3 65.3 + - - +
46D ALA* 3.3 4.1 + - - +
47D GLU* 3.1 24.1 + - - +
53D LYS* 3.2 26.9 + - - +
55D PRO* 3.2 28.9 - - + -
58D PHE* 3.3 26.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLN* 3.1 16.0 - - - +
40D CYS 2.7 18.4 + - - -
41D PHE* 2.9 13.7 + - - -
43D HIS* 1.3 76.4 - - - +
45D ILE* 1.3 61.3 + - - +
47D GLU* 3.2 16.6 + - - +
48D LEU* 3.6 12.5 + - - +
144D LEU* 3.9 25.4 - - - -
152D PHE 2.8 22.5 + - - -
153D ASP 3.5 7.3 - - - -
154D ALA* 4.0 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 3.0 44.3 + - + +
42D TYR 3.9 6.3 - - - +
44D SER* 1.3 76.2 - - - +
46D ALA* 1.3 62.9 + - - +
47D GLU 3.2 0.7 + - - -
48D LEU* 3.2 4.1 + - - +
49D PHE* 3.0 26.6 + - + +
61D VAL* 3.8 21.5 - - + -
108D LEU* 4.0 15.9 - - + -
112D LEU* 5.3 7.6 - - + -
116D ILE* 4.5 20.0 - - + -
142D LEU* 4.3 19.0 - - + +
144D LEU* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR 2.9 18.1 + - - +
43D HIS* 3.3 6.9 + - - +
45D ILE* 1.3 76.6 - - - +
47D GLU* 1.3 60.5 + - - +
49D PHE* 4.7 0.7 - - - -
50D PHE* 3.2 44.9 + - + +
53D LYS* 4.2 7.8 - - + +
57D SER* 3.7 29.2 - - - -
58D PHE* 3.9 9.4 - - - +
61D VAL* 4.3 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 4.1 22.8 - - + +
34D GLN* 3.9 19.4 + - - +
43D HIS 3.1 11.4 + - - +
44D SER 3.5 11.0 - - - +
45D ILE 3.2 0.4 - - - -
46D ALA* 1.3 76.6 - - - +
48D LEU* 1.3 61.6 + - + +
50D PHE 4.1 7.4 - - - +
53D LYS* 4.1 29.3 + - + +
154D ALA* 4.2 11.4 - - + -
156D ARG* 2.9 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 4.8 0.2 - - + -
44D SER 3.9 8.7 - - - +
45D ILE 3.2 3.6 + - - +
47D GLU* 1.3 79.9 - - + +
49D PHE* 1.3 62.5 + - - +
50D PHE 3.6 3.6 - - - +
142D LEU* 4.0 25.7 - - + +
143D ASN 3.3 42.8 - - - +
144D LEU* 3.9 14.8 - - + -
154D ALA* 4.1 13.5 - - + -
155D LEU 3.4 19.7 - - - +
156D ARG* 3.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN* 6.5 1.8 - - + -
45D ILE* 3.0 22.9 + - + +
46D ALA* 4.5 2.5 - - - +
48D LEU* 1.3 79.8 - - - +
50D PHE* 1.3 92.9 + + + +
61D VAL* 6.1 2.7 - - + -
64D HIS* 4.7 9.9 - + - -
112D LEU* 3.9 40.4 - - + -
114D THR* 4.4 14.6 - - + -
142D LEU* 4.4 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA* 3.2 40.3 + - + +
47D GLU 4.1 12.0 - - - +
48D LEU 4.4 2.9 - - - +
49D PHE* 1.3 110.5 - + - +
51D ASP* 1.3 64.9 + - - +
52D VAL* 3.4 18.7 - - - +
57D SER* 3.8 30.5 - - - -
60D LYS* 3.8 42.8 - - + -
61D VAL* 4.5 9.9 - - + -
64D HIS* 5.3 1.8 - + - -
156D ARG* 5.4 1.2 + - - -
----------------------------------------------------------
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