Contacts of the helix formed by residues 32 - 48 (chain D) in PDB entry 4IP8
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 SER 32 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D MET* 5.1 4.5 + - - +
29D TYR* 2.7 33.0 + - - +
31D GLY* 1.3 78.4 - - - +
33D ASP* 1.3 70.9 + - - +
34D LYS 3.4 2.5 - - - -
35D TYR* 3.2 5.6 + - - +
36D PHE* 3.2 46.4 + - - -
97D PRO* 3.9 22.7 - - - -
100D LEU* 4.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 6.0 0.9 - - - -
24D MET* 3.8 24.9 - - - +
29D TYR 5.3 1.2 - - - +
31D GLY* 3.5 4.2 + - - -
32D SER* 1.3 81.9 + - - +
34D LYS* 1.3 83.1 + - - +
36D PHE* 3.3 2.8 + - - +
37D HIS* 3.0 37.8 + - - +
66D GLN* 4.7 11.9 + - - -
71D HIS* 5.2 7.1 - - - -
79D ASP* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLY* 5.2 8.4 + - - +
32D SER 3.4 0.8 - - - -
33D ASP* 1.3 98.2 + - - +
35D TYR* 1.3 62.8 + - - +
37D HIS* 3.4 8.0 - - + +
38D ALA* 2.9 25.1 + - - +
75D ASP* 5.3 0.9 - - - -
78D ALA* 4.4 24.5 - - + +
79D ASP* 3.3 25.0 + - - +
82D ALA* 3.7 8.0 - - + +
95D PHE* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLY 5.5 0.2 + - - -
32D SER* 3.2 9.3 + - - +
34D LYS* 1.3 79.0 - - - +
36D PHE* 1.3 73.5 + + - +
38D ALA* 3.3 2.1 + - - +
39D ARG* 2.8 48.4 + - - +
92D PRO* 3.3 30.6 - - + +
93D ASN* 3.4 21.5 + - - -
95D PHE* 3.5 24.6 + - - +
96D ARG* 3.1 30.7 + - - -
97D PRO* 4.2 5.4 - - + -
100D LEU* 3.6 23.6 - - + -
104D TYR* 2.5 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ALA* 3.5 28.0 - - - +
23D ASP* 3.6 22.9 - - + -
24D MET* 3.5 42.0 - - + -
27D ALA* 4.1 9.0 - - + -
32D SER* 3.2 45.5 + - - +
33D ASP 3.9 3.1 - - - +
35D TYR* 1.3 84.6 - + - +
37D HIS* 1.3 61.3 + - - +
39D ARG* 3.8 23.1 - - - +
40D GLY* 2.9 24.1 + - - -
100D LEU* 4.1 7.4 - - + -
104D TYR* 3.9 26.5 - + + -
203D P4C 4.3 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D MET* 4.5 9.6 - - + -
33D ASP* 3.0 34.1 + - + +
34D LYS* 3.4 9.9 - - - +
36D PHE* 1.3 77.3 - - - +
38D ALA* 1.3 61.9 + - - +
40D GLY* 4.0 0.3 - - - -
41D ASN* 3.0 31.2 + - - -
62D ARG* 3.3 40.9 + - - -
66D GLN* 4.2 9.2 + - - -
79D ASP* 3.5 40.7 + - + -
82D ALA* 4.0 9.4 - - + -
83D ASN* 3.5 13.7 - - - +
203D P4C 3.3 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LYS 2.9 17.5 + - - +
35D TYR 3.7 3.4 - - - +
37D HIS* 1.3 74.9 - - - +
39D ARG* 1.3 59.2 + - - +
41D ASN* 3.5 0.8 + - - -
42D TYR* 2.8 30.8 + - - +
82D ALA 3.5 21.8 - - - +
85D TRP* 4.8 0.2 - - + -
86D GLY* 3.5 11.0 - - - +
92D PRO* 3.9 17.7 - - + -
95D PHE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP 4.9 0.2 + - - -
19D ARG* 3.6 26.3 + - - +
20D ALA* 3.5 24.8 - - - +
23D ASP* 2.9 29.4 + - - -
35D TYR* 2.8 34.5 + - + +
36D PHE* 3.8 21.5 - - - +
38D ALA* 1.3 70.4 - - - +
40D GLY* 1.3 62.1 + - - +
42D TYR* 3.7 2.4 - - + +
43D ASP* 2.9 56.3 + - - +
92D PRO* 3.7 20.6 - - + +
103D LYS 4.7 1.4 + - - -
104D TYR* 3.1 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP* 4.3 7.6 - - - +
17D MET* 3.3 19.7 - - - +
20D ALA* 3.5 24.8 - - - +
36D PHE 2.9 13.1 + - - -
37D HIS 4.0 0.4 - - - -
39D ARG* 1.3 76.4 - - - +
41D ASN* 1.3 61.1 + - - +
43D ASP* 3.3 5.6 + - - +
44D ALA* 3.0 19.2 + - - +
203D P4C 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D MET* 3.7 12.4 - - - +
37D HIS 3.0 25.7 + - - +
38D ALA 4.0 1.6 - - - +
40D GLY* 1.3 70.9 - - - +
42D TYR* 1.3 60.5 + - - +
44D ALA* 3.9 0.9 - - - +
45D ALA* 2.9 32.7 + - - +
55D ALA* 3.1 13.4 - - - +
59D SER* 3.1 13.0 + - - -
62D ARG* 4.3 0.2 - - - +
83D ASN* 3.0 44.2 + - - +
87D ARG* 2.8 40.4 + - + +
----------------------------------------------------------
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 ALA 2.8 19.5 + - - +
39D ARG* 3.7 4.5 - - + +
41D ASN* 1.3 76.3 - - - +
43D ASP* 1.3 76.4 + - - +
45D ALA* 3.8 2.4 - - - +
46D LYS* 3.2 47.1 + - + +
86D GLY* 3.3 21.5 + - - +
89D GLY* 3.4 24.7 - - - -
90D LYS 3.6 17.7 - - - -
91D ASP* 4.9 1.3 - - - -
92D PRO* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP* 3.0 33.4 - - + +
19D ARG* 4.0 18.4 + - - +
39D ARG* 2.9 52.7 + - - +
40D GLY* 3.6 3.0 + - - +
42D TYR* 1.3 90.8 - - - +
44D ALA* 1.3 62.2 + - - +
46D LYS* 3.3 20.5 + - - +
47D ARG* 3.6 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLY* 3.6 26.5 - - - +
16D ASP* 3.5 9.3 + - - +
17D MET* 4.2 2.7 - - + -
40D GLY 3.0 15.3 + - - +
41D ASN 3.9 0.2 - - - +
43D ASP* 1.3 73.9 - - - +
45D ALA* 1.3 66.1 + - - +
47D ARG* 2.9 22.0 + - - +
51D GLY* 3.2 26.4 - - - +
55D ALA* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN 2.9 18.8 + - - +
42D TYR* 3.8 5.4 - - - +
44D ALA* 1.3 76.3 - - - +
46D LYS* 1.3 62.2 + - - +
48D GLY* 3.1 17.7 + - - +
51D GLY 4.3 0.2 - - - -
52D VAL* 3.9 25.4 - - + +
55D ALA* 5.0 0.2 - - - +
86D GLY 4.6 0.7 - - - +
87D ARG* 3.5 30.1 - - + +
89D GLY* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR* 3.2 39.1 + - + +
43D ASP* 3.4 14.8 - - - +
44D ALA 3.1 0.8 - - - -
45D ALA* 1.3 76.0 - - - +
47D ARG* 1.3 61.9 + - - +
48D GLY* 3.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLU* 3.4 37.1 - - - +
12D ASP* 3.5 23.8 + - + +
13D GLY 4.0 11.4 - - - +
15D ARG* 3.8 6.9 - - - +
16D ASP* 2.9 39.5 + - - +
19D ARG* 5.1 2.6 - - - +
43D ASP 3.6 3.1 + - - +
44D ALA 2.9 17.3 + - - +
46D LYS* 1.3 80.8 - - - +
48D GLY* 1.3 54.8 + - - +
51D GLY* 4.3 1.1 - - - -
201D SO4 3.0 49.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLU* 3.9 1.8 - - - -
45D ALA 3.1 10.3 + - - +
46D LYS 3.2 0.8 - - - -
47D ARG* 1.3 81.3 - - - +
49D PRO* 1.3 69.0 - - - +
50D GLY 3.1 2.9 - - - -
51D GLY 2.7 20.3 + - - -
52D VAL* 2.9 16.9 + - - +
----------------------------------------------------------
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