Contacts of the helix formed by residues 2 - 28 (chain B) in PDB entry 4IP9
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 2 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 4.7 9.3 - - - -
1B ARG* 1.4 77.1 - - - +
3B PHE* 1.3 55.5 + - - +
5B SER* 3.5 8.1 + - - -
6B PHE* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 5.8 3.1 - - + -
69A PHE* 4.2 30.6 - + + -
1B ARG 3.3 2.5 - - - +
2B SER* 1.3 75.0 - - - +
4B PHE* 1.3 74.5 + + + +
6B PHE* 3.3 4.6 + + - +
7B LEU* 3.1 60.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.4 12.9 + - - +
3B PHE* 1.3 90.9 - + + +
5B SER* 1.4 57.8 + - - +
7B LEU* 3.5 6.9 + - + +
8B GLY 3.2 20.4 + - - -
201B P4C 3.3 87.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.2 14.6 + - - +
2B SER* 3.7 11.2 - - - -
3B PHE 3.3 0.2 - - - -
4B PHE* 1.4 72.9 - - - +
6B PHE* 1.4 53.6 - - - +
8B GLY* 3.2 3.3 + - - +
9B GLU* 2.8 49.5 + - - +
201B P4C 3.2 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.4 39.3 - - + -
68A PHE* 3.5 43.3 - + + -
69A PHE* 3.6 13.0 - + + -
2B SER 3.0 15.8 + - - +
3B PHE* 3.4 9.6 - + - +
5B SER* 1.4 73.4 - - - +
7B LEU* 1.4 61.7 + - + +
9B GLU* 3.5 9.5 + - - -
10B ALA* 3.0 22.9 + - - +
49B PRO* 3.5 11.7 - - + -
50B GLY* 3.3 33.4 - - - -
53B TRP* 3.7 37.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.5 21.8 - - + -
3B PHE* 3.1 49.9 + - + +
4B PHE* 3.9 10.1 - - + +
5B SER 3.3 0.2 - - - -
6B PHE* 1.4 77.1 - - + +
8B GLY* 1.3 60.6 + - - +
10B ALA* 3.2 9.6 + - + +
11B PHE* 3.0 49.9 + - + -
53B TRP* 5.0 5.6 - - + -
201B P4C 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE 3.2 10.5 + - - -
5B SER* 3.6 4.0 - - - -
7B LEU* 1.3 74.1 - - - +
9B GLU* 1.4 57.1 + - - +
11B PHE* 3.4 6.4 + - - +
12B ASP* 3.0 38.9 + - - +
201B P4C 3.8 22.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 2.8 33.8 + - - +
6B PHE* 3.5 12.9 - - - +
8B GLY* 1.4 73.1 - - - +
10B ALA* 1.3 52.2 + - - +
12B ASP* 3.5 5.0 + - - +
13B GLY* 2.8 31.7 + - - -
47B ARG* 3.3 35.6 - - + +
48B GLY* 3.9 5.7 - - - -
49B PRO* 3.3 15.6 - - - +
50B GLY 3.0 18.9 + - - -
51B GLY* 3.6 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE 3.0 15.2 + - - +
7B LEU* 3.2 14.8 + - + +
9B GLU* 1.3 73.4 - - - +
11B PHE* 1.4 55.4 + - + +
13B GLY 3.1 1.6 + - - -
14B ALA* 2.8 33.2 + - - +
50B GLY 3.4 19.5 - - - +
53B TRP* 3.7 27.6 - - + -
54B ALA* 3.4 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.0 46.2 + - + +
8B GLY* 3.4 6.5 + - - +
10B ALA* 1.4 76.0 - - + +
12B ASP* 1.3 60.7 + - - +
14B ALA* 3.2 7.6 - - + +
15B ARG* 2.9 35.9 + - + +
201B P4C 5.4 7.4 - - + -
202B P4C 4.5 26.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 3.0 23.0 + - - +
9B GLU* 3.7 5.8 - - - +
11B PHE* 1.3 74.0 - - - +
13B GLY* 1.3 60.1 + - - +
15B ARG* 2.8 37.8 + - - +
16B ASP* 2.9 35.7 + - - +
47B ARG* 3.6 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU 2.8 19.2 + - - -
10B ALA 3.1 4.2 + - - -
12B ASP* 1.3 71.8 - - - +
14B ALA* 1.4 51.4 + - - +
16B ASP* 3.3 3.7 + - - +
17B MET* 2.9 39.4 + - - +
44B ALA* 3.6 29.1 - - - +
47B ARG* 4.1 0.8 - - - +
51B GLY* 4.2 6.1 - - - -
54B ALA* 4.5 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA 2.8 12.4 + - - +
11B PHE* 3.2 14.6 - - + +
13B GLY* 1.4 75.0 - - - +
15B ARG* 1.3 56.4 + - - +
17B MET* 3.4 3.3 + - - +
18B TRP* 2.9 27.7 + - - +
54B ALA* 4.2 2.3 - - + +
58B ILE* 3.7 25.8 - - + +
202B P4C 3.8 29.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 2.9 24.7 + - + +
12B ASP* 2.8 46.9 + - - +
14B ALA* 1.3 76.7 - - - +
16B ASP* 1.4 51.2 + - - +
18B TRP* 3.2 3.6 + - - +
19B ARG* 2.8 35.1 + - - +
47B ARG* 4.1 14.4 - - - +
202B P4C 3.7 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP 2.9 15.9 + - - +
13B GLY 3.3 5.4 + - - +
15B ARG* 1.4 71.2 - - - +
17B MET* 1.4 64.6 + - - +
19B ARG* 2.8 36.6 + - - +
20B ALA* 3.2 22.2 + - - +
39B ARG* 4.9 0.7 + - - -
40B GLY* 3.7 6.0 - - - -
43B ASP* 3.6 27.0 - - + +
44B ALA* 3.8 6.3 - - - +
47B ARG* 2.7 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY 2.9 19.4 + - - +
14B ALA 3.6 5.8 - - - +
16B ASP* 1.4 72.8 - - - +
18B TRP* 1.3 65.5 + - - +
20B ALA* 3.3 10.4 + - - +
21B TYR* 3.2 47.0 + - + +
37B HIS* 6.2 0.2 - - - -
40B GLY* 3.4 31.6 - - - +
41B ASN* 3.6 17.7 - - - +
44B ALA* 4.3 0.9 - - + -
55B ALA* 4.1 19.5 - - - +
58B ILE* 3.8 36.8 - - + -
59B SER* 3.7 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 2.9 15.5 + - - +
15B ARG 3.2 8.0 + - - +
17B MET* 1.3 76.2 - - - +
19B ARG* 1.3 58.5 + - - +
21B TYR* 3.2 8.6 + - + +
22B SER* 2.9 39.9 + - - -
25B ARG* 4.1 18.9 - - - +
202B P4C 3.5 54.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG 2.8 18.8 + - - +
16B ASP* 2.8 36.9 + - - +
17B MET 3.3 0.2 - - - -
18B TRP* 1.3 75.0 - - - +
20B ALA* 1.3 56.5 + - - +
22B SER* 3.6 7.1 - - - -
23B ASP* 2.9 46.6 + - - +
39B ARG* 3.7 17.9 - - - +
43B ASP* 2.9 29.9 + - - +
47B ARG* 5.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 3.2 6.0 + - - +
17B MET* 3.4 10.5 - - - +
18B TRP 3.3 0.2 - - - -
19B ARG* 1.3 76.0 - - - +
21B TYR* 1.4 62.6 + - + +
23B ASP 3.5 0.2 + - - -
24B MET* 2.9 27.5 + - - +
36B PHE* 3.4 35.9 - - + +
39B ARG* 3.4 14.7 - - - +
40B GLY* 3.6 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 3.2 48.4 + - + +
18B TRP* 3.2 8.7 + - + +
20B ALA* 1.4 75.7 - - + +
22B SER* 1.3 64.8 + - - +
24B MET* 3.3 23.4 + - + +
25B ARG* 3.1 44.1 + - - +
36B PHE* 5.1 4.0 - - + -
37B HIS* 2.9 49.3 - + - -
58B ILE* 5.0 7.0 - - + -
62B ARG* 3.0 28.5 + - + -
83B ASN* 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 2.9 28.4 + - - -
19B ARG* 3.6 8.7 - - - -
21B TYR* 1.3 74.6 - - - +
23B ASP* 1.4 59.3 + - - +
25B ARG* 3.3 26.7 + - - +
26B GLU* 3.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 2.9 27.7 + - - +
20B ALA 3.6 4.5 - - - +
22B SER* 1.4 76.4 + - - +
24B MET* 1.4 58.9 + - - +
26B GLU* 3.2 13.1 + - - +
27B ALA* 2.9 33.3 + - - +
36B PHE* 3.7 15.9 - - + -
39B ARG* 2.8 30.1 + - - +
103B LYS 5.3 1.0 - - - +
104B TYR* 3.7 19.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 2.9 18.5 + - - +
21B TYR* 3.3 31.2 + - + +
23B ASP* 1.4 74.7 - - - +
25B ARG* 1.3 61.3 + - + +
27B ALA* 3.8 1.7 + - - +
28B ASN* 3.3 19.9 + - - -
29B TYR 4.8 1.0 + - - -
32B SER* 4.2 8.5 + - - +
33B ASP* 3.7 46.2 - - + +
36B PHE* 3.7 31.6 - - + -
37B HIS* 5.0 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 4.1 25.3 + - - +
21B TYR* 3.1 31.7 + - - +
22B SER* 3.4 31.9 + - - +
24B MET* 1.3 74.2 - - + +
26B GLU* 1.3 65.0 + - - +
28B ASN* 3.7 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER 3.1 13.4 + - - +
23B ASP* 3.2 15.3 + - - +
25B ARG* 1.3 75.1 - - - +
27B ALA* 1.4 64.7 + - - +
28B ASN* 3.4 4.0 + - - +
103B LYS* 3.5 18.3 + - - +
104B TYR* 2.7 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP 2.9 20.0 + - - +
24B MET 4.0 4.0 - - - +
26B GLU* 1.4 72.4 - - - +
28B ASN* 1.4 65.9 + - - +
29B TYR* 3.1 8.8 + - - +
36B PHE* 4.1 8.1 - - + -
100B LEU* 3.9 21.1 - - + -
101B PRO* 5.5 0.9 - - + -
104B TYR* 3.4 29.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET 3.3 12.6 + - - -
25B ARG* 3.7 12.9 + - - +
26B GLU 3.3 4.6 - - - +
27B ALA* 1.4 77.9 - - - +
29B TYR* 1.3 61.0 + - - +
30B ILE* 3.8 9.9 + - - +
----------------------------------------------------------
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