Contacts of the helix formed by residues 3 - 19 (chain D) in PDB entry 4B86
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 3 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ASN* 1.3 89.0 + - + +
4D VAL* 1.3 56.4 + - - +
5D ASN 3.6 0.4 - - - -
6D ALA* 4.0 16.2 - - + +
7D THR* 2.7 30.3 + - - +
65D TYR* 3.2 29.4 - - + +
93D ASN* 3.7 21.8 - - - +
95D GLN* 3.9 17.0 - - + +
96D LEU* 3.8 15.7 - - + -
99D LEU* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 4 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLN* 4.0 7.9 - - - +
241B GLN* 3.4 37.7 - - + +
244B GLU* 4.6 8.5 - - - +
2D ASN* 3.6 21.9 + - - +
3D PRO* 1.3 71.2 - - - +
5D ASN* 1.3 68.9 + - - +
7D THR* 3.0 5.7 + - - -
8D ALA* 2.9 38.9 + - + +
61D THR* 5.7 4.9 - - + -
63D GLN* 3.9 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D PRO 3.6 0.2 - - - -
4D VAL* 1.3 81.7 - - - +
6D ALA* 1.3 58.5 - - - +
8D ALA* 3.8 4.2 - - - +
9D LEU* 3.0 38.4 + - + +
41D SER* 4.5 12.3 - - - +
63D GLN* 2.7 41.7 + - - +
65D TYR* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D PRO* 4.0 17.9 + - + +
4D VAL 3.3 0.2 - - - -
5D ASN* 1.3 77.2 - - - +
7D THR* 1.3 60.3 + - - +
9D LEU* 3.4 1.9 + - - -
10D TYR* 2.9 29.1 + - - +
38D PHE* 3.8 5.5 - - - -
41D SER* 3.8 17.9 - - - +
42D LEU* 3.5 31.6 - - + -
65D TYR* 5.6 0.7 - - + -
96D LEU* 5.0 0.9 - - + -
99D LEU* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.7 9.6 - - + -
236A GLN* 4.1 8.7 - - - +
233B ILE* 5.0 2.4 - - + +
237B GLN* 3.3 37.0 + - - +
3D PRO 2.7 23.4 + - - +
4D VAL 3.0 10.2 + - - -
6D ALA* 1.3 74.0 - - - +
8D ALA* 1.3 64.1 + - - +
10D TYR* 3.3 2.7 + - - +
11D ILE* 2.9 32.8 + - - +
95D GLN* 4.4 6.7 - - - +
99D LEU* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLN* 5.6 0.6 - - - +
4D VAL* 2.9 26.0 + - + +
5D ASN* 3.8 5.2 - - - +
7D THR* 1.3 76.2 - - - +
9D LEU* 1.3 57.4 + - + +
11D ILE* 3.2 12.8 + - - +
12D SER* 3.0 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ASN* 3.0 25.1 + - + +
6D ALA 3.9 0.7 - - - +
8D ALA* 1.3 76.3 - - + +
10D TYR* 1.3 59.1 + - - +
12D SER* 3.4 5.4 + - - +
13D ALA* 2.9 31.7 + - - +
34D LEU* 3.9 29.7 - - + +
37D TYR* 3.4 35.0 - - + +
38D PHE* 3.7 22.3 - - + +
41D SER* 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 3.4 21.0 - - + +
229A GLN* 3.1 29.3 + - + +
232A LEU* 4.5 10.5 - - + -
230B LEU* 4.0 16.8 - - + -
233B ILE* 4.6 2.5 - - + -
6D ALA 2.9 18.0 + - - +
7D THR* 3.3 6.0 + - - +
9D LEU* 1.3 71.5 - - - +
11D ILE* 1.3 64.9 + - + +
13D ALA* 4.6 0.9 - - - -
14D SER* 2.9 48.7 + - - -
38D PHE* 3.5 31.3 - + + -
99D LEU* 3.8 20.0 - - + -
102D CYS* 3.5 38.3 - - + -
106D LEU* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.1 23.3 - - + +
233B ILE* 4.3 14.6 - - + +
234B GLU* 3.6 38.4 - - + +
237B GLN* 5.0 4.3 - - + -
7D THR* 2.9 26.8 + - - +
8D ALA* 3.2 10.3 + - - +
10D TYR* 1.3 77.3 - - + +
12D SER* 1.3 58.0 + - - +
14D SER* 3.9 0.7 - - - -
15D ARG* 2.9 74.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ALA 3.0 17.5 + - - -
9D LEU* 3.8 9.1 - - - +
11D ILE* 1.3 78.7 - - - +
13D ALA* 1.3 57.3 + - - +
15D ARG* 3.4 5.9 + - - +
16D LEU* 2.9 37.4 + - - +
34D LEU* 3.9 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU 2.9 21.9 + - - +
10D TYR 4.0 2.7 - - - +
12D SER* 1.3 73.7 - - - +
14D SER* 1.3 56.5 + - - +
16D LEU* 3.1 7.2 + - - +
17D VAL* 2.9 36.1 + - - +
34D LEU* 3.7 15.9 - - + +
35D LEU* 4.5 13.5 - - + -
38D PHE* 4.2 13.9 - - + -
106D LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 4.7 1.0 - - - +
229A GLN* 4.6 0.9 + - - -
230B LEU* 3.6 25.8 - - - -
10D TYR* 2.9 46.0 + - - -
13D ALA* 1.3 75.4 - - - +
15D ARG* 1.3 58.6 + - - +
18D LEU* 2.9 43.7 + - - +
106D LEU* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 4.6 9.9 - - + -
230B LEU* 3.7 16.0 - - + +
231B ASP* 3.3 36.4 + - - +
234B GLU* 2.6 45.3 + - - +
11D ILE* 2.9 41.4 + - - +
12D SER* 3.6 7.0 - - - +
14D SER* 1.3 76.9 - - - +
16D LEU* 1.3 60.8 + - + +
19D ASN* 3.1 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 2.9 22.6 + - - +
13D ALA* 3.1 9.2 + - - +
15D ARG* 1.3 80.9 - - + +
17D VAL* 1.3 61.2 + - + +
19D ASN* 3.9 1.3 - - - -
20D TYR* 3.4 16.8 + - - -
27D ALA* 6.1 0.2 - - - +
30D GLU* 3.9 28.0 - - + +
31D ILE* 3.6 47.5 - - + +
34D LEU* 3.9 27.1 - - + -
35D LEU* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA 2.9 23.2 + - - +
14D SER 4.1 2.5 - - - +
16D LEU* 1.3 74.5 - - - +
18D LEU* 1.3 63.8 + - + +
20D TYR* 3.4 19.1 + - - +
31D ILE* 4.0 24.2 - - + -
35D LEU* 4.7 1.8 - - + -
106D LEU* 4.3 13.0 - - + -
109D TYR* 3.8 27.9 + - + -
110D ILE* 3.7 41.7 - - + -
115D LEU* 4.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.9 10.5 - - + -
225A ILE* 5.7 1.6 - - + -
229A GLN* 5.4 0.9 - - - +
223B LYS* 3.8 42.8 - - + +
226B LEU* 3.4 38.8 - - + -
227B LEU* 3.7 22.2 - - + +
230B LEU* 4.9 2.9 - - + -
14D SER* 2.9 38.2 + - - +
17D VAL* 1.3 79.2 - - + +
19D ASN* 1.3 64.3 + - - +
20D TYR 3.4 1.5 + - - -
106D LEU* 5.1 5.8 - - + -
109D TYR* 4.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 3.2 35.5 - - - +
15D ARG* 3.1 22.5 + - - +
16D LEU* 3.9 3.6 - - - +
18D LEU* 1.3 76.3 - - - +
20D TYR* 1.3 65.2 + - - +
21D ASP* 2.9 10.4 + - - +
----------------------------------------------------------
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