Contacts of the helix formed by residues 7 - 23 (chain D) in PDB entry 5FN4
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 7 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG 3.9 1.4 + - - -
6D VAL* 1.3 75.8 - - - +
8D ASN* 1.3 66.1 - - - +
9D GLU* 4.4 11.8 - - - +
10D GLU* 3.1 25.1 + - - +
11D LYS* 3.1 27.0 + - - +
47D TYR* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 1.3 71.3 - - - +
9D GLU* 1.3 73.9 + - - +
11D LYS* 3.2 7.3 + - - +
12D LEU* 2.9 27.2 + - - +
47D TYR* 3.4 51.8 + - + +
48D THR* 2.8 29.7 + - - -
49D GLU* 3.1 28.0 - - - +
53D ILE* 5.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 4.5 10.6 - - - +
8D ASN* 1.3 93.1 + - - +
10D GLU* 1.3 58.7 + - - +
12D LEU* 3.2 12.5 + - + +
13D ASN* 2.9 29.2 + - - +
49D GLU* 4.1 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL* 3.8 19.7 - - + -
7D SER* 3.1 21.0 + - - +
8D ASN 3.2 0.4 - - - -
9D GLU* 1.3 80.3 - - - +
11D LYS* 1.3 56.0 + - - +
13D ASN* 3.2 22.8 + - - +
14D LEU* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 3.7 29.8 + - + +
4D GLU* 3.5 38.1 + - - +
6D VAL* 3.1 32.5 - - + +
7D SER 3.1 23.1 + - - +
8D ASN* 3.3 9.0 - - - +
10D GLU* 1.3 76.9 - - - +
12D LEU* 1.3 57.7 + - - +
14D LEU* 3.2 9.8 + - - +
15D CYS* 2.9 29.3 + - - +
37D PHE* 4.3 14.5 - - + -
40D GLU* 5.4 6.2 + - + +
47D TYR* 4.2 21.5 - - + +
53D ILE* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASN 2.9 12.5 + - - +
9D GLU* 3.2 11.4 + - + +
11D LYS* 1.3 77.2 - - - +
13D ASN* 1.3 60.6 + - + +
15D CYS* 3.2 3.3 + - + +
16D ARG* 2.9 33.7 + - + +
49D GLU* 3.3 35.2 - - + +
52D GLN* 4.8 20.2 - - + +
53D ILE* 3.9 28.2 - - + +
56D TYR* 5.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 6.0 2.2 - - - -
9D GLU 2.9 13.0 + - - +
10D GLU* 3.2 27.6 + - - +
12D LEU* 1.3 78.8 - - + +
14D LEU* 1.3 58.0 + - - +
16D ARG* 3.2 23.0 + - - +
17D LYS* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 4.0 31.0 - - + +
216B LYS* 5.2 13.9 - - + -
217B GLY* 5.4 2.7 - - - +
3D LEU* 5.5 10.1 - - + -
6D VAL* 6.1 2.9 - - + -
10D GLU* 2.9 29.3 + - + +
11D LYS* 3.3 12.3 - - - +
13D ASN* 1.3 77.6 - - - +
15D CYS* 1.3 58.9 + - - +
17D LYS* 3.2 5.7 + - + +
18D TYR* 2.9 72.0 + - + +
36D TRP* 5.6 5.2 - - + -
37D PHE* 4.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS 2.9 10.1 + - - +
12D LEU* 3.4 9.6 - - + +
14D LEU* 1.3 77.7 - - - +
16D ARG* 1.3 57.0 + - - +
18D TYR* 3.2 3.6 + - - +
19D TYR* 2.9 27.9 + - - +
33D ASN* 3.9 10.9 + - - -
37D PHE* 3.4 38.1 - - + -
53D ILE* 4.2 20.2 - - + -
56D TYR* 4.5 25.1 - - - -
57D VAL* 4.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 2.9 18.5 + - + +
13D ASN* 3.4 24.5 + - - +
15D CYS* 1.3 77.2 - - - +
17D LYS* 1.3 61.5 + - - +
19D TYR* 3.2 8.9 + - + +
20D LEU* 2.9 37.4 + - - +
56D TYR* 4.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 3.9 44.5 - - + +
13D ASN* 2.9 34.2 + - - +
14D LEU* 3.5 10.5 - - - +
16D ARG* 1.3 82.2 - - - +
18D TYR* 1.3 61.4 + - + +
20D LEU* 3.2 17.2 + - + +
21D GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 3.0 30.5 - - + +
215B TRP* 4.4 9.4 + + - -
217B GLY* 3.2 24.7 + - - -
218B PRO* 4.3 0.3 - - - +
14D LEU* 2.9 40.1 + - + +
15D CYS 3.2 4.0 + - - +
17D LYS* 1.3 78.5 - - + +
19D TYR* 1.3 57.0 - - - +
21D GLY* 3.2 3.0 + - - +
22D GLY* 2.9 25.5 + - - -
29D LEU* 3.8 33.3 - - + +
30D TRP* 4.1 3.8 - - - -
32D VAL* 4.2 15.7 - - + -
33D ASN* 3.2 44.9 - - + +
36D TRP* 4.4 13.2 - + - -
37D PHE* 5.5 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D CYS* 2.9 13.2 + - - +
16D ARG* 3.4 11.7 - - - +
18D TYR* 1.3 76.3 - - - +
20D LEU* 1.3 65.4 + - - +
22D GLY 3.2 2.1 + - - -
23D PHE* 3.1 45.4 + + + +
30D TRP* 3.3 21.6 + + - +
33D ASN* 4.1 3.5 - - - +
56D TYR* 3.8 31.6 - + + -
59D ARG* 3.0 37.3 + - + +
60D SER* 3.2 42.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG* 2.9 21.0 + - - +
17D LYS* 3.3 20.4 - - + +
19D TYR* 1.3 80.6 - - - +
21D GLY* 1.3 62.6 + - - +
23D PHE* 3.3 19.3 + - + +
24D ALA* 3.9 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LYS 2.9 13.9 + - - -
18D TYR 3.2 4.0 + - - -
20D LEU* 1.3 77.9 - - - +
22D GLY* 1.3 55.4 + - - +
24D ALA* 3.0 31.6 + - - +
26D LEU* 4.4 4.1 - - - +
29D LEU* 4.3 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D TYR 2.9 9.9 + - - -
19D TYR 3.2 0.6 + - - -
21D GLY* 1.3 72.5 - - - +
23D PHE* 1.3 59.5 + - - +
24D ALA 3.1 6.5 + - - -
25D PHE 4.1 0.9 + - - -
26D LEU* 3.8 26.1 + - - +
29D LEU* 4.3 2.8 - - - +
30D TRP* 3.3 44.6 - - - -
67D TRP* 5.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D TYR* 3.1 33.3 + + + +
20D LEU* 3.3 14.3 + - + +
22D GLY* 1.3 75.2 - - - +
24D ALA* 1.3 56.9 - - - +
25D PHE 3.9 1.7 + - - -
30D TRP* 3.6 21.9 - + - -
67D TRP* 5.7 2.8 + - - -
----------------------------------------------------------
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