Contacts of the helix formed by residues 2 - 20 (chain D) in PDB entry 4XYN
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN 4.8 1.8 - - - -
40C GLU* 2.5 54.7 + - - -
43C HIS* 4.6 1.4 + - - -
1D MET* 1.3 72.3 - - - +
3D GLU* 1.3 59.5 + - - +
4D LEU 3.5 3.9 + - - -
5D GLU* 2.9 24.3 + - - -
6D LYS* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 3 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA* 4.3 18.8 - - + +
14C VAL* 6.0 4.0 - - + -
2D SER* 1.3 75.8 - - - +
4D LEU* 1.3 56.9 + - - +
6D LYS* 2.9 35.7 + - - +
7D ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 5.7 1.3 - - - -
11C LEU* 3.4 28.5 - - + -
14C VAL* 4.0 28.8 - - + +
36C LEU* 3.9 22.2 - - + -
40C GLU* 4.0 9.0 - - + +
41C LEU* 3.9 33.4 - - + -
74C PHE* 4.4 6.7 - - + -
78C VAL* 4.7 4.5 - - + -
2D SER* 3.1 9.6 + - - +
3D GLU* 1.3 75.8 - - - +
5D GLU* 1.3 66.8 + - - +
7D ALA* 3.1 4.8 + - - +
8D MET* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU 3.4 15.5 - - - +
41C LEU* 3.1 23.2 - - + +
43C HIS* 2.9 53.3 + - - +
44C PHE* 3.5 19.5 + - + -
1D MET* 3.3 19.2 - - + +
2D SER* 2.9 29.8 + - - +
4D LEU* 1.3 75.8 - - - +
6D LYS* 1.3 59.1 + - - +
8D MET* 3.0 7.1 + - - +
9D VAL* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.6 36.8 + - + -
2D SER 2.9 21.6 + - - +
3D GLU* 2.9 35.0 + - - +
5D GLU* 1.3 75.5 - - - +
7D ALA* 1.3 58.3 + - - +
9D VAL* 3.1 6.4 + - - +
10D ALA* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 3.6 37.2 - - - +
10C ALA* 4.1 6.3 - - + -
11C LEU* 4.0 14.4 - - + -
3D GLU 2.9 20.0 + - - +
4D LEU* 3.1 6.7 + - - +
6D LYS* 1.3 77.6 - - - +
8D MET* 1.3 56.4 + - - +
10D ALA* 3.3 4.9 + - - +
11D LEU* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 5.1 1.3 - - + -
41C LEU* 3.6 36.6 - - + -
44C PHE* 3.8 24.7 - - + -
77C PHE* 6.3 0.4 - - + -
78C VAL* 4.3 18.4 - - + -
81C VAL* 3.8 24.0 - - + -
82C THR* 3.2 32.0 - - + +
4D LEU* 2.9 34.0 + - + +
5D GLU 3.0 7.2 + - - +
7D ALA* 1.3 77.9 - - - +
9D VAL* 1.3 61.8 + - - +
11D LEU* 3.2 7.4 + - - +
12D ILE* 3.2 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 4.2 12.8 - - + -
85C CYS* 5.2 2.7 - - - -
89C PHE* 5.0 21.8 - - + -
1D MET* 4.0 18.8 - - + -
5D GLU 2.9 18.2 + - - +
6D LYS* 3.1 8.2 + - - +
8D MET* 1.3 76.4 - - - +
10D ALA* 1.3 57.1 + - - +
12D ILE* 3.4 8.1 + - + +
13D ASP* 2.8 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 4.5 22.5 - - + +
4C LEU* 5.6 1.6 - - - -
7C ALA* 3.8 18.4 - - + -
6D LYS 2.9 13.2 + - - +
7D ALA* 3.4 10.5 - - - +
9D VAL* 1.3 78.6 - - - +
11D LEU* 1.3 57.2 + - - +
13D ASP* 3.6 7.8 - - - +
14D VAL* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.4 30.5 - - + +
7C ALA* 4.4 9.9 - - + -
8C MET* 5.0 2.9 - - + -
11C LEU* 4.6 15.3 - - + -
78C VAL* 4.9 2.5 - - + -
82C THR* 4.3 11.2 - - + +
7D ALA 3.0 20.3 + - - +
8D MET* 3.2 7.8 + - + +
10D ALA* 1.3 71.7 - - - +
12D ILE* 1.3 65.8 + - - +
14D VAL* 3.3 8.1 - - - +
15D PHE* 3.2 24.3 + - - +
71D PHE* 4.1 2.2 - - - -
74D PHE* 3.8 4.8 - - + -
75D MET* 3.7 39.3 - - + -
78D VAL* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C THR* 4.0 7.6 - - + +
85C CYS* 3.5 31.9 - - - -
86C HIS* 4.0 21.3 - - + +
89C PHE* 3.9 22.2 - - + -
8D MET 3.2 16.7 + - - +
9D VAL* 3.7 9.2 - - + +
11D LEU* 1.3 76.9 - - - +
13D ASP* 1.3 64.1 + - - +
15D PHE* 3.5 2.8 + - - +
16D HIS* 3.0 49.1 + - + +
71D PHE* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 6.0 3.5 - - - +
9D VAL* 2.8 22.2 + - + +
10D ALA* 3.6 8.6 - - - +
11D LEU 3.2 0.2 - - - -
12D ILE* 1.3 79.5 - - - +
14D VAL* 1.3 63.5 + - - +
16D HIS* 3.1 12.5 + - - +
17D GLN* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 6.0 3.4 - - + -
4C LEU* 4.1 23.1 - - + +
10D ALA 2.9 15.5 + - - +
11D LEU* 3.3 15.9 - - - +
13D ASP* 1.3 75.8 - - - +
15D PHE* 1.3 66.9 + - - +
17D GLN* 3.4 12.2 + - - +
18D TYR* 3.2 40.6 + - + +
36D LEU* 4.1 7.0 - - + +
40D GLU* 3.6 31.0 - - + -
74D PHE* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C HIS* 4.2 7.9 - + - -
11D LEU 3.2 13.4 + - - +
12D ILE 3.7 3.6 - - - +
13D ASP 3.1 0.4 - - - -
14D VAL* 1.3 84.2 - - - +
16D HIS* 1.3 68.0 + + - +
18D TYR* 3.7 0.9 - - - +
19D SER* 2.7 49.8 + - - -
26D HIS* 3.3 24.5 - - - -
28D LEU* 3.3 32.7 - - + +
36D LEU* 4.7 3.4 - - - -
69D CYS 3.7 3.6 - - - -
70D ASP 3.5 17.9 - - - -
71D PHE* 3.3 41.3 - + + -
74D PHE* 3.5 28.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C HIS* 4.1 22.9 - + - -
89C PHE* 4.7 19.2 + + + +
90C GLU* 5.5 4.0 - - - -
12D ILE* 3.0 45.6 + - + +
13D ASP* 3.1 11.9 + - - +
15D PHE* 1.3 84.0 - + - +
17D GLN* 1.3 65.5 + - + +
18D TYR 2.9 1.6 + - - -
19D SER* 3.3 6.9 + - - -
20D GLY* 3.2 21.1 + - - -
25D LYS 5.7 1.0 + - - -
26D HIS* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASP* 2.9 46.3 + - - +
14D VAL* 3.8 14.4 - - - +
15D PHE 3.3 0.4 - - - -
16D HIS* 1.3 76.8 - - + +
18D TYR* 1.3 70.7 + - + +
20D GLY 5.2 0.2 - - - -
21D ARG* 3.4 26.1 + - - +
40D GLU* 5.3 1.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
14D VAL* 3.2 31.6 - - + +
15D PHE 3.3 0.8 + - - -
16D HIS 3.0 0.2 - - - -
17D GLN* 1.3 90.8 - - + +
19D SER* 1.3 63.3 + - - +
20D GLY 3.3 3.0 + - - -
21D ARG* 3.5 45.3 + - - +
28D LEU* 3.9 8.5 - - + -
32D GLU* 3.2 30.1 - - - +
35D GLU* 3.5 7.6 - - + -
36D LEU* 3.3 53.4 - - + -
39D ASN* 3.6 15.0 - - - +
40D GLU* 2.3 35.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 2.7 50.3 + - - -
16D HIS* 3.3 13.3 + - - -
18D TYR* 1.3 72.7 - - - +
20D GLY* 1.3 59.4 + - - +
24D ASP 3.0 9.4 - - - +
25D LYS* 3.2 16.3 + - - -
27D LYS 3.7 17.0 - - - -
28D LEU* 3.7 10.7 - - - +
501D CA 2.2 27.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D HIS 3.2 14.0 + - - -
17D GLN 5.2 0.7 - - - -
19D SER* 1.3 78.4 + - - +
21D ARG* 1.3 66.2 + - - +
22D GLU 3.5 0.8 + - - -
25D LYS* 3.4 44.5 - - - +
----------------------------------------------------------
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