Contacts of the helix formed by residues 9 - 24 (chain D) in PDB entry 1XFB
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 9 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PRO* 6.0 0.7 - - - -
8D LEU* 1.3 76.4 - - - +
10D ALA* 1.3 64.4 + - - +
11D GLU* 3.3 13.9 + - - +
12D GLN* 2.6 41.5 + - - +
13D LYS* 3.0 23.0 + - - +
68I ASP* 6.1 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
9D SER* 1.3 74.3 - - - +
11D GLU* 1.3 70.2 + - + +
13D LYS* 3.4 12.5 + - - +
14D LYS* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER* 3.6 13.2 - - - +
10D ALA* 1.3 79.5 - - + +
12D GLN* 1.3 64.4 + - + +
14D LYS* 3.1 10.6 - - - +
15D GLU* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ALA 4.2 2.4 - - - +
8D LEU* 3.3 26.7 - - + +
9D SER* 2.6 41.9 + - - +
11D GLU* 1.3 74.5 - - + +
13D LYS* 1.3 65.5 + - - +
14D LYS 3.2 0.2 + - - -
15D GLU* 3.2 13.5 + - - +
16D LEU* 3.0 29.5 + - + +
179D GLN 5.4 1.3 + - - +
180D GLN* 4.8 10.9 + - - +
182D GLY* 6.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 4.6 14.9 - - - +
8D LEU* 3.8 33.0 - - + +
9D SER 3.0 19.6 + - - +
10D ALA* 3.7 9.9 - - - +
12D GLN* 1.3 76.3 - - - +
14D LYS* 1.3 64.0 + - - +
16D LEU* 3.3 1.2 + - - -
17D SER* 2.9 21.8 + - - -
223D TYR* 3.3 54.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA 3.1 13.4 + - - +
11D GLU* 3.1 13.5 - - - +
13D LYS* 1.3 76.7 - - - +
15D GLU* 1.3 65.3 + - - +
17D SER* 3.0 12.3 + - - -
18D ASP* 2.8 56.3 + - - +
223D TYR* 5.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLU 3.0 8.6 + - - +
12D GLN* 3.2 13.9 + - - +
14D LYS* 1.3 79.0 - - - +
16D LEU* 1.3 63.1 + - + +
18D ASP* 3.8 8.0 - - - +
19D ILE* 2.9 44.7 + - + +
139D LYS* 2.9 31.3 + - - -
182D GLY* 4.1 15.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
8D LEU* 3.5 33.7 - - + -
12D GLN* 3.0 16.6 + - + +
13D LYS 3.6 4.9 - - - +
15D GLU* 1.3 77.1 - - + +
17D SER* 1.3 64.9 + - - +
19D ILE* 3.2 3.0 + - + -
20D ALA* 2.9 20.8 + - - +
179D GLN* 3.8 29.4 - - + +
182D GLY* 3.7 11.4 - - - +
183D ILE 3.6 42.8 - - - +
184D VAL* 3.2 18.5 - - + +
223D TYR* 4.3 2.7 - - + -
226D GLY* 4.0 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LYS 2.9 17.2 + - - -
14D LYS* 3.5 13.2 + - - -
16D LEU* 1.3 75.7 - - - +
18D ASP* 1.3 65.4 + - - +
20D ALA* 3.2 2.4 + - - +
21D LEU* 3.0 41.0 + - - +
223D TYR* 4.2 10.8 - - - -
225D GLU* 3.5 27.0 + - - +
226D GLY* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 2.8 49.2 + - - +
15D GLU* 3.8 7.0 + - - +
17D SER* 1.3 77.2 + - - +
19D ILE* 1.3 66.0 + - + +
21D LEU* 2.9 13.3 + - - +
22D ARG* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLU* 2.9 28.2 + - + +
16D LEU* 3.5 4.5 - - - +
18D ASP* 1.3 77.9 - - + +
20D ALA* 1.3 63.7 + - - +
22D ARG* 3.3 16.3 + - - +
23D ILE* 3.1 39.8 + - + +
104D VAL* 4.2 5.4 - - + -
139D LYS* 3.7 20.4 - - - +
144D ASP* 3.5 50.9 - - + +
182D GLY 4.1 3.6 - - - +
184D VAL* 3.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU 2.9 14.4 + - - +
17D SER 3.4 8.5 - - - +
19D ILE* 1.3 76.5 - - - +
21D LEU* 1.3 62.8 + - - +
23D ILE* 3.2 18.0 + - - +
24D VAL* 3.2 17.7 + - - +
184D VAL* 3.9 21.7 - - + +
225D GLU 4.1 6.3 - - - +
226D GLY* 4.6 0.9 - - - -
227D THR 4.4 2.0 - - - +
228D LEU* 4.5 4.1 - - + +
266D PRO* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D SER* 3.0 33.6 + - - +
18D ASP* 2.9 11.0 + - - +
20D ALA* 1.3 71.8 - - - +
22D ARG* 1.3 65.5 + - + +
24D VAL* 3.4 7.8 + - + +
25D ALA* 2.9 25.3 + - - +
225D GLU 5.8 0.2 - - - +
266D PRO* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ASP* 2.9 23.5 + - + +
19D ILE* 3.7 18.3 - - - +
20D ALA 3.3 0.2 - - - -
21D LEU* 1.3 77.8 - - + +
23D ILE* 1.3 65.3 + - - +
25D ALA* 3.3 17.9 + - - +
28D LYS* 4.2 6.6 - - - +
75D GLY* 4.3 3.1 - - - +
102D GLY* 3.0 32.5 + - - -
103D ILE 4.6 1.6 + - - -
104D VAL* 3.8 28.2 - - + +
144D ASP* 5.2 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 3.1 23.3 - - + +
20D ALA* 3.2 8.2 + - - +
22D ARG* 1.3 79.0 - - - +
24D VAL* 1.3 59.5 + - + +
25D ALA 3.4 1.7 + - - -
28D LYS* 3.9 9.4 - - - +
29D GLY* 4.5 2.1 - - - +
30D ILE* 3.6 36.8 - - + -
75D GLY* 3.6 20.1 + - - -
76D GLY* 4.4 7.6 - - - +
104D VAL* 3.7 18.8 - - + -
145D PHE* 3.6 42.6 - - + -
184D VAL* 5.2 1.3 - - + -
228D LEU* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ALA 3.4 13.9 - - - +
21D LEU* 4.0 12.8 - - + +
23D ILE* 1.3 76.9 - - + +
25D ALA* 1.3 69.8 + - - +
26D PRO* 3.5 2.3 - - - +
28D LYS 4.5 5.6 - - - -
30D ILE* 6.0 0.4 - - + -
228D LEU* 3.7 24.9 - - + -
266D PRO* 4.2 17.0 - - + +
267D GLY* 4.2 6.3 - - - -
268D VAL 5.0 0.4 - - - +
269D THR* 3.8 23.1 - - + -
297D ALA* 3.7 30.9 - - + +
299D THR* 4.3 11.3 - - + +
----------------------------------------------------------
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