Contacts of the helix formed by residues 8 - 23 (chain X) in PDB entry 1XDM
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 THR 8 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X ALA 5.7 0.2 - - - +
7X LEU* 1.3 81.2 - - - +
9X GLN* 1.3 69.0 + - - +
10X GLU* 4.5 7.2 + - - +
11X GLN* 2.7 48.0 + - - +
12X LYS* 3.1 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 9 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364W SO4 3.6 21.7 + - - -
8X THR* 1.3 69.7 - - - +
10X GLU* 1.3 62.2 + - - +
12X LYS* 2.6 59.3 + - - +
13X LYS* 3.4 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X THR* 3.2 7.4 + - - +
9X GLN* 1.3 79.5 - - - +
11X GLN* 1.3 59.3 + - - +
12X LYS 3.1 0.4 - - - -
13X LYS* 3.2 32.6 + - + +
14X GLU* 3.6 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 11 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X ALA 5.2 0.2 - - - +
7X LEU* 3.4 19.7 - - + +
8X THR* 2.7 40.3 + - - +
10X GLU* 1.3 74.9 + - - +
12X LYS* 1.3 60.1 + - - -
14X GLU* 3.8 11.3 + - + +
15X LEU* 3.4 25.2 + - + +
178X GLN 2.8 27.0 + - - +
179X GLN* 2.9 23.5 + - - +
181X GLY* 4.1 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364W SO4 3.3 25.4 + - - +
7X LEU* 4.4 22.5 + - + -
8X THR 3.1 10.6 + - - +
9X GLN* 2.6 52.8 + - - +
11X GLN* 1.3 75.3 - - - +
13X LYS* 1.3 58.1 + - - +
14X GLU 3.1 0.2 - - - -
15X LEU* 3.0 5.2 + - - +
16X SER* 2.5 39.8 + - - -
222X TYR* 3.4 51.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X GLN 3.4 4.6 + - - +
10X GLU* 3.2 23.5 + - + +
12X LYS* 1.3 79.6 - - - +
14X GLU* 1.3 52.4 + - - +
16X SER* 3.5 5.8 - - - -
17X GLU* 2.6 70.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X GLU 3.6 6.5 + - - +
11X GLN* 4.0 13.7 - - + +
12X LYS 3.1 0.6 - - - -
13X LYS* 1.3 77.0 - - - +
15X LEU* 1.3 57.4 + - + +
17X GLU* 4.3 5.6 - - - -
18X ILE* 2.6 51.2 + - + +
138X LYS* 3.3 33.1 + - - -
181X GLY* 3.4 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X LEU* 3.8 15.3 - - + -
11X GLN* 3.4 14.0 + - + +
12X LYS 3.0 7.3 + - - +
14X GLU* 1.3 78.9 - - + +
16X SER* 1.3 57.0 + - - +
18X ILE* 4.5 0.2 - - - -
19X ALA* 3.0 27.5 + - - +
178X GLN* 3.2 47.6 - - - +
181X GLY* 3.8 18.8 - - - +
182X LEU 2.8 36.8 - - - +
183X VAL* 3.3 17.6 - - + +
222X TYR* 4.4 4.5 - - + -
225X GLY* 3.8 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X LYS 2.5 23.8 + - - -
13X LYS* 3.5 6.5 - - - -
15X LEU* 1.3 68.7 - - - +
17X GLU* 1.3 67.7 + - - +
18X ILE 2.9 2.8 + - - -
19X ALA* 3.0 4.0 + - - +
20X GLN* 3.0 41.1 + - - +
222X TYR* 4.2 13.7 + - - -
224X GLU* 4.1 18.2 + - - +
225X GLY* 4.3 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13X LYS* 2.6 65.6 + - + +
14X GLU* 3.8 5.6 - - - +
16X SER* 1.3 73.6 - - - +
18X ILE* 1.3 51.0 + - + +
20X GLN* 4.4 9.8 - - - +
21X SER* 2.5 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X GLU* 2.6 48.9 + - + +
15X LEU 3.7 3.6 - - - +
17X GLU* 1.3 74.1 - - + +
19X ALA* 1.3 62.1 + - - +
21X SER* 2.6 19.6 + - - +
22X ILE* 2.9 29.6 - - + +
103X VAL* 4.9 6.3 - - + -
138X LYS* 3.5 27.8 - - - +
143X ASP* 3.6 41.3 - - + +
144X PHE* 4.5 0.4 - - + -
181X GLY 4.1 3.6 - - - +
183X VAL* 3.7 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15X LEU 3.0 17.2 + - - +
16X SER 3.8 2.5 - - - +
18X ILE* 1.3 76.6 - - - +
20X GLN* 1.3 60.8 + - - +
22X ILE* 3.6 13.6 - - - +
23X VAL* 3.5 18.9 - - - +
183X VAL* 3.5 14.6 - - + -
225X GLY* 4.2 5.2 - - - -
226X THR 3.4 25.4 - - - +
227X LEU* 3.6 11.4 - - + +
265X PRO* 4.1 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16X SER* 3.0 31.8 + - - +
17X GLU* 4.4 7.7 - - - +
19X ALA* 1.3 73.7 - - - +
21X SER* 1.3 58.3 - - - +
22X ILE 2.9 5.2 - - - -
23X VAL* 2.9 37.5 + - - +
24X ALA* 3.1 5.7 + - - -
224X GLU 5.7 0.9 - - - +
265X PRO* 3.9 24.5 - - + +
296X LYS* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X GLU 2.5 25.0 + - - -
18X ILE* 2.6 19.6 + - - -
20X GLN* 1.3 76.6 - - - +
22X ILE* 1.3 60.7 + - - +
24X ALA* 4.3 9.9 - - - +
27X LYS* 4.0 17.7 + - - -
74X GLY 3.8 8.4 - - - +
103X VAL* 5.6 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18X ILE* 2.9 26.7 - - + +
19X ALA* 3.6 10.1 - - - +
20X GLN 2.9 1.0 - - - -
21X SER* 1.3 81.1 - - - +
23X VAL* 1.3 64.3 + - + +
24X ALA 3.7 0.9 - - - -
27X LYS* 3.7 8.7 - - - +
28X GLY 3.8 2.1 - - - +
29X ILE* 3.2 37.2 - - + -
74X GLY* 3.7 20.9 - - - -
75X GLY* 4.2 7.4 - - - -
103X VAL* 4.0 14.1 - - + -
144X PHE* 3.3 36.8 - - + -
183X VAL* 5.4 0.7 - - + -
227X LEU* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X ALA 3.5 17.9 - - - +
20X GLN* 2.9 11.2 - - - +
22X ILE* 1.3 81.0 - - + +
24X ALA* 1.3 58.5 - - - +
26X GLY* 5.0 0.9 - - - -
27X LYS 3.0 26.9 - - - +
28X GLY* 4.6 0.9 - - - -
227X LEU* 4.1 16.8 - - + -
265X PRO 4.5 4.9 - - - +
266X GLY* 4.4 10.8 - - - -
268X CYS* 3.4 17.3 - - - -
296X LYS* 3.6 27.2 - - + +
298X SER* 3.3 24.2 - - - +
----------------------------------------------------------
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