Contacts of the helix formed by residues 16 - 32 (chain D) in PDB entry 2XLR
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 GLY 16 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLY 3.6 2.6 - - - -
15D ALA* 1.3 78.3 - - - +
17D PRO* 1.3 73.8 - - - +
18D SER 3.3 0.2 - - - -
19D GLY 3.1 2.2 + - - +
20D MET* 2.9 29.8 + - - +
49D GLY 3.7 0.9 - - - -
50D GLY* 3.5 20.2 - - - -
166D CYS 5.1 0.2 + - - -
500D FAD 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLY* 1.3 83.1 - - - +
18D SER* 1.3 57.8 + - - +
20D MET* 3.4 10.8 + - + +
21D ALA* 2.8 30.8 + - - +
49D GLY* 3.6 16.6 - - - +
52D TRP* 3.9 8.5 - - + -
112D ILE* 4.4 9.2 - - + -
115D ARG* 5.5 0.5 + - - -
327D PHE* 3.8 22.7 - - + -
330D PHE* 3.9 17.4 - - + +
500D FAD 3.4 37.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PRO* 1.3 73.1 - - - +
19D GLY* 1.3 59.3 + - - +
21D ALA* 3.3 3.8 + - - +
22D GLN* 3.0 26.3 + - - +
166D CYS* 3.8 16.3 - - - -
318D ILE* 3.5 35.8 + - - +
330D PHE* 3.5 20.3 - - - -
500D FAD 2.6 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 4.0 5.3 - - - +
14D GLY 3.4 24.7 + - - -
15D ALA* 4.7 1.6 - - - -
16D GLY 3.1 6.0 + - - +
18D SER* 1.3 76.4 - - - +
20D MET* 1.3 66.2 + - - +
22D GLN* 3.1 3.7 + - - +
23D LEU* 3.0 30.2 + - - +
41D CYS* 5.5 0.2 - - - -
166D CYS* 3.7 15.2 - - - +
500D FAD 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA* 3.8 16.1 - - + +
16D GLY 2.9 25.4 + - - +
17D PRO* 3.5 9.9 - - + +
19D GLY* 1.3 74.5 - - - +
21D ALA* 1.3 58.5 + - - +
23D LEU* 3.2 10.5 + - + +
24D ARG* 2.9 32.1 + - - +
48D TRP* 3.7 34.8 - - + -
49D GLY* 4.2 8.3 - - - +
112D ILE* 4.1 23.3 - - + +
113D LYS* 4.4 3.6 - - + -
115D ARG* 4.8 2.9 - - - +
116D VAL* 3.2 48.5 - - + +
125D ILE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PRO 2.8 18.3 + - - +
18D SER 3.4 7.0 - - - +
20D MET* 1.3 75.4 - - - +
22D GLN* 1.3 60.8 + - - +
24D ARG* 3.3 1.2 + - - +
25D ALA* 2.9 24.9 + - - +
115D ARG* 4.0 13.6 - - - +
330D PHE* 4.1 15.7 - - + +
331D ASP* 3.5 20.2 - - - +
334D ALA* 3.7 13.6 - - + +
335D TRP* 4.1 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 3.6 28.3 - - + -
18D SER 3.0 13.6 + - - +
19D GLY* 3.1 10.7 + - - +
21D ALA* 1.3 76.9 - - - +
23D LEU* 1.3 62.4 + - - +
25D ALA* 4.1 2.6 - - - +
26D PHE* 3.3 40.9 + - + -
164D VAL* 3.6 23.9 - - + +
166D CYS* 4.8 3.6 - - - -
318D ILE* 3.8 3.0 - - + +
334D ALA* 3.2 38.9 + - + +
337D ALA* 3.6 15.7 - - - +
338D ARG 4.0 4.4 - - - +
341D ILE* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 3.7 22.0 - - + -
15D ALA* 6.0 0.4 - - + -
19D GLY 3.0 19.4 + - - +
20D MET* 3.6 9.2 - - + +
22D GLN* 1.3 77.0 - - - +
24D ARG* 1.3 57.0 + - - +
26D PHE* 3.2 7.7 + - - +
27D GLN* 3.0 26.9 + - - +
39D LEU* 4.0 17.3 - - + +
41D CYS* 4.3 13.2 - - + -
121D VAL* 3.9 31.3 - - + +
124D TYR* 3.8 24.6 - - + -
125D ILE* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D MET 2.9 17.1 + - - +
21D ALA 3.8 2.0 - - - +
22D GLN 3.3 0.2 - - - -
23D LEU* 1.3 78.1 - - - +
25D ALA* 1.3 62.1 + - - +
27D GLN* 2.9 35.9 + - - +
28D SER* 3.0 34.5 + - - -
88D ASP* 2.8 37.2 + - - +
89D TYR* 5.8 0.2 - - - +
115D ARG* 3.0 53.3 - - - +
116D VAL* 4.9 7.9 - - + -
118D LYS* 6.1 2.6 - - - +
119D ALA* 3.5 18.9 - - + +
121D VAL* 4.5 2.9 - - - -
335D TRP* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA 2.9 16.6 + - - +
22D GLN* 3.6 8.3 - - - +
23D LEU 3.2 0.2 - - - -
24D ARG* 1.3 78.0 - - - +
26D PHE* 1.3 62.2 + - - +
28D SER* 3.5 0.7 + - - -
29D ALA 3.3 7.8 + - - -
334D ALA 3.9 20.2 - - - +
335D TRP* 3.5 32.8 - - + -
338D ARG* 2.7 30.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 4.4 12.1 - - + -
12D ILE* 4.9 1.6 - - + -
22D GLN* 3.3 44.1 + - + -
23D LEU 3.2 7.9 + - - +
25D ALA* 1.3 78.2 - - - +
27D GLN* 1.3 63.4 + - - +
29D ALA 3.3 1.6 + - - -
30D GLN* 3.1 17.8 + - - +
36D ILE* 3.4 25.4 - - + +
37D PRO* 3.5 33.9 - - + -
39D LEU* 3.9 32.8 - - + -
338D ARG* 3.6 29.8 - - + +
341D ILE* 4.1 23.3 - - + -
342D MET* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU 3.0 16.5 + - - +
24D ARG* 2.9 33.6 + - - +
26D PHE* 1.3 72.7 - - - +
28D SER* 1.3 61.7 + - - +
30D GLN* 3.0 17.6 + - - +
31D GLU* 2.8 48.7 + - - +
36D ILE* 5.0 2.9 - - - -
39D LEU* 5.6 0.4 - - - +
119D ALA* 3.5 31.5 + - - +
121D VAL* 3.8 14.8 - - + -
124D TYR* 5.7 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ARG* 3.0 23.9 + - - -
25D ALA 3.6 9.2 - - - -
26D PHE 3.3 0.2 - - - -
27D GLN* 1.3 76.6 + - - +
29D ALA* 1.3 68.1 + - - +
31D GLU* 3.2 7.9 + - - +
32D LYS* 3.1 37.6 + - - +
88D ASP* 5.4 0.3 + - - -
335D TRP* 3.6 24.9 - - - -
338D ARG* 4.3 3.4 - - - -
389D ASP* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA 3.3 10.2 + - - +
26D PHE 3.3 9.8 + - - +
27D GLN 3.2 0.8 - - - -
28D SER* 1.3 78.6 - - - +
30D GLN* 1.3 62.3 + - - +
32D LYS* 3.2 15.7 + - - +
33D GLY 3.4 0.7 + - - -
34D ALA* 3.1 21.9 + - + +
36D ILE* 4.1 11.2 - - + -
338D ARG* 3.9 24.2 - - - +
342D MET* 4.4 2.5 - - - -
344D ARG* 4.3 17.8 + - - +
389D ASP* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE 3.1 8.9 + - - +
27D GLN* 3.0 19.2 + - - +
29D ALA* 1.3 77.1 - - - +
31D GLU* 1.3 66.2 + - - +
32D LYS 3.1 1.6 - - - -
33D GLY* 2.9 14.6 + - - -
34D ALA 3.5 19.7 - - - +
36D ILE* 3.8 29.1 - - + +
124D TYR* 4.5 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 2.8 32.3 + - - +
28D SER* 3.6 11.2 - - - +
30D GLN* 1.3 77.8 + - - +
32D LYS* 1.3 59.5 + - + +
33D GLY* 3.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER* 3.1 22.9 + - - +
29D ALA* 3.7 9.0 - - - +
30D GLN 3.1 1.2 - - - -
31D GLU* 1.3 79.2 - - + +
33D GLY* 1.3 57.5 + - - +
34D ALA* 3.5 2.2 + - - -
389D ASP* 3.9 31.5 + - - +
----------------------------------------------------------
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