Contacts of the helix formed by residues 37 - 49 (chain B) in PDB entry 2XQL
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 TYR 37 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.7 23.1 - + + -
26A PRO* 4.7 4.9 - - + -
29A ARG* 3.9 20.0 - - - -
30A VAL* 4.7 7.5 - - + +
33A LEU* 3.7 24.7 - - + +
55A LEU* 5.0 2.8 - - + +
36B SER* 1.3 88.0 - - - +
38B SER* 1.3 66.6 + - - +
39B ILE 3.0 3.1 - - - -
40B TYR* 2.7 32.6 + + - -
41B VAL* 2.9 19.1 + - + -
63B ASN* 2.7 21.4 + - - +
66B VAL* 3.4 38.5 - - + +
67B ASN* 3.4 28.1 + - - -
70B PHE* 4.6 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER 3.6 10.9 + - - -
37B TYR* 1.3 75.7 - - - +
39B ILE* 1.3 66.9 + - - +
41B VAL* 3.4 11.8 - - - +
42B TYR* 3.0 23.9 + - - +
59B MET* 3.5 18.4 - - - +
63B ASN* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 6.2 0.7 - - - +
36B SER 5.3 2.0 - - - +
37B TYR 2.8 4.4 + - - -
38B SER* 1.3 77.0 - - - +
40B TYR* 1.3 79.2 + - + +
42B TYR* 3.1 4.6 + - - +
43B LYS* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.0 24.5 - - - +
25A PHE* 3.8 23.1 - - + -
26A PRO* 3.4 40.7 - - + +
29A ARG* 3.7 28.2 + - - -
36B SER 4.2 1.8 - - - -
37B TYR* 2.7 25.1 + + - +
39B ILE* 1.3 88.0 - - + +
41B VAL* 1.3 54.6 + - - +
43B LYS* 2.8 18.4 + - - +
44B VAL* 2.7 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.2 5.3 - - + -
59A THR* 4.2 12.1 - - + -
63A LEU* 3.5 21.9 - - + +
37B TYR* 2.9 28.1 + - + +
38B SER* 3.4 8.5 - - - +
40B TYR* 1.3 73.0 - - - +
42B TYR* 1.3 56.0 + - - +
44B VAL* 3.4 7.7 + - - -
45B LEU* 2.9 26.4 + - + +
54B ILE* 5.1 1.1 - - + -
59B MET* 3.2 33.7 - - + -
62B MET* 4.0 27.1 - - + -
63B ASN* 4.8 1.8 - - - +
66B VAL* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER 3.0 20.5 + - - +
39B ILE* 3.3 4.7 - - - +
41B VAL* 1.3 75.1 - - - +
43B LYS* 1.3 69.8 + - + +
45B LEU* 3.0 22.7 + - + +
46B LYS* 3.0 24.8 + - + +
52B THR 5.9 0.4 - - - -
53B GLY* 5.0 7.3 - - - -
54B ILE* 4.2 30.7 - - + -
59B MET* 3.8 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.8 35.5 + - + +
39B ILE* 2.9 43.6 + - + +
40B TYR* 2.8 17.9 + - - +
42B TYR* 1.3 77.9 - - + +
44B VAL* 1.3 60.7 + - - +
46B LYS* 3.1 31.5 - - + +
47B GLN* 3.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 4.1 13.2 - - + -
25A PHE* 3.5 30.1 - - + -
56A GLU* 4.1 10.5 - - + +
59A THR* 4.3 5.4 - - + -
60A ALA* 3.7 40.4 - - + +
63A LEU* 4.4 2.2 - - + -
40B TYR 2.7 23.5 + - - +
41B VAL* 3.7 6.3 - - - +
43B LYS* 1.3 70.5 - - - +
45B LEU* 1.3 65.3 + - - +
47B GLN* 3.1 18.9 + - - +
48B VAL* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.8 21.7 - - + +
78A ILE* 4.2 12.3 - - + -
41B VAL* 2.9 14.8 + - + +
42B TYR* 3.0 19.7 + - + +
44B VAL* 1.3 77.4 - - - +
46B LYS* 1.3 56.1 + - - +
48B VAL* 2.9 17.3 + - + +
49B HIS* 2.6 45.9 + - + +
52B THR 3.4 26.5 - - - +
53B GLY* 4.1 3.8 - - - +
54B ILE* 3.7 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 3.0 22.1 + - + +
43B LYS* 3.1 27.6 - - + +
45B LEU* 1.3 76.2 - - - +
47B GLN* 1.3 68.3 + - + +
49B HIS 3.7 9.0 - - - -
50B PRO* 3.0 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.4 30.0 + - - +
56A GLU* 3.9 11.4 + - - +
60A ALA* 5.5 5.5 - - - +
43B LYS 3.6 8.1 - - - +
44B VAL* 3.1 21.6 + - - +
45B LEU 3.1 0.2 - - - -
46B LYS* 1.3 84.6 - - + +
48B VAL* 1.3 56.0 + - - +
50B PRO* 4.7 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 4.3 13.7 - - + +
63A LEU* 4.5 5.4 - - + +
64A GLU* 3.5 54.2 - - + +
44B VAL 3.1 11.4 + - - +
45B LEU* 2.9 27.8 + - + +
47B GLN* 1.3 80.8 - - + +
49B HIS* 1.3 82.4 + - + +
50B PRO* 3.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 3.8 26.2 - - - -
67A GLY* 3.5 25.6 - - - -
68A ASN* 2.8 32.1 + - - -
71A ARG* 3.4 29.8 + - - +
45B LEU* 2.6 24.7 + - + +
46B LYS* 3.7 3.8 - - - -
48B VAL* 1.3 103.1 + - + +
50B PRO* 1.3 60.0 - - - +
51B ASP* 2.9 12.8 + - - -
52B THR* 3.4 30.6 + - - +
----------------------------------------------------------
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