Contacts of the helix formed by residues 31 - 45 (chain A) in PDB entry 1XJB
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 LYS 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 5.6 2.4 - - - -
25A ALA* 4.3 16.4 + - - +
27A ALA* 5.1 10.3 - - - +
29A VAL 3.4 9.8 + - - +
30A PRO* 1.3 70.7 - - - +
32A SER* 1.3 64.7 + - - +
34A ALA* 3.1 17.9 + - + +
55A TYR 3.5 16.5 + - - +
56A ASN* 3.3 44.4 - - - +
57A ASN* 4.5 7.4 - - + -
60A GLN* 3.3 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 3.1 15.9 - - - +
31A LYS* 1.3 79.2 - - - +
33A LYS* 1.3 68.2 + - - +
35A LEU* 3.0 26.1 + - - +
36A GLU* 3.8 3.5 + - - +
60A GLN* 4.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.9 12.8 - - + -
30A PRO* 3.1 32.8 + - + +
32A SER* 1.3 80.8 + - - +
34A ALA* 1.3 56.5 + - - +
35A LEU 3.2 0.2 - - - -
36A GLU* 3.6 7.5 + - + +
37A ALA* 3.1 28.4 + - - +
272A TYR* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 4.8 0.4 - - - +
30A PRO 4.4 0.2 + - - -
31A LYS* 3.1 16.2 + - + +
32A SER 3.1 0.2 + - - -
33A LYS* 1.3 76.2 - - - +
35A LEU* 1.3 65.1 + - - +
37A ALA* 4.3 0.2 - - - -
38A VAL* 3.0 31.0 + - + +
57A ASN* 4.2 20.2 - - + +
60A GLN* 4.1 12.6 - - + -
61A VAL* 4.4 5.8 - - + -
272A TYR* 3.5 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 3.0 15.3 + - - +
34A ALA* 1.3 80.6 - - - +
36A GLU* 1.3 63.6 + - + +
39A LYS* 3.2 44.0 + - + +
60A GLN* 3.6 35.6 - - + +
63A LEU* 4.0 19.5 - - + -
64A ALA* 3.6 22.7 - - - +
67A SER* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER 3.8 3.2 + - - +
33A LYS* 3.6 9.9 + - + +
34A ALA 3.4 0.4 - - - -
35A LEU* 1.3 80.2 - - + +
37A ALA* 1.3 64.5 + - - +
39A LYS* 3.4 26.2 + - - +
40A LEU* 3.0 53.0 + - + +
43A GLU* 5.1 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.0 9.9 - - + -
33A LYS 3.1 19.3 + - - +
34A ALA 3.7 3.8 - - - +
36A GLU* 1.3 78.1 - - - +
38A VAL* 1.3 57.5 + - - +
40A LEU* 3.0 7.5 + - - +
41A ALA* 2.8 27.9 + - - +
272A TYR* 3.6 42.0 - - + +
277A ILE* 3.8 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.9 11.2 - - + -
23A THR* 3.7 31.0 - - + -
34A ALA* 3.0 19.2 + - - +
37A ALA* 1.3 74.8 - - - +
39A LYS* 1.3 63.5 + - - +
41A ALA* 3.2 2.9 + - - +
42A ILE* 2.9 26.8 + - + +
49A ILE* 3.4 31.6 - - + -
61A VAL* 4.1 15.7 - - + +
64A ALA* 3.4 25.1 - - + -
65A ILE* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.2 34.4 + - + +
36A GLU* 3.5 26.5 + - - +
38A VAL* 1.3 77.4 - - - +
40A LEU* 1.3 62.3 + - - +
42A ILE* 3.4 0.7 + - - +
43A GLU* 3.0 34.1 + - - +
64A ALA* 3.7 20.9 - - + +
67A SER* 4.0 26.2 + - - +
68A LYS* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 3.0 50.0 + - + +
37A ALA* 3.0 5.1 + - - +
39A LYS* 1.3 77.0 - - - +
41A ALA* 1.3 52.8 + - - +
43A GLU* 3.2 21.9 + - + +
44A ALA* 2.7 36.6 + - - +
272A TYR 5.4 3.1 - - - +
274A GLU* 3.5 53.2 - - + +
277A ILE* 3.9 17.9 - - + +
278A ARG* 5.6 1.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.5 42.0 - - + -
37A ALA 2.8 13.2 + - - +
38A VAL* 3.4 9.2 - - + +
39A LYS 3.2 0.2 - - - -
40A LEU* 1.3 77.5 - - - +
42A ILE* 1.3 60.5 + - + +
44A ALA 3.2 1.7 + - - -
45A GLY 3.2 5.4 + - - -
46A PHE* 2.9 37.0 + - + +
49A ILE* 5.8 0.7 - - + -
277A ILE* 3.7 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 2.9 27.2 + - + +
39A LYS 3.8 3.8 - - - +
41A ALA* 1.3 71.7 - - - +
43A GLU* 1.3 67.2 + - - +
45A GLY* 3.0 14.0 + - - -
46A PHE* 3.8 11.7 + - + +
47A HIS* 5.8 2.9 + - + +
49A ILE* 3.8 29.4 - - + -
64A ALA 4.4 0.4 - - - +
65A ILE* 4.2 14.4 - - + +
68A LYS* 3.9 38.8 - - + -
73A SER* 5.4 2.7 - - - -
74A VAL* 4.2 20.4 - - + -
79A ILE* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 5.1 2.1 - - - +
39A LYS* 3.0 33.5 + - - +
40A LEU* 3.5 25.1 + - + +
42A ILE* 1.3 78.1 - - - +
44A ALA* 1.3 60.7 + - - +
45A GLY* 3.4 0.9 + - - -
68A LYS* 3.0 33.7 + - + +
73A SER* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU 2.7 20.5 + - - +
41A ALA 3.6 5.8 - - - +
42A ILE 3.2 0.2 - - - -
43A GLU* 1.3 73.4 - - - +
45A GLY* 1.3 56.8 + - - +
277A ILE* 3.9 20.4 - - + +
278A ARG* 4.1 26.5 - - + -
281A VAL* 3.6 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE 3.0 11.5 + - - -
43A GLU 3.2 1.0 - - - -
44A ALA* 1.3 80.7 - - - +
46A PHE* 1.4 66.4 + - - +
47A HIS* 3.2 22.9 - - - -
281A VAL* 4.4 7.4 - - - -
1002A ACT 3.3 14.6 - - - +
----------------------------------------------------------
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