Contacts of the helix formed by residues 30 - 42 (chain B) in PDB entry 1XK4
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 30 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 3.4 44.9 - - + -
24B GLY* 3.9 7.6 - - - -
25B ASN* 2.9 24.0 + - - +
28B ALA* 3.7 13.2 - - + -
29B VAL* 1.3 76.3 - - - +
31B ARG* 1.3 68.2 + - - +
32B ASP 3.3 1.6 - - - -
33B ASP* 2.9 25.1 + - - +
34B LEU* 2.9 19.4 + - - +
55B PHE* 3.5 5.8 - - - -
64B GLY 3.5 18.2 - - - +
65B ALA* 4.0 7.4 - - + -
2502B CA 3.6 7.0 - - - -
68C THR 2.5 30.9 + - - -
69C ASN* 4.8 3.6 - - - -
70C ALA* 5.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 1.3 75.1 - - - +
32B ASP* 1.3 62.8 + - - +
34B LEU* 3.5 3.5 + - - +
35B LYS* 3.1 21.1 + - - +
51B ALA* 5.1 3.3 - - - +
52B ASP* 4.1 27.6 + - - +
55B PHE* 3.5 53.6 - - + +
56B LYS* 5.2 9.1 - - - +
64B GLY* 4.9 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 3.9 12.5 - - - +
30B TYR* 3.3 1.4 - - - +
31B ARG* 1.3 77.0 - - - +
33B ASP* 1.3 61.0 + - - +
35B LYS* 3.3 20.6 + - - +
36B LYS* 2.8 57.6 + - - +
22J ILE 3.4 23.8 - - - +
23J LYS* 3.6 20.7 - - - +
24J GLY 4.2 0.9 + - - -
26J PHE* 3.9 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.7 24.4 - - + +
22B ILE* 3.3 35.3 - - + +
23B LYS* 3.4 17.7 + - - +
28B ALA 4.4 0.9 - - - +
29B VAL* 3.6 15.7 - - + -
30B TYR* 2.9 39.7 + - - +
32B ASP* 1.3 77.7 - - - +
34B LEU* 1.3 58.8 + - - +
36B LYS* 3.2 5.8 + - - +
37B LEU* 2.8 27.4 + - - +
26J PHE* 4.9 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.4 18.7 - - + +
30B TYR 2.9 14.9 + - - +
31B ARG 3.8 4.0 - - - +
33B ASP* 1.3 74.1 - - - +
35B LYS* 1.3 60.7 + - - +
37B LEU* 3.1 13.2 + - + +
38B LEU* 2.8 37.7 + - + +
51B ALA 4.0 7.6 - - - +
54B TRP* 4.1 10.3 - - + -
55B PHE* 3.7 47.3 - - + +
58B LEU* 4.1 21.8 - - + -
66B VAL* 4.8 6.5 - - + -
71B PHE* 5.4 2.0 - - + -
74B LEU* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ARG 3.1 14.9 + - - +
32B ASP* 3.4 24.0 - - - +
34B LEU* 1.3 74.8 - - - +
36B LYS* 1.3 58.6 + - + +
38B LEU* 3.4 2.7 + - - +
39B GLU* 3.0 59.8 + - + +
51B ALA* 3.7 28.9 - - + +
23J LYS* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.8 13.5 + - + -
22B ILE* 4.4 11.2 - - + -
32B ASP* 2.8 38.4 + - - +
33B ASP* 3.5 7.9 - - - +
34B LEU 3.2 0.2 - - - -
35B LYS* 1.3 76.1 - - + +
37B LEU* 1.3 65.0 + - - +
39B GLU* 3.5 9.7 + - - +
40B THR* 3.1 30.4 + - - +
24J GLY* 3.0 34.7 + - - +
26J PHE* 3.3 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.8 3.8 - - + +
16B TYR* 5.1 2.9 - - - -
19B TYR* 3.6 44.6 - - + -
29B VAL* 5.2 6.7 - - + -
33B ASP 2.8 17.4 + - - +
34B LEU* 3.5 17.7 - - + +
36B LYS* 1.3 74.5 - - - +
38B LEU* 1.3 61.8 + - + +
41B GLU* 2.8 48.7 + - + +
42B SER* 5.6 1.8 - - - -
71B PHE* 3.7 30.1 - - + -
74B LEU* 4.0 25.6 - - + -
8D LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 2.8 35.3 + - + +
35B LYS* 3.8 3.6 - - - +
37B LEU* 1.3 73.2 - - + +
39B GLU* 1.3 62.9 + - + +
42B SER* 2.5 40.3 + - - +
46B ILE* 4.0 19.7 - - + +
47B ARG* 3.1 17.5 - - + +
50B GLY 4.9 0.2 - - - -
51B ALA* 3.7 33.7 - - + +
54B TRP* 3.9 29.2 - - + -
74B LEU* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 3.0 58.9 + - + +
36B LYS* 3.8 8.9 - - - +
37B LEU 3.2 0.4 - - - -
38B LEU* 1.3 78.6 - - + +
40B THR* 1.3 61.3 + - - +
42B SER 4.6 0.7 - - - +
47B ARG* 3.6 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.2 25.5 + - - +
36B LYS* 3.1 13.6 + - - +
39B GLU* 1.3 79.6 - - - +
41B GLU* 1.3 67.1 + - - +
42B SER 3.7 1.3 - - - +
6D SER* 3.5 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.8 13.7 - - + -
18B LYS* 2.6 34.6 + - - -
19B TYR* 3.7 26.6 + - + +
37B LEU* 2.8 25.2 + - + +
40B THR* 1.3 81.7 - - - +
42B SER* 1.3 58.1 + - - +
78B MET* 4.1 2.3 - - - +
6D SER* 2.8 29.1 + - - -
7D GLN* 3.6 3.5 + - - +
8D LEU* 3.2 47.5 + - + +
9D GLU* 3.6 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.8 1.3 - - - -
38B LEU* 2.5 37.3 + - - +
39B GLU 4.6 1.6 - - - +
40B THR 5.0 0.5 - - - -
41B GLU* 1.3 79.1 - - - +
43B PRO* 1.3 69.0 + - - +
46B ILE* 3.8 17.6 - - - +
47B ARG* 3.0 37.6 + - - +
78B MET* 4.0 12.1 - - - -
9D GLU* 3.3 6.4 - - - +
----------------------------------------------------------
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