Contacts of the helix formed by residues 42 - 54 (chain D) in PDB entry 3U8Z
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 42 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LYS 4.6 4.3 - - - +
41D TRP* 1.3 76.3 - - - +
43D GLY* 1.3 66.3 + - - +
44D LYS* 3.2 2.2 - - + +
45D ASP* 2.7 26.5 + - - +
46D LEU 3.4 8.1 + - - -
77D MET 3.4 12.1 - - - +
78D ASP* 3.3 43.2 + - - +
79D LYS 3.4 10.8 - - - +
80D LYS* 3.9 14.4 - - + +
81D VAL* 3.7 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LYS* 1.3 71.5 - - - +
44D LYS* 1.3 50.3 + - - +
46D LEU* 3.4 3.5 + - - +
47D PHE* 2.9 34.8 + - - +
75D LEU* 3.9 11.4 - - - +
76D LYS 3.4 18.6 - - - -
77D MET* 3.4 10.5 + - - +
79D LYS 2.9 13.3 + - - -
81D VAL* 3.7 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU* 5.2 21.0 + - - +
42D LYS* 3.2 2.0 - - + -
43D GLY* 1.3 74.0 - - - +
45D ASP* 1.3 61.4 + - - +
47D PHE* 5.7 0.7 - - + -
48D ASP* 2.9 52.7 + - - +
77D MET* 3.0 46.8 + - + +
78D ASP* 5.4 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D TRP* 3.6 42.6 - - + -
42D LYS* 2.7 37.8 + - - +
44D LYS* 1.3 77.0 - - - +
46D LEU* 1.3 63.5 + - - +
48D ASP* 4.2 3.2 - - - +
49D LEU* 3.3 23.2 + - - +
52D ARG* 5.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.0 16.6 - - + -
26D ILE* 4.3 13.0 - - + -
35D PHE* 4.6 13.0 - - + -
37D CYS* 4.4 22.4 - - + -
41D TRP* 4.1 5.5 - - - -
42D LYS 3.4 1.8 + - - +
43D GLY 3.4 7.5 + - - +
45D ASP* 1.3 76.4 - - - +
47D PHE* 1.4 64.2 + - - +
49D LEU* 3.3 11.5 + - + +
50D VAL* 3.2 30.0 + - + +
64D LEU* 4.0 15.0 - - + -
75D LEU* 4.3 1.3 - - + -
81D VAL* 4.0 27.1 - - + -
94D PHE* 3.9 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLY 2.9 21.4 + - - +
44D LYS* 3.9 2.0 - - + +
45D ASP 3.5 0.2 - - - -
46D LEU* 1.4 72.3 - - - +
48D ASP* 1.3 69.7 + - - +
50D VAL* 3.2 6.4 + - - +
51D CYS* 3.1 46.7 + - - -
59D THR* 3.4 35.7 - - + -
62D PHE* 3.5 23.8 - - + -
63D GLY* 3.8 6.1 - - - -
64D LEU* 4.0 23.1 - - + +
77D MET* 3.7 26.7 - - + -
96D PHE* 3.6 27.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 3.7 26.7 - - - +
44D LYS* 2.9 43.9 + - - +
45D ASP* 4.4 2.9 - - - +
47D PHE* 1.3 84.9 - - - +
49D LEU* 1.4 59.7 + - - +
51D CYS* 3.8 6.3 - - - +
52D ARG* 2.9 44.3 + - - +
59D THR* 5.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 5.4 9.0 - - + +
35D PHE* 3.7 36.6 - - + -
36D ASN 4.6 6.1 - - - +
41D TRP* 3.6 30.7 - - + -
45D ASP 3.3 14.4 + - - +
46D LEU* 3.4 13.2 - - + +
48D ASP* 1.4 73.2 - - - +
50D VAL* 1.3 55.7 + - - +
52D ARG* 3.5 25.4 + - + +
53D THR* 2.7 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 3.8 34.1 - - + -
28D THR* 5.1 1.8 - - + -
33D MET* 5.4 1.1 - - - -
35D PHE* 3.8 31.4 - - + -
46D LEU* 3.2 17.9 + - + +
47D PHE* 3.2 7.4 + - - +
49D LEU* 1.3 73.3 - - - +
51D CYS* 1.3 62.5 + - - +
53D THR* 3.2 5.4 + - - -
54D LEU* 3.2 31.1 + - + +
64D LEU* 4.6 4.9 - - + -
96D PHE* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 4.3 3.6 - - - -
47D PHE* 3.1 48.9 + - - +
48D ASP* 3.8 7.9 - - - +
50D VAL* 1.3 76.3 - - - +
52D ARG* 1.3 54.9 + - - +
54D LEU* 3.2 3.7 + - - -
55D GLY 3.0 8.1 + - - -
56D LEU* 2.8 62.8 + - + +
59D THR* 3.6 24.0 - - + -
96D PHE* 4.0 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 5.5 0.4 - - - +
113B ILE* 4.2 0.3 - - - +
116B HIS* 3.4 47.2 - - + +
148B ALA 5.1 8.6 + - - -
149B LYS* 5.0 13.3 + - - +
198B ARG* 4.3 33.2 + - - +
201B ASP* 4.5 15.9 - - - -
204B GLU* 5.2 0.7 - - - -
41D TRP* 6.0 2.2 - - - -
45D ASP 5.8 0.4 + - - -
48D ASP* 2.9 33.8 + - - +
49D LEU* 3.8 27.7 - - + +
50D VAL 3.4 0.2 - - - -
51D CYS* 1.3 74.2 - - - +
53D THR* 1.4 61.5 + - - +
55D GLY* 3.2 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 3.8 34.7 + - + +
31B ALA* 4.3 0.7 - - + -
33B MET* 3.9 26.9 - - + -
54B LEU* 3.7 10.0 - - - +
113B ILE* 3.2 17.8 - - - +
117B LEU* 5.8 0.2 - - - +
33D MET* 4.8 5.6 - - - -
35D PHE* 3.2 29.7 - - + -
49D LEU* 2.7 21.1 + - - +
50D VAL 3.3 10.1 - - - -
52D ARG* 1.4 76.3 - - - +
54D LEU* 1.3 58.6 + - + +
55D GLY 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR 3.7 19.5 - - - +
54B LEU* 3.5 24.3 - - + +
113B ILE* 4.2 1.7 - - - +
28D THR* 4.3 9.4 - - + -
33D MET* 3.7 30.1 - - + -
50D VAL* 3.2 24.7 + - + +
51D CYS* 3.2 6.5 + - - +
53D THR* 1.3 81.5 - - + +
55D GLY* 1.3 62.3 + - - +
56D LEU* 4.4 4.5 - - + -
96D PHE* 4.0 30.7 - - + -
113D ILE* 3.4 28.4 - - + +
117D LEU* 4.4 11.4 - - + -
----------------------------------------------------------
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