Contacts of the helix formed by residues 35 - 44 (chain C) in PDB entry 5LSW
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 ARG 35 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU 3.5 9.0 - - - -
29C LEU* 3.1 23.6 + - + +
30C SER 3.1 25.0 + - - -
31C SER 3.0 13.9 + - - +
32C PRO* 3.6 32.1 + - + +
34C THR* 1.3 77.9 - - - +
36C GLU* 1.3 57.3 + - - +
38C ALA* 3.2 2.0 + - - +
39C LEU* 2.8 45.4 + - + +
65C ALA* 3.7 23.2 - - - +
66C LEU* 5.9 0.4 - - - -
68C GLN* 3.8 30.7 + - - +
69C GLU* 2.9 34.3 + - - +
72C ASN* 5.1 2.8 - - - +
89C ARG* 3.9 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PRO 4.6 2.7 + - - +
34C THR 3.4 0.6 - - - -
35C ARG* 1.3 78.3 - - - +
37C ASN* 1.3 62.7 + - - +
39C LEU* 3.5 12.8 + - - +
40C LEU* 3.2 20.5 + - + +
85C HIS* 2.8 38.7 + - - -
88C ASN* 5.7 1.6 + - - -
89C ARG* 3.3 45.5 + - + +
92C ASN* 5.1 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TRP* 4.5 0.5 + - - -
28C GLU* 4.5 2.1 - - - +
34C THR* 3.5 8.8 + - - +
35C ARG 3.3 0.4 - - - -
36C GLU* 1.3 76.7 - - - +
38C ALA* 1.3 69.3 + - - +
40C LEU* 3.1 17.8 + - - +
41C GLU* 3.0 33.5 + - - +
304C TRS 3.0 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TRP* 3.2 38.4 - - - +
28C GLU* 3.8 13.7 + - + +
29C LEU* 3.7 11.9 - - + -
34C THR 3.2 14.7 + - - +
35C ARG 3.2 7.2 + - - +
37C ASN* 1.3 80.9 + - - +
39C LEU* 1.3 62.4 + - - +
41C GLU* 4.0 0.2 - - - +
42C LEU* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.6 13.4 - - + +
35C ARG* 2.8 33.9 + - + +
36C GLU* 3.6 8.3 - - - +
37C ASN 3.3 0.2 - - - -
38C ALA* 1.3 75.4 - - - +
40C LEU* 1.3 63.4 + - - +
42C LEU* 4.1 2.8 - - - +
43C SER* 3.0 27.0 + - - -
66C LEU* 3.5 31.6 - - + -
69C GLU* 4.0 22.7 - - + +
89C ARG* 4.2 22.0 - - + +
92C ASN* 4.0 14.4 - - + +
93C ALA* 3.9 15.9 - - + -
96C LEU* 4.0 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 3.2 10.5 + - + +
37C ASN* 3.1 22.8 + - - +
39C LEU* 1.3 78.0 - - - +
41C GLU* 1.3 67.1 + - + +
43C SER* 2.8 20.2 + - - +
44C LYS* 3.3 41.7 + - + +
88C ASN* 5.8 2.7 - - - +
92C ASN* 3.8 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TRP* 3.5 55.9 - - + +
37C ASN* 3.0 31.7 + - - +
38C ALA 4.0 1.8 - - - +
40C LEU* 1.3 81.6 - - - +
42C LEU* 1.3 64.4 + - - +
44C LYS* 3.2 26.6 + - - +
45C LYS* 3.3 28.6 + - - +
304C TRS 4.1 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.8 30.5 - - + +
25C TRP* 3.6 26.9 - - + +
26C ILE* 3.8 23.6 - - + +
29C LEU* 3.7 31.0 - - + -
38C ALA 2.9 21.3 + - - +
39C LEU 4.2 0.2 - - - +
41C GLU* 1.3 76.3 - - - +
43C SER* 1.3 63.9 + - - +
45C LYS* 3.0 17.8 + - + +
46C ARG* 3.2 10.7 + - - -
52C LEU* 4.1 11.7 - - + +
56C LEU* 4.6 1.8 - - + -
96C LEU* 4.0 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU 3.0 16.8 + - - -
40C LEU* 2.8 20.1 + - - +
42C LEU* 1.3 76.0 - - - +
44C LYS* 1.3 64.2 + - - +
46C ARG* 3.3 19.8 + - - +
92C ASN* 3.3 37.3 + - - -
95C ALA* 4.5 10.8 - - - +
96C LEU* 4.0 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.4 43.1 - - + +
41C GLU* 3.2 22.8 + - - +
42C LEU 3.2 0.8 - - - -
43C SER* 1.3 81.2 + - - +
45C LYS* 1.3 70.8 + - - +
46C ARG 3.3 1.1 + - - -
47C GLU* 4.5 5.7 + - - +
48C SER* 4.5 5.2 + - - -
----------------------------------------------------------
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