Contacts of the helix formed by residues 44 - 54 (chain C) in PDB entry 3S9L
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 SER 44 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 3.8 17.5 - - - +
42C LYS* 4.0 0.7 - - - +
43C ALA* 1.3 79.7 - - - +
45C TYR* 1.3 65.6 + - - +
46C LEU* 3.5 17.3 + - - +
47C ASP* 3.1 26.5 + - - +
48C CYS* 3.4 9.2 + - - -
161C CYS* 5.1 0.4 - - - -
179C CYS* 3.9 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 4.0 11.5 - - + +
44C SER* 1.3 73.0 - - - +
46C LEU* 1.3 92.3 + - + +
48C CYS* 3.0 19.4 + - + +
49C ILE* 3.1 30.3 + - + +
60C VAL* 6.1 2.2 - - + -
62C LEU* 3.5 30.0 - - + +
66C LEU* 3.3 47.8 - - + +
69C ASP* 4.1 15.6 + - + -
122C LEU* 4.3 7.4 + - - +
161C CYS* 3.7 21.9 - - + +
179C CYS* 3.7 18.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A GLU* 5.3 9.0 - - - +
44C SER* 3.1 10.9 - - - +
45C TYR* 1.3 107.1 - - + +
47C ASP* 1.3 62.1 + - - +
49C ILE* 3.6 10.9 + - + +
50C ARG* 3.1 68.3 + - + +
69C ASP* 5.2 11.9 - - + +
75C ASN* 5.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 4.0 15.4 - - + +
43C ALA* 3.4 28.8 + - - +
44C SER* 3.1 20.2 + - - +
46C LEU* 1.3 81.9 - - - +
48C CYS* 1.3 57.7 + - - +
50C ARG* 4.0 19.6 + - - +
51C ALA* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C CYS* 2.0 55.1 - - + -
11C VAL* 4.0 16.4 - - - -
42C LYS* 3.7 10.1 - - - -
44C SER 3.4 7.8 + - - -
45C TYR* 3.0 11.1 + - - +
47C ASP* 1.3 78.3 - - - +
49C ILE* 1.3 64.7 + - - +
51C ALA* 3.4 2.9 + - - +
52C ILE* 3.2 29.2 + - - +
60C VAL* 3.9 21.8 - - + -
62C LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.1 34.0 + - + +
46C LEU* 4.0 11.9 - - + +
48C CYS* 1.3 75.2 - - - +
50C ARG* 1.3 63.1 + - + +
51C ALA 3.4 0.3 + - - -
52C ILE* 3.5 1.2 + - - -
53C ALA* 3.5 15.8 + - - +
60C VAL* 5.2 0.4 - - + -
62C LEU* 4.3 17.5 - - + -
66C LEU 4.1 11.9 - - - +
69C ASP* 4.5 4.7 - - + -
70C ALA* 3.6 37.0 - - + +
75C ASN* 3.7 20.1 - - + +
77C LEU* 3.2 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A GLU* 3.8 22.8 + - - +
666A THR* 4.9 3.2 + - - -
46C LEU* 3.1 51.8 + - + +
47C ASP* 4.0 18.3 + - - +
48C CYS 3.3 0.2 - - - -
49C ILE* 1.3 76.7 - - + +
51C ALA* 1.3 61.4 + - - +
53C ALA* 3.7 6.0 + - - +
54C ALA* 3.4 20.6 + - - +
56C GLU* 4.7 0.4 - - - +
75C ASN* 4.0 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C CYS* 4.9 4.5 - - - -
40C VAL* 5.4 5.2 - - + -
47C ASP 3.1 20.1 + - - +
48C CYS* 3.6 8.5 - - - +
49C ILE 3.2 0.2 - - - -
50C ARG* 1.3 76.4 - - - +
52C ILE* 1.3 62.9 + - - +
53C ALA 3.2 0.2 - - - -
54C ALA 3.0 7.3 + - - -
56C GLU* 2.9 54.3 + - + +
57C ALA* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C CYS 3.2 13.8 + - - +
49C ILE 3.5 4.9 + - - +
51C ALA* 1.3 76.3 - - - +
53C ALA* 1.3 59.8 + - - +
55C ASN 3.2 6.9 + - - -
57C ALA* 3.7 24.7 - - + +
58C ASP 4.0 12.3 - - - +
59C ALA* 3.5 31.2 - - - +
60C VAL* 3.8 20.9 - - + -
77C LEU* 3.5 27.6 - - + -
252C VAL 3.6 11.0 - - - +
253C ALA* 4.5 0.2 - - - -
254C ARG* 2.9 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE 3.5 9.6 + - - +
50C ARG* 3.7 11.9 - - - +
51C ALA 3.2 0.6 - - - -
52C ILE* 1.3 80.3 - - - +
54C ALA* 1.3 57.1 + - - +
55C ASN* 3.2 2.2 + - - +
74C PRO* 4.4 6.3 - - + +
75C ASN* 3.8 34.3 - - - +
77C LEU* 4.6 0.4 - - - +
254C ARG* 4.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ARG 3.4 14.0 + - - +
51C ALA 3.0 6.0 + - - +
53C ALA* 1.3 76.3 - - - +
55C ASN* 1.3 78.2 + - - +
56C GLU* 2.9 28.3 + - + +
----------------------------------------------------------
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