Contacts of the helix formed by residues 39 - 47 (chain C) in PDB entry 4YC3
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 39 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU 3.7 2.2 + - - -
38C MET* 1.3 72.7 - - - +
40C GLU* 1.3 65.2 + - - +
41C GLU* 3.8 12.6 + - - +
42C GLU* 2.8 42.3 + - - +
43C TRP* 3.0 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 1.3 74.8 - - - +
41C GLU* 1.3 72.9 + - - +
42C GLU 3.1 0.3 + - - -
43C TRP* 3.3 28.6 + - + +
44C ARG* 2.8 67.0 + - - +
52C LEU* 4.4 13.5 - - - +
53C GLY* 3.8 19.7 + - - -
54C TRP 4.1 6.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
39C SER* 3.3 11.9 + - - +
40C GLU* 1.3 79.7 + - - +
42C GLU* 1.3 63.1 + - + +
44C ARG* 3.4 8.5 + - - +
45C ARG* 2.9 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PRO* 4.2 6.1 - - - +
36C HIS* 3.0 30.7 + - - -
37C LEU 4.1 0.3 - - - +
38C MET* 3.3 30.5 - - + +
39C SER* 2.8 41.2 + - - +
40C GLU 3.1 1.0 - - - -
41C GLU* 1.3 80.2 - - + +
43C TRP* 1.3 59.5 + - - +
45C ARG* 3.1 39.0 + - - +
46C LEU* 3.4 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 3.4 33.0 + - + +
39C SER 3.0 21.0 + - - -
40C GLU* 3.4 25.5 - - + +
42C GLU* 1.3 76.7 - - - +
44C ARG* 1.3 99.2 + - + +
46C LEU* 3.2 19.1 - - + +
48C VAL* 3.4 44.4 + - + +
50C GLN* 3.4 39.0 - - + -
51C SER 4.1 3.4 - - - -
54C TRP* 3.7 23.7 + - + -
55C VAL* 5.1 0.2 - - - +
56C HIS* 4.3 5.0 - - + +
67C LEU* 4.9 0.7 - - + -
69C PHE* 3.6 32.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU* 2.8 57.2 + - - +
41C GLU* 3.7 8.7 - - - +
42C GLU 3.2 0.2 - - - -
43C TRP* 1.3 86.9 - - + +
45C ARG* 1.3 61.0 + - - +
46C LEU 3.2 1.2 + - - -
47C GLY* 3.2 14.6 + - - -
48C VAL 3.9 11.0 + - - +
49C GLN* 4.6 3.6 - - - +
50C GLN 2.8 38.6 + - - +
51C SER 3.2 14.1 + - - -
52C LEU* 4.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 2.9 40.8 + - - +
42C GLU* 3.1 33.1 + - - +
44C ARG* 1.3 77.1 - - - +
46C LEU* 1.3 60.3 + - - +
47C GLY 3.4 0.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
6C ILE* 4.9 0.4 - - - -
24C LEU* 4.0 7.0 - - + -
28C LEU* 3.4 48.1 - - + +
31C GLN* 3.9 37.5 - - + +
32C VAL* 4.0 13.7 - - + -
38C MET* 3.5 35.2 - - + -
42C GLU 3.4 5.9 + - - +
43C TRP* 3.2 14.6 - - - +
45C ARG* 1.3 81.6 - - - +
47C GLY* 1.3 54.0 + - - +
48C VAL* 3.6 4.5 - - + +
67C LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.4 19.5 - - - +
8C TYR* 4.2 0.7 + - - -
44C ARG 3.2 10.5 + - - -
45C ARG 3.4 1.2 + - - -
46C LEU* 1.3 77.9 - - - +
48C VAL* 1.3 64.2 + - - +
49C GLN* 3.0 25.9 + - - +
----------------------------------------------------------
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