Contacts of the helix formed by residues 63 - 70 (chain C) in PDB entry 4STD
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 ALA 63 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 3.8 15.3 - - + -
43C ALA 3.5 19.1 - - - +
44C PRO* 2.9 18.9 + - + +
46C LEU* 3.8 12.5 - - - +
61C MET 3.9 0.2 + - - -
62C PRO* 1.3 69.3 - - - +
64C GLU* 1.3 63.5 + - + +
66C PHE* 3.1 4.5 + - - +
67C VAL* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.6 35.4 + - - +
62C PRO* 3.2 4.3 + - + +
63C ALA* 1.3 79.0 - - + +
65C GLU* 1.3 63.5 + - + +
67C VAL* 3.8 5.5 - - - +
68C GLY* 2.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C MET* 3.8 17.0 - - + +
62C PRO* 3.0 36.8 + - + +
64C GLU* 1.3 76.5 - - + +
66C PHE* 1.3 60.6 + - - +
68C GLY* 3.2 2.4 + - - +
69C MET* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 4.7 0.2 - - - -
30C TYR* 3.3 23.8 - + - -
38C LEU* 4.1 11.2 - - + -
42C ILE* 3.7 30.3 - - + -
46C LEU* 3.6 30.7 - - + -
48C ILE* 3.7 29.6 - - + -
50C TYR* 4.3 8.1 - - - -
61C MET* 3.5 14.8 - - - -
62C PRO 3.0 10.9 + - - +
63C ALA 3.1 7.0 - - - +
65C GLU* 1.3 77.0 - - - +
67C VAL* 1.3 64.4 + - + +
69C MET* 3.0 17.2 + - + +
70C VAL* 3.1 34.4 + - + +
144C PHE* 3.8 16.6 - + - -
147C LEU* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 3.9 31.2 - - + +
38C LEU* 4.3 14.1 - - + -
39C ARG* 3.9 33.0 - - + +
42C ILE* 3.4 24.5 - - + -
63C ALA 2.8 25.5 + - - +
64C GLU* 4.0 7.9 - - - +
66C PHE* 1.3 72.4 - - + +
68C GLY* 1.3 54.3 + - - +
70C VAL* 3.7 7.3 - - - +
71C SER* 2.6 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU 2.8 19.0 + - - -
65C GLU* 3.5 3.1 - - - -
66C PHE 3.1 0.4 - - - -
67C VAL* 1.3 77.6 - - - +
69C MET* 1.3 56.5 + - - +
71C SER* 3.5 6.5 + - - -
72C SER* 3.1 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 4.6 5.4 - - + -
50C TYR* 3.3 44.6 - - + +
54C LEU* 5.9 0.2 - - - -
58C TRP* 4.9 6.1 - - - -
61C MET* 4.2 21.8 - - + -
65C GLU 2.9 15.5 + - - +
66C PHE* 3.0 7.6 + - + +
68C GLY* 1.3 74.7 - - - +
70C VAL* 1.3 74.8 + - + +
71C SER 3.2 1.3 - - - -
72C SER* 2.8 26.2 + - - -
75C VAL* 3.0 12.5 - - + +
169C PHE* 3.5 45.5 - - + -
175C BFS 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.8 18.8 - - + +
35C TRP* 3.6 24.0 - - + -
38C LEU* 3.9 17.7 - - + -
50C TYR* 4.8 2.5 - - - +
66C PHE* 3.1 37.4 + - + +
67C VAL 3.7 8.1 - - - +
69C MET* 1.3 84.5 - - + +
71C SER* 1.3 61.1 + - - +
75C VAL* 3.3 8.9 - - - +
76C LEU* 2.8 37.6 + - + +
175C BFS 4.6 10.5 - - + -
----------------------------------------------------------
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