Contacts of the helix formed by residues 66 - 71 (chain A) in PDB entry 3RQ5
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 VAL 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY* 4.8 0.2 - - - -
36A SER 3.7 34.1 - - - +
37A ASP* 4.1 0.2 - - - +
40A PRO* 3.8 27.6 - - + +
43A ALA* 4.2 1.8 - - + -
62A THR* 3.4 23.3 - - - +
63A SER* 2.9 15.7 + - - +
65A ASN* 1.3 80.0 - - - +
67A ILE* 1.3 67.2 + - - +
68A PRO 3.3 0.7 - - - -
69A LEU* 2.9 23.7 + - + +
70A ILE* 3.5 20.2 + - + +
278A GOL 3.9 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 3.6 23.1 - - + +
63A SER 3.8 3.4 - - - +
64A GLU* 3.6 11.0 - - - +
66A VAL* 1.3 76.9 - - - +
68A PRO* 1.3 70.6 - - + +
70A ILE* 3.0 15.2 + - - +
71A VAL* 3.3 17.4 + - + +
79A TYR* 3.8 50.5 - - + -
80A TRP 5.3 0.2 - - - +
81A ARG* 4.0 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.4 12.3 - - - +
65A ASN* 3.6 14.6 - - - +
66A VAL 3.5 2.7 - - - -
67A ILE* 1.3 96.1 - - + +
69A LEU* 1.3 64.8 + - + +
70A ILE 3.3 0.2 - - - -
71A VAL* 4.5 6.2 - - + +
72A PRO* 3.2 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 4.0 20.0 - - + -
44A LEU* 4.1 16.2 - - - +
65A ASN 3.8 9.4 - - - +
66A VAL* 2.9 14.9 + - + +
68A PRO* 1.3 86.0 - - + +
70A ILE* 1.3 61.9 + - + +
72A PRO* 4.1 5.4 - - - +
73A VAL* 4.6 4.7 - - - +
278A GOL 3.8 39.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO 5.6 0.2 - - - +
43A ALA* 3.8 26.9 - - + -
44A LEU* 4.2 26.7 - - + +
60A ILE* 4.1 26.7 - - + -
62A THR* 4.2 13.2 - - + -
66A VAL* 3.7 22.2 - - + +
67A ILE 3.0 3.2 + - - +
69A LEU* 1.3 81.4 - - + +
71A VAL* 1.3 65.0 + - - +
72A PRO* 3.4 1.6 - - - -
73A VAL* 3.0 6.8 + - - +
74A LEU* 2.9 39.7 + - + -
79A TYR* 3.2 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.3 23.5 + - + +
68A PRO* 4.5 4.5 - - + +
70A ILE* 1.3 75.4 - - - +
72A PRO* 1.3 70.7 - - + +
74A LEU 4.2 3.4 - - - -
75A PRO* 3.1 37.3 - - + +
79A TYR* 3.4 30.1 - - + +
----------------------------------------------------------
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