Contacts of the helix formed by residues 60 - 68 (chain A) in PDB entry 1O0L
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 THR 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 4.9 16.7 + - - +
57A PHE* 3.4 43.3 + - + +
58A ARG 4.0 1.3 - - - -
59A ARG* 1.3 73.4 + - - +
61A PHE* 1.3 74.8 + - - +
62A SER* 3.1 9.0 + - - +
63A ASP* 3.9 6.8 + - - +
64A LEU* 3.4 21.8 - - - +
101A VAL* 4.3 20.2 - - + -
102A PHE* 6.1 4.5 - - + -
105A ALA* 4.9 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 4.3 24.0 - - + -
25A LYS* 4.2 36.3 - - + -
54A GLU* 4.8 6.3 - - - -
60A THR* 1.3 90.8 + - - +
62A SER* 1.3 62.8 + - - +
63A ASP 3.6 0.2 - - - -
64A LEU* 3.4 15.3 - - + -
65A ALA* 3.4 10.6 + - - +
105A ALA* 4.2 17.9 - - + -
108A ALA* 4.9 6.7 - - + -
109A GLU* 3.2 48.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.4 37.8 - - - +
61A PHE* 1.3 72.6 - - - +
63A ASP* 1.3 74.4 + - - +
64A LEU 3.1 1.3 - - - -
65A ALA* 3.1 7.6 + - - +
66A ALA* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 4.0 18.7 + - - +
60A THR 3.9 5.7 + - - +
62A SER* 1.3 87.2 + - - +
64A LEU* 1.3 61.8 + - + +
66A ALA* 3.6 9.1 - - - +
67A GLN* 2.9 40.0 + - - +
102A PHE* 6.0 4.2 - - + -
178A VAL* 3.6 16.8 - - - +
180A LEU* 3.3 28.6 - - + +
181A GLY* 3.2 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR 3.4 10.8 - - - +
61A PHE* 3.4 33.2 - - + +
63A ASP* 1.3 81.4 - - + +
65A ALA* 1.3 61.0 + - - +
67A GLN* 3.9 3.7 - - - +
68A LEU* 3.2 32.2 + - + +
102A PHE* 4.3 7.4 - - + +
105A ALA* 3.2 35.9 - - + +
106A LEU* 3.5 45.1 - - + +
109A GLU* 3.4 22.2 - - + +
180A LEU* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE 3.4 8.6 + - - +
62A SER* 3.1 8.8 + - - +
64A LEU* 1.3 79.6 - - - +
66A ALA* 1.3 56.0 + - - +
67A GLN 3.2 0.2 - - - -
68A LEU* 3.2 4.0 + - - +
69A HIS* 2.7 48.8 + - + +
109A GLU* 4.1 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER 2.8 17.3 + - - +
63A ASP* 3.6 4.3 - - - +
65A ALA* 1.3 77.0 - - - +
67A GLN* 1.3 62.4 + - - +
69A HIS* 3.3 21.5 - - - +
70A VAL* 4.6 2.8 + - - +
180A LEU 3.2 19.3 - - - +
181A GLY* 4.2 2.0 - - - -
182A ALA* 3.2 44.1 - - - +
183A LEU 4.4 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP 2.9 27.7 + - - +
64A LEU 3.9 3.4 - - - +
66A ALA* 1.3 73.7 - - - +
68A LEU* 1.3 68.8 + - + +
69A HIS 3.1 8.7 + - - -
70A VAL* 3.9 9.9 - - - +
71A THR 3.9 14.0 - - - +
75A ALA* 4.5 12.4 - - + +
78A ARG* 4.0 37.0 + - - +
79A PHE* 4.6 2.6 + - - -
106A LEU* 3.3 36.7 - - - +
180A LEU* 3.3 46.5 - - + +
182A ALA* 5.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.2 24.9 + - + +
65A ALA* 3.2 6.0 + - - +
67A GLN* 1.3 86.5 - - + +
69A HIS* 1.3 59.6 + - - +
70A VAL 3.5 1.4 - - - -
71A THR* 4.5 5.0 + - - +
72A PRO* 3.7 29.8 - - + -
75A ALA* 5.2 9.0 - - + -
106A LEU* 4.5 17.5 - - + +
109A GLU* 5.8 2.9 - - + -
110A SER* 4.1 19.3 - - - +
113A LYS* 3.0 29.2 + - + -
115A MET* 3.4 36.6 - - + +
118A LEU* 5.6 1.8 - - + -
----------------------------------------------------------
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