Contacts of the helix formed by residues 66 - 76 (chain D) in PDB entry 2AOB
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 PRO 66 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D LYS 3.9 0.8 - - - -
65D ILE* 1.3 75.4 - - - +
67D ARG* 1.3 67.3 + - - +
68D ALA* 2.8 9.3 + - + +
69D LYS* 3.1 15.8 + - + +
70D ALA* 3.4 9.2 + - - +
86D ARG* 4.3 3.1 - - - +
89D GLU* 3.4 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PRO* 1.3 72.2 - - - +
68D ALA* 1.3 57.8 + - - +
70D ALA* 3.5 4.3 - - - +
71D GLU* 3.0 31.4 - - - +
86D ARG* 3.8 22.2 - - - +
89D GLU* 4.4 4.4 + - - +
107D HIS* 3.2 39.2 - - + +
2301D S1S 2.7 89.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PRO* 2.8 10.2 + - + -
67D ARG* 1.3 76.8 - - - +
69D LYS* 1.3 59.6 + - - +
71D GLU* 3.5 19.0 + - - +
72D GLU* 3.6 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 4.7 14.9 - - + +
66D PRO* 3.1 9.9 + - + +
68D ALA* 1.3 75.2 - - - +
70D ALA* 1.3 66.4 + - - +
72D GLU* 4.0 10.5 - - + +
73D MET* 3.6 18.0 + - - +
84D LEU* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 5.0 3.7 - - + +
66D PRO 3.4 4.9 + - - -
67D ARG 3.5 11.9 - - - +
68D ALA 3.3 1.0 - - - -
69D LYS* 1.3 78.1 - - - +
71D GLU* 1.3 58.6 + - - +
73D MET* 3.4 2.8 + - - +
74D LEU* 3.0 34.3 + - - +
84D LEU* 4.3 14.8 - - + -
86D ARG* 4.0 17.7 - - - +
98D SER* 3.5 31.4 - - - +
107D HIS* 4.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ARG* 3.0 29.2 - - - +
68D ALA* 3.7 11.0 - - - +
69D LYS 3.3 0.4 - - - -
70D ALA* 1.3 73.2 - - - +
72D GLU* 1.3 52.5 + - - +
75D SER* 2.5 46.1 + - - +
105D VAL* 3.7 31.5 + - + +
107D HIS* 2.8 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ALA 3.6 8.8 + - - +
69D LYS* 4.1 12.1 - - + +
70D ALA 3.3 0.4 - - - -
71D GLU* 1.3 79.1 - - - +
73D MET* 1.3 65.0 + - - +
75D SER* 3.5 14.9 + - - -
76D LYS* 3.7 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE* 5.1 8.7 - - + -
62D PHE* 5.9 4.9 - - + -
69D LYS 3.6 8.8 + - - +
70D ALA 3.4 8.0 + - - +
72D GLU* 1.3 79.7 - - - +
74D LEU* 1.3 63.7 + - + +
76D LYS* 3.3 17.2 + - - +
77D GLN* 4.0 10.7 + - - +
84D LEU* 4.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE* 3.8 29.8 - - + -
70D ALA 3.0 18.2 + - - +
73D MET* 1.3 72.6 - - - +
75D SER* 1.3 65.6 + - - +
77D GLN* 3.2 24.2 + - + +
82D ALA* 3.7 22.9 - - + +
83D PHE* 4.0 4.0 - - - -
84D LEU* 3.9 11.4 - - + -
98D SER* 3.4 46.0 - - - +
99D VAL* 3.9 4.0 - - - +
100D LYS* 3.9 14.9 - - + +
105D VAL* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU* 2.5 33.0 + - - +
72D GLU* 3.6 9.3 - - - -
73D MET 3.4 0.2 - - - -
74D LEU* 1.3 73.4 - - - +
76D LYS* 1.3 59.4 + - - +
77D GLN 3.1 7.5 + - - +
103D ASN 5.5 3.4 + - - -
105D VAL* 4.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLU 3.7 5.7 + - - +
73D MET* 3.3 12.7 + - - +
74D LEU 3.3 1.4 - - - -
75D SER* 1.3 75.9 - - - +
77D GLN* 1.3 66.2 + - - +
78D ARG* 3.8 1.0 + - - +
----------------------------------------------------------
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