Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 1ORR
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 ASN 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP* 2.9 17.2 + - + +
60A ARG* 1.3 75.6 - - - +
62A LYS* 1.3 68.4 + - - +
63A ASN* 3.3 10.5 + - - +
64A ASP* 2.8 39.6 + - - +
65A VAL* 3.1 24.4 + - - +
106A ASN* 3.7 1.6 - - - -
58B ASP* 5.1 0.4 + - - +
60B ARG* 3.3 29.4 + - - +
98B GLU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG 3.5 2.2 + - - -
61A ASN* 1.3 72.4 - - - +
63A ASN* 1.3 58.7 + - - +
65A VAL* 3.2 2.1 + - - +
66A THR* 2.9 45.9 + - - +
105A LEU 5.5 0.2 - - - -
106A ASN* 3.5 36.8 + - + +
109A GLU* 3.7 33.5 + - - +
113A GLN* 5.4 6.0 - - - +
94C CYS* 4.5 19.4 - - - +
62D LYS* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 3.3 9.8 + - - +
62A LYS* 1.3 78.2 - - - +
64A ASP* 1.3 64.5 + - - +
66A THR* 3.9 4.6 - - - -
67A ARG* 3.0 47.2 + - - +
92B ASN* 3.0 28.3 + - - +
94B CYS* 3.7 26.3 - - - +
95B MET* 3.7 20.6 - - - +
98B GLU* 4.5 4.4 + - - +
62D LYS* 4.9 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.2 14.4 - - + -
56A HIS 5.5 0.9 - - - -
57A GLY* 3.7 5.6 - - - -
58A ASP 2.9 25.8 + - - +
61A ASN* 2.8 28.1 + - - +
63A ASN* 1.3 76.2 + - - +
65A VAL* 1.3 62.8 + - - +
67A ARG* 4.1 5.0 - - - +
68A LEU* 3.2 21.7 + - - +
60B ARG* 2.8 42.2 + - - -
95B MET* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.2 5.8 - - + -
58A ASP 4.2 1.6 - - - +
59A ILE* 3.5 43.5 - - + +
61A ASN 3.1 16.2 + - - +
62A LYS 3.2 3.1 + - - +
64A ASP* 1.3 75.3 - - - +
66A THR* 1.3 65.1 + - - +
68A LEU* 3.1 10.8 + - + +
69A ILE* 3.0 22.2 + - + +
106A ASN* 3.8 11.7 - - + +
107A LEU* 3.7 44.9 - - + +
110A ALA* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 2.9 35.5 + - - +
63A ASN* 3.9 6.1 - - - -
65A VAL* 1.3 75.9 - - - +
67A ARG* 1.3 64.8 + - + +
69A ILE* 3.2 2.9 + - - +
70A THR* 3.0 27.3 + - + +
106A ASN 5.0 1.9 + - - -
110A ALA* 4.1 14.9 - - + +
114A TYR* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 3.0 41.8 + - - +
64A ASP* 4.1 4.0 - - - +
66A THR* 1.3 77.9 - - + +
68A LEU* 1.3 57.0 + - - +
70A THR* 3.4 7.9 + - - +
71A LYS* 2.8 36.0 + - + +
91B ASP* 3.0 45.3 + - - -
92B ASN* 3.2 37.9 + - - +
112D ARG* 6.0 1.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
5A LEU* 3.6 31.2 - - + -
7A THR* 5.0 2.7 - - + -
29A ILE* 4.1 16.8 - - + -
31A PHE* 3.8 36.1 - - + -
55A VAL* 4.2 13.2 - - + -
59A ILE* 6.2 0.2 - - + -
64A ASP 3.2 14.4 + - - +
65A VAL* 3.1 16.8 + - + +
67A ARG* 1.3 77.5 - - - +
69A ILE* 1.3 60.2 + - + +
71A LYS* 4.7 0.2 - - - -
72A TYR* 3.0 60.2 + - + +
74A PRO* 4.8 0.3 - - - +
107A LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.9 20.0 - - + -
65A VAL* 3.0 13.5 + - + +
66A THR 3.8 5.6 - - - +
68A LEU* 1.3 77.0 - - + +
70A THR* 1.3 60.5 + - + +
73A MET* 2.7 32.2 + - - +
74A PRO* 4.1 14.1 - - + -
77A CYS* 6.2 0.2 - - + -
107A LEU* 3.8 27.1 - - + -
110A ALA* 3.7 34.1 - - + +
111A VAL* 4.2 9.2 - - + +
114A TYR* 4.7 3.6 - - + -
115A ASN* 3.7 30.5 - - + +
118A CYS* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 3.0 21.7 + - + +
67A ARG* 3.4 10.4 + - - +
69A ILE* 1.3 73.0 - - - +
71A LYS* 1.3 69.7 + - - +
73A MET* 3.5 20.0 - - - +
114A TYR* 3.6 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 2.8 21.5 + - + +
70A THR* 1.3 84.8 + - - +
72A TYR* 1.3 101.6 + - + +
73A MET* 4.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 3.0 22.3 + - + +
29A ILE* 4.0 31.9 - - + -
53A GLU* 3.3 38.1 + - + -
55A VAL* 3.6 30.2 - - + +
68A LEU* 3.0 40.5 + - + +
71A LYS* 1.3 120.6 + - + +
73A MET* 1.3 71.9 + - - +
74A PRO* 3.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 2.8 22.1 + - - +
69A ILE 2.7 28.8 + - - +
70A THR* 3.5 23.1 - - - +
71A LYS 4.7 1.3 - - - +
72A TYR* 1.3 72.1 - - - +
74A PRO* 1.3 71.0 - - - +
75A ASP* 4.4 2.8 - - - +
114A TYR* 3.4 25.4 - - - +
115A ASN* 3.3 27.5 - - - +
----------------------------------------------------------
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