Contacts of the strand formed by residues 66 - 78 (chain A) in PDB entry 2ORY
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 2.9 39.1 - - + +
64A PRO 3.6 1.6 - - - +
65A PHE* 1.3 78.2 - - - +
67A ILE* 1.3 66.9 + - - +
68A PHE 4.1 3.1 + - - -
69A ASN* 4.4 12.3 + - + +
70A ASP* 4.0 7.2 - - - +
96B SER* 4.9 0.2 - - - -
98B SER* 4.0 10.7 + - - -
99B ASP* 2.9 26.4 + - - -
267B GLN* 4.6 5.8 + - - +
305B LEU* 3.5 28.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
66A THR* 1.3 80.9 - - - +
68A PHE* 1.3 83.3 + - + +
69A ASN 3.0 3.8 - - - -
70A ASP* 2.8 33.5 + - - +
92A THR* 2.8 31.4 - - + +
93A ASN* 5.2 9.9 - - + -
96A SER* 6.5 0.9 - - - -
99B ASP* 3.0 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 4.1 0.4 + - - -
67A ILE* 1.3 95.3 - - + +
69A ASN* 1.3 62.1 + - - +
92A THR* 2.6 21.9 + - + -
96A SER* 6.0 1.8 - - - -
99A ASP* 3.5 46.4 - - + -
100A TRP* 4.7 14.8 - - + +
175A LYS* 2.8 20.4 + - - +
67B ILE* 4.4 8.7 - - + -
68B PHE* 4.0 11.4 - + - -
99B ASP* 3.5 46.4 + - + +
103B ASN* 3.2 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.5 20.5 - - + -
66A THR* 4.4 14.2 + - + +
67A ILE 3.0 1.0 - - - +
68A PHE* 1.3 87.4 - - - +
70A ASP* 1.3 68.4 + - - +
71A ALA* 4.1 3.3 - - - +
106A MET* 4.9 4.3 - - - +
175A LYS* 4.4 8.2 + - - +
98B SER* 5.0 0.2 + - - -
103B ASN* 5.0 2.3 + - - +
266B TYR* 3.4 59.9 + - + +
267B GLN* 4.5 2.6 + - - -
270B LEU* 4.0 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 5.5 7.6 - - + +
61A TYR* 3.4 4.7 - - - +
62A THR* 3.0 35.9 - - + +
63A MET 4.4 0.2 + - - -
66A THR 4.0 5.4 - - - +
67A ILE* 2.8 43.6 + - - +
68A PHE 3.5 0.6 - - - -
69A ASN* 1.3 82.1 - - - +
71A ALA* 1.3 61.3 + - - +
90A ARG* 5.0 5.8 - - - +
91A GLY* 3.3 20.6 - - - +
92A THR* 3.5 14.8 + - - +
175A LYS* 5.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.6 4.3 - - - +
61A TYR* 2.8 43.0 + - + +
69A ASN 3.6 5.4 + - - +
70A ASP* 1.3 78.8 - - - +
72A MET* 1.3 64.5 + - - +
90A ARG* 3.4 16.2 + - - +
91A GLY* 4.3 3.4 - - - -
135A THR* 4.7 9.2 - - - +
136A LEU* 4.5 15.9 - - + -
139A LEU* 5.4 1.6 - - + -
179A LEU* 5.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 3.4 26.0 - - - +
33A ILE* 4.1 12.6 - - + -
37A MET* 3.4 31.9 - - + -
58A PRO* 3.7 9.0 - - + -
59A ALA 3.4 13.2 - - - +
60A VAL* 3.9 17.0 - - + -
71A ALA* 1.3 78.5 - - - +
73A MET* 1.3 80.3 + - - +
74A TYR* 3.5 24.0 - - + -
88A ALA 5.0 0.2 - - - +
89A ILE* 3.5 3.8 - - - +
90A ARG* 2.8 62.4 + - + +
136A LEU* 4.8 2.0 - - - -
139A LEU* 5.0 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
56A TRP* 3.2 32.9 - - + -
58A PRO* 3.7 0.2 - - - +
59A ALA 3.0 29.4 + - - -
72A MET* 1.3 80.3 - - - +
74A TYR* 1.3 65.8 + - - +
87A ILE* 3.8 18.4 - - + -
88A ALA 3.3 13.7 - - - +
89A ILE* 3.7 25.6 - - + -
136A LEU* 3.3 46.0 - - + +
139A LEU* 4.3 3.8 - - + +
152A ILE* 3.9 17.9 - - + -
183A LEU* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.8 29.5 + - - +
15A MET* 3.4 25.2 - - + +
16A SER* 3.4 19.1 - - - -
37A MET* 3.3 31.6 - - + -
54A VAL* 4.6 7.4 - - + -
56A TRP* 3.1 17.3 - - - +
57A GLY 4.3 0.4 - - - -
58A PRO* 3.9 16.2 - - + -
72A MET* 3.5 13.7 - - + -
73A MET* 1.3 74.9 - - - +
75A VAL* 1.3 66.4 + - - +
76A ILE* 3.0 33.4 - - + -
87A ILE* 3.5 5.4 - - - +
88A ALA* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.6 3.8 - - - +
55A VAL* 3.0 30.0 + - + +
56A TRP* 2.8 31.7 + - + +
74A TYR* 1.3 81.4 - - - +
76A ILE* 1.3 63.8 + - - +
85A TYR* 4.0 32.5 - - + -
86A VAL 3.1 11.7 - - - +
87A ILE* 4.0 11.7 - - + -
152A ILE* 3.4 33.2 - - + -
155A PHE* 4.6 7.0 - - + -
156A LEU* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.7 23.1 - - + -
15A MET* 4.8 2.9 - - + -
41A LEU* 4.4 5.2 - - + -
52A TRP* 3.5 40.8 - - + -
53A GLU 3.4 11.7 - - - +
54A VAL* 4.5 3.6 - - + +
74A TYR* 3.0 41.1 - - + -
75A VAL* 1.3 75.5 - - - +
77A GLN* 1.3 63.1 + - - +
78A LYS 4.3 0.3 + - - -
84A GLU 4.1 0.2 - - - +
85A TYR* 3.4 3.3 - - - +
86A VAL* 2.8 66.8 + - + +
88A ALA* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 3.6 4.2 - - - -
53A GLU* 2.8 33.9 + - + +
55A VAL* 3.3 27.6 - - + +
76A ILE* 1.3 75.2 - - - +
78A LYS* 1.3 72.9 + - - +
79A LYS* 3.3 3.0 + - - -
81A ALA 4.5 9.5 - - - +
82A GLU* 5.6 0.3 - - - -
83A GLY 4.8 3.3 + - - -
84A GLU 3.5 8.3 - - - +
85A TYR* 3.4 28.0 + - + -
159A LYS* 2.6 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.8 1.6 - - - +
50A ASP* 3.2 48.0 + - + +
51A ASP 3.9 1.3 - - - +
52A TRP* 3.8 31.6 - - + -
77A GLN* 1.3 76.7 - - - +
79A LYS* 1.3 70.3 + - - +
80A GLY 3.6 0.2 + - - -
81A ALA* 3.2 36.4 - - + +
84A GLU* 3.1 43.2 + - + +
----------------------------------------------------------
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