Contacts of the strand formed by residues 67 - 73 (chain B) in PDB entry 5AYR
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 TYR 67 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 3.9 23.7 - - + +
171A GLU* 4.8 5.9 - - - +
172A ASN* 6.1 1.3 - - - -
175A LYS* 5.6 3.1 + - - -
271A PRO* 4.3 18.2 - - + -
55B THR* 3.9 12.6 - - + -
56B TYR 3.6 13.5 - - - -
57B TYR* 4.2 5.8 - - + -
61B LEU 4.5 2.0 - - - -
62B HIS* 2.7 48.2 + + - -
65B ASN* 4.2 26.3 + - + -
66B ILE* 1.3 80.5 - - - +
68B PRO* 1.3 64.3 - - - +
69B PHE* 3.6 4.5 - - - +
82B TYR* 3.3 1.6 - - - -
83B ILE* 2.8 56.8 + - + +
87B HIS* 5.3 4.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.8 24.0 - - + -
11B ILE* 4.1 18.2 - - + -
23B TRP* 3.8 31.6 - - + -
55B THR* 3.4 1.4 - - - -
56B TYR* 2.8 40.8 + - + +
61B LEU* 3.9 7.6 - - + -
66B ILE* 3.6 10.8 - - + +
67B TYR* 1.3 89.8 - - - +
69B PHE* 1.3 61.1 - - - +
81B GLY 3.3 9.9 - - - +
82B TYR* 3.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 4.2 18.6 - - + -
7B LEU* 4.0 2.4 - - - +
54B TYR 2.9 15.9 - - - +
55B THR* 4.1 11.2 - - + +
56B TYR* 4.4 1.3 - - - -
67B TYR 3.6 7.0 - - - +
68B PRO* 1.3 74.7 - - - +
70B ILE* 1.3 69.7 + - - +
71B LEU* 3.9 27.6 - - + -
79B ALA* 4.4 1.8 - - + -
80B ILE 4.3 2.0 - - - -
81B GLY* 2.9 54.4 + - - +
82B TYR* 3.2 33.0 - - - -
83B ILE* 3.7 3.4 - - + -
89B MET* 4.0 19.7 - - + -
90B ASP 4.0 3.1 - - - -
91B PHE* 3.9 28.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.3 12.8 - - + -
4B GLU* 4.2 22.4 - - + +
7B LEU* 4.0 16.2 - - + -
54B TYR* 2.8 42.6 + - + -
56B TYR* 3.8 26.0 - - + +
69B PHE* 1.3 80.0 - - - +
71B LEU* 1.3 65.7 + - - +
72B TYR* 3.4 31.4 - - + +
77B LEU* 3.5 19.3 - - + -
79B ALA 3.3 6.7 - - - +
80B ILE* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 4.0 13.0 - - + -
35B ILE* 4.3 11.2 - - + -
36B LEU* 3.8 26.2 - - + -
51B LEU* 4.5 12.8 - - + -
52B GLN 3.6 1.8 - - - +
53B THR* 3.6 32.3 - - + -
54B TYR 4.6 0.4 - - - +
69B PHE* 3.9 20.2 - - + -
70B ILE* 1.3 83.1 - - - +
72B TYR* 1.3 62.5 + - - +
77B LEU* 3.7 4.3 - - - +
78B ILE* 2.8 35.0 + - + -
79B ALA* 2.8 32.7 + - + +
89B MET* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.2 10.9 - - - +
51B LEU* 3.3 9.1 - - - +
52B GLN* 2.8 41.3 + - + +
54B TYR* 3.5 29.8 - + + +
70B ILE* 3.4 22.2 - - + +
71B LEU* 1.3 74.6 - - - +
73B TYR* 1.3 58.5 + - - +
74B GLN 3.6 13.5 - - - +
75B LYS* 3.8 16.2 - - - -
76B GLN 3.3 6.1 - - - -
77B LEU* 3.5 43.1 - - + +
78B ILE* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 3.5 44.4 - - + +
50B ILE* 3.4 24.5 - - + -
51B LEU* 4.0 6.3 - - + -
72B TYR* 1.3 70.8 - - - +
74B GLN* 1.3 88.9 + - + +
76B GLN* 2.7 47.2 + - + +
78B ILE* 3.4 21.4 - - + +
97B THR* 3.6 21.3 - - + -
----------------------------------------------------------
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