Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 1H8O
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 ASP 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS 3.9 3.6 - - - -
27B LYS* 2.9 34.9 - - - +
69B GLY* 3.4 18.1 - - - -
70B SER 3.7 5.1 + - - +
72B THR* 1.3 104.8 - - - +
74B PHE* 1.3 63.8 - - - +
75B THR* 4.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 5.9 0.2 - - + -
25B THR* 3.6 4.2 - - - -
26B CYS* 2.8 45.0 + - + +
28B ALA* 4.5 5.4 - - + -
32B VAL* 3.4 33.9 - - + -
33B GLY 3.5 23.1 - - - -
34B THR* 4.3 6.3 - - - -
36B VAL* 3.5 36.6 - - + -
38B TRP* 4.4 13.7 - - + +
54B ALA* 4.1 10.8 - - + -
68B SER 3.5 5.4 - - - +
69B GLY 4.0 4.7 - - - -
70B SER* 3.6 16.4 - - - -
71B GLY 3.7 7.0 - - - -
72B THR* 3.8 19.3 - - - -
73B ASP* 1.3 74.2 - - - +
75B THR* 1.3 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 4.3 9.4 - - - +
24B ILE 3.7 4.7 - - - +
25B THR* 3.9 24.3 - - + +
38B TRP* 4.1 4.5 - - - -
66B THR 3.4 4.2 - - - +
67B GLY* 3.5 0.5 - - - -
68B SER* 2.8 53.8 + - - +
69B GLY* 5.5 0.3 - - - -
73B ASP* 4.4 4.7 + - - +
74B PHE* 1.3 80.6 + - - +
76B LEU* 1.3 62.6 + - - +
77B THR* 3.8 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL 4.2 0.2 - - - +
23B SER* 3.7 0.9 - - - -
24B ILE* 2.9 45.7 + - + +
38B TRP* 3.3 60.4 - - + +
50B LEU* 5.0 2.2 - - + -
51B ILE* 4.6 8.7 - - + -
65B PHE* 4.2 19.1 - - + -
66B THR 3.8 9.4 - - - +
67B GLY* 4.6 0.7 - - - -
75B THR* 1.3 72.0 - - - +
77B THR* 1.3 72.2 + - - +
78B ILE* 4.2 4.1 + - + +
89B TYR* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 4.3 23.4 + - - +
22B VAL 3.4 11.2 - - - +
23B SER* 3.2 17.2 + - - +
64B ARG 3.2 4.2 - - - +
65B PHE* 3.5 2.3 - - - -
66B THR* 2.8 49.7 + - - -
68B SER* 5.3 1.7 + - - -
75B THR* 3.8 11.8 + - - +
76B LEU* 1.3 75.3 - - - +
78B ILE* 1.3 70.8 + - - +
79B SER* 4.6 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP 3.9 1.7 - - - +
21B ARG* 3.4 2.8 - - - -
22B VAL* 2.9 43.9 + - + +
24B ILE* 4.9 7.0 - - + -
64B ARG* 3.7 7.4 - - + -
65B PHE* 3.4 37.7 - - + -
76B LEU* 4.3 7.9 - - + +
77B THR* 1.3 77.7 - - - +
79B SER* 1.3 69.3 + - - +
81B VAL* 4.2 12.0 - - + +
85B ASP* 3.8 21.8 - - + +
89B TYR* 3.7 28.9 - - + +
107B LEU* 4.0 13.2 - - + -
----------------------------------------------------------
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