Contacts of the strand formed by residues 96 - 100 (chain B) in PDB entry 1OZ7
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 CYS 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.2 34.3 - - + -
65B TRP* 3.5 25.0 - - + -
68B LEU 3.8 2.5 - - - -
69B THR* 3.7 9.9 - - - +
95B HIS* 1.3 76.0 - - - +
97B PHE* 1.3 64.7 + - - +
98B ILE* 4.5 0.3 - - - +
107B THR 3.6 0.2 - - - +
108B ARG* 3.5 1.6 - - - -
109B ARG* 3.0 31.8 + - - +
111B CYS* 2.0 46.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.2 37.0 - + - -
92A GLU* 3.2 23.6 - - - -
65B TRP* 3.4 6.6 - - - -
66B ILE* 3.2 35.2 + - + +
68B LEU* 2.8 48.9 + - + +
70B ASP* 4.1 8.3 - - + -
95B HIS 3.8 6.7 - - - -
96B CYS* 1.3 75.1 - - - +
98B ILE* 1.3 68.1 + - - +
106B TRP* 3.5 27.8 - + + -
107B THR 3.5 3.6 - - - -
108B ARG* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.6 7.0 - - + -
64B VAL 3.5 15.5 - - - +
65B TRP* 3.4 18.8 - - + -
66B ILE* 3.8 7.2 - - - -
96B CYS 4.5 1.3 - - - +
97B PHE* 1.3 83.5 - - - +
99B TYR* 1.3 71.4 + - - +
100B LYS* 4.0 17.5 - - + -
106B TRP* 3.0 6.1 - - - +
107B THR* 2.7 49.6 + - + +
109B ARG* 4.6 10.3 - - + -
115B PHE* 3.1 51.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 5.5 2.5 - + - -
42B PHE* 4.1 13.7 - + + -
48B VAL* 3.3 35.9 - - + +
52B ILE* 3.4 21.4 - - + +
62B ASP 3.7 0.2 - - - +
63B LEU* 3.2 24.8 + - - +
64B VAL* 3.1 28.2 + - + +
66B ILE* 4.0 9.4 - - + +
98B ILE* 1.3 75.3 - - - +
100B LYS* 1.3 79.1 + - - +
101B ASN* 3.4 27.1 + - - -
104B ASN* 3.7 18.2 + - - +
105B GLN* 3.8 11.7 - - - -
106B TRP* 3.6 27.4 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP 3.4 3.8 - - - -
63B LEU* 3.9 30.7 - - + -
98B ILE* 4.0 9.6 - - + -
99B TYR* 1.3 77.8 - - - +
101B ASN* 1.3 60.0 + - - +
102B THR* 4.6 4.7 - - - +
103B ASP* 3.3 32.6 + - + +
104B ASN* 2.9 24.1 + - - -
105B GLN 3.1 12.9 + - - +
107B THR* 3.9 33.7 + - - +
109B ARG* 5.5 10.6 - - - +
----------------------------------------------------------
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