Contacts of the strand formed by residues 85 - 91 (chain C) in PDB entry 2BKU
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 85 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.9 1.8 - - - -
12C LYS 3.6 11.9 - - - +
13C LEU* 3.4 24.8 - - - -
14C VAL* 3.1 23.0 + - - +
61C PHE* 4.1 9.2 - - - -
83C ALA* 3.4 3.7 - - - +
84C GLN* 1.3 79.4 - - - +
86C ALA* 1.3 64.1 + - - +
115C ILE* 3.8 7.6 - - - +
116C PRO* 3.3 17.7 - - + +
164C LEU* 3.9 11.2 - - + -
168C LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.7 1.6 - - - -
14C VAL* 3.2 26.9 - - + +
85C CYS* 1.3 80.7 - - - +
87C ILE* 1.3 66.6 + - - +
88C ILE 4.2 0.2 - - - -
108C LEU* 3.6 28.0 - - + -
115C ILE* 4.0 6.3 - - + -
116C PRO 3.2 6.3 + - - +
117C ILE* 3.3 8.3 - - + -
118C VAL 3.0 23.5 + - - -
164C LEU* 4.1 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.2 11.0 - - + -
14C VAL 3.0 7.2 + - - +
15C LEU* 3.4 26.6 - - + -
16C VAL* 2.9 30.2 + - - +
26C PHE* 4.4 8.3 - - + -
86C ALA* 1.3 77.9 - - - +
88C ILE* 1.3 70.8 + - - +
89C MET* 4.2 6.5 - - + -
118C VAL* 3.4 10.1 - - + +
120C CYS* 4.0 20.4 - - - -
160C PRO* 4.0 20.9 - - + -
161C PHE* 4.2 27.8 - - + -
164C LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 3.4 18.8 - - + +
87C ILE* 1.3 74.0 - - - +
89C MET* 1.3 64.4 + - - +
101C VAL* 4.2 20.0 - - + +
104C TRP* 4.1 18.4 - - + -
105C HIS* 3.7 42.4 - - + +
108C LEU* 4.0 6.5 - - + -
117C ILE* 3.9 24.0 - - + -
118C VAL 2.8 10.9 + - - +
119C LEU* 3.4 21.9 - - + +
120C CYS* 2.9 26.3 + - - -
144C LEU* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 4.1 16.2 - - + -
16C VAL 2.8 14.6 + - - +
17C GLY* 3.3 21.3 - - - -
18C ASP 4.1 2.6 + - - -
21C THR* 3.9 10.7 + - - +
22C GLY 3.9 25.8 - - - +
23C LYS* 4.0 13.0 - - + -
26C PHE* 3.9 35.0 - - + -
87C ILE* 4.0 9.1 - - + -
88C ILE* 1.3 78.8 - - - +
90C PHE* 1.3 72.0 + - - +
97C THR 5.0 0.9 - - - +
101C VAL* 5.2 0.9 - - - +
104C TRP* 5.4 0.5 - - - -
120C CYS* 3.5 20.4 - - + +
122C ASN* 3.8 20.6 - - + -
149C ILE* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 4.0 10.5 - - - -
89C MET* 1.3 73.7 - - - +
91C ASP* 1.3 68.5 + - - +
92C VAL* 4.0 12.6 - - + -
97C THR 3.2 25.6 - - - +
98C TYR* 3.7 33.2 - + + -
101C VAL* 3.9 7.2 - - + -
119C LEU* 3.7 23.3 - - + -
120C CYS 2.9 13.4 + - - +
121C GLY* 3.6 18.6 - - - -
122C ASN* 2.8 30.5 + - - +
131C VAL* 4.1 11.9 - - + -
136C ILE* 3.7 17.3 - - + -
146C TYR* 3.6 28.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLY 4.1 2.5 - - - +
21C THR* 3.6 20.4 - - + +
90C PHE* 1.3 74.6 - - - +
92C VAL* 1.3 59.9 + - - +
93C THR* 2.9 31.3 + - - +
94C SER* 2.9 28.4 + - - +
97C THR* 2.8 29.1 + - + +
122C ASN 3.8 3.4 - - - -
123C LYS* 3.1 45.9 + - - +
131C VAL* 4.5 0.5 - - - +
----------------------------------------------------------
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