Contacts of the strand formed by residues 88 - 96 (chain B) in PDB entry 3BX9
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 PHE 88 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 4.1 24.0 - - + -
68B THR* 3.6 20.9 - - - -
79B PHE* 4.9 4.3 - - + -
80B PHE* 3.7 52.0 - + + -
83B SER* 4.1 6.1 - - - +
84B PHE* 3.7 7.6 - + - -
87B GLY* 1.3 79.1 - - - +
89B THR* 1.3 78.9 + - - +
90B TRP* 4.4 7.2 - + - -
108B THR* 2.9 69.3 + - + +
117B TYR* 5.9 0.2 - + - -
179B ARG 3.1 18.2 - - - +
180B SER* 4.0 3.6 - - - -
181B LYS* 3.4 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 4.2 2.6 + - - -
88B PHE* 1.3 82.6 - - - +
90B TRP* 1.3 62.8 + - - +
91B GLU* 2.9 17.1 + - - -
106B GLN* 3.1 16.4 - - - +
107B ASP* 3.4 26.9 - - + +
178B TYR* 3.4 3.6 - - - -
179B ARG* 2.8 47.1 + - - +
181B LYS* 4.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER* 3.7 24.7 - - - -
63B NRQ 3.1 41.2 + - - -
67B LYS* 4.4 9.6 - - + -
88B PHE* 4.4 14.8 - + - -
89B THR* 1.3 74.4 - - - +
91B GLU* 1.3 73.1 + - - +
92B ARG* 3.7 38.1 - - + -
104B ALA* 3.5 38.1 - - + -
105B THR* 3.4 0.7 - - - -
106B GLN* 2.8 70.4 + - + -
119B VAL* 4.6 1.3 - - + -
176B THR* 4.1 1.3 - - + -
177B THR 3.1 4.5 - - - +
178B TYR* 3.4 28.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.9 23.9 + - - +
122A ARG* 3.2 28.2 + - - +
124A VAL* 3.9 21.1 - - + +
89B THR* 2.9 27.9 + - - -
90B TRP* 1.3 85.4 - - - +
92B ARG* 1.3 60.7 + - - +
104B ALA 3.3 5.2 - - - -
105B THR* 3.7 12.3 - - + -
106B GLN 4.3 0.9 + - - +
175B LYS 4.0 0.5 - - - +
176B THR* 3.4 1.6 - - - -
177B THR* 2.7 58.6 + - - +
179B ARG* 4.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.1 6.4 - - - +
60B THR* 2.8 42.1 + - - -
61B SER* 4.6 0.8 + - - +
63B NRQ 2.7 42.3 + - - -
90B TRP* 3.7 34.6 - - + -
91B GLU* 1.3 75.0 - - - +
93B VAL* 1.3 65.5 + - - +
94B THR* 3.5 24.5 - - - +
102B LEU* 3.9 1.3 - - - +
103B THR* 3.2 7.3 - - - -
104B ALA* 2.9 37.8 + - + +
174B LEU* 3.8 13.7 - - - +
175B LYS 3.3 11.4 - - - +
176B THR* 2.9 25.6 + - - +
178B TYR* 3.6 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 4.3 22.9 - - + -
124A VAL* 3.9 23.6 - - + -
125A ASN* 4.1 2.5 - - - +
92B ARG* 1.3 73.5 - - - +
94B THR* 1.3 62.0 + - - +
95B THR* 3.9 13.9 + - - +
101B VAL* 3.9 25.8 - - + -
102B LEU 3.6 2.7 - - - -
103B THR* 4.0 13.5 - - + -
173B ASN 3.7 2.1 - - - +
174B LEU* 3.7 1.0 - - - -
175B LYS* 3.0 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 5.0 3.6 + - - -
92B ARG* 3.5 24.3 - - - +
93B VAL* 1.3 70.8 - - - +
95B THR* 1.3 62.4 + - - +
96B TYR* 3.5 29.3 + - + +
100B GLY 3.8 0.7 - - - +
101B VAL* 3.4 5.2 - - - +
102B LEU* 2.8 50.3 + - - +
172B CYS* 3.6 23.1 - - + -
173B ASN 3.4 3.6 - - - -
174B LEU* 3.6 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.9 16.1 + - - +
94B THR* 1.3 72.9 - - - +
96B TYR* 1.3 71.4 + - - +
97B GLU* 5.2 1.4 - - - +
99B GLY* 5.6 1.6 - - - +
100B GLY 3.6 7.0 - - - +
101B VAL* 4.5 13.5 - - + +
172B CYS* 3.2 4.0 - - - -
173B ASN* 2.9 40.7 + - - +
175B LYS* 6.0 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.5 31.6 + - + +
94B THR* 3.5 24.6 - - + +
95B THR* 1.3 81.9 - - - +
97B GLU* 1.3 59.2 + - - +
98B ASP* 3.1 20.2 - - - +
99B GLY* 3.0 19.8 + - - -
100B GLY* 2.9 22.7 + - - +
102B LEU* 4.8 3.6 - - + -
126B PHE* 3.8 26.9 - + - -
132B VAL* 4.7 2.0 - - + -
140B TRP* 3.5 33.3 - + - -
162B LEU* 4.3 13.5 - - + -
170B LEU* 3.9 22.9 - - + -
171B ILE 3.7 3.8 - - - -
172B CYS* 3.7 18.0 - - + -
----------------------------------------------------------
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