Contacts of the strand formed by residues 88 - 96 (chain F) in PDB entry 3BXB
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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F NRQ 5.9 0.2 - - - -
67F LYS* 3.9 23.8 - - + -
68F THR* 3.4 27.1 - - - -
79F PHE* 4.9 4.3 - + + -
80F PHE* 3.6 48.9 - + + -
83F SER* 4.0 11.4 - - - +
84F PHE* 3.5 17.0 - + - -
87F GLY* 1.3 78.6 - - - +
89F THR* 1.3 74.4 + - - +
90F TRP* 4.6 5.2 - + - -
108F THR* 2.8 61.1 + - + +
117F TYR* 6.0 0.4 - + - -
178F TYR* 5.3 0.4 - + - -
179F ARG 3.5 14.1 - - - +
180F SER* 4.4 1.3 - - - -
181F LYS* 3.6 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F PHE* 1.3 82.8 - - - +
90F TRP* 1.3 65.8 + - - +
106F GLN* 3.3 15.0 - - - +
107F ASP* 3.6 25.6 - - + +
108F THR 4.6 0.2 - - - +
178F TYR* 3.6 2.8 - - - -
179F ARG* 3.0 37.9 + - - +
181F LYS* 4.5 11.7 - - + -
21G ASN* 2.5 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F SER* 3.7 22.4 - - - -
63F NRQ 2.9 43.6 + - - -
67F LYS* 4.3 17.9 - - + -
88F PHE* 4.6 6.1 - + - -
89F THR* 1.3 74.6 - - - +
91F GLU* 1.3 74.5 + - - +
92F ARG* 3.6 34.1 - - + -
104F ALA* 3.6 31.2 - - + -
105F THR* 3.4 2.1 - - - -
106F GLN* 2.7 79.2 + - + +
119F VAL* 4.3 2.0 - - + -
176F THR* 4.4 1.8 - - + -
177F THR 3.4 5.4 - - - +
178F TYR* 3.6 25.4 - + + -
21G ASN* 4.2 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F TRP* 1.3 73.8 - - - +
92F ARG* 1.3 62.4 + - - +
104F ALA 3.4 6.3 - - - +
105F THR* 4.5 6.5 - - + -
175F LYS 3.9 0.2 - - - +
176F THR* 3.0 6.3 - - - +
177F THR* 2.9 40.0 + - - +
179F ARG* 2.3 35.9 + - - -
20G ASN* 3.2 35.3 - - - +
21G ASN* 3.1 32.9 + - - +
124G VAL* 3.9 16.4 - - + -
125G ASN* 3.5 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F THR* 3.1 32.7 + - - -
61F SER* 4.6 1.4 + - - +
63F NRQ 2.4 31.9 + - - +
67F LYS* 4.7 0.2 - - - +
90F TRP* 3.6 32.1 - - + -
91F GLU* 1.3 76.3 - - - +
93F VAL* 1.3 64.5 + - - +
94F THR* 3.5 15.0 - - - +
102F LEU 3.8 1.1 - - - +
103F THR* 3.3 5.9 - - - -
104F ALA* 2.9 35.1 + - + +
145F GLU* 5.2 0.8 + - - -
174F LEU* 3.5 30.1 - - - +
175F LYS 3.2 12.8 - - - +
176F THR* 3.4 20.3 + - + +
178F TYR* 3.8 19.2 + - - -
124G VAL* 3.9 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ARG* 1.3 73.5 - - - +
94F THR* 1.3 63.6 + - - +
95F THR* 4.0 11.2 + - - +
101F VAL* 3.6 28.3 - - + -
102F LEU 3.6 2.9 - - - -
103F THR* 4.1 2.9 - - + -
173F ASN* 3.7 1.7 - - - +
174F LEU* 3.5 2.4 - - - -
175F LYS* 2.9 65.0 + - + +
101G VAL* 4.1 26.2 - - + -
124G VAL* 3.6 20.4 - - + +
125G ASN* 4.4 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F THR* 5.0 3.6 + - - +
92F ARG* 3.5 14.4 - - - +
93F VAL* 1.3 72.9 - - - +
95F THR* 1.3 63.5 + - - +
96F TYR* 3.7 25.9 + - + +
100F GLY 3.8 0.9 - - - +
101F VAL* 3.3 6.4 - - - +
102F LEU* 2.9 49.3 + - - +
172F CYS* 3.7 24.0 - - + -
173F ASN 3.3 5.8 - - - +
174F LEU* 3.4 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F VAL* 4.0 15.4 + - - +
94F THR* 1.3 74.8 + - - +
96F TYR* 1.3 71.4 + - - +
97F GLU* 3.8 2.6 + - - +
99F GLY 6.0 0.7 - - - -
100F GLY 3.8 5.8 - - - +
101F VAL* 4.4 14.5 - - + +
172F CYS* 3.3 5.2 - - - -
173F ASN* 2.8 44.3 + - - +
175F LYS* 5.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ILE* 3.5 32.0 + - + +
94F THR* 3.7 22.5 - - + +
95F THR* 1.3 83.1 - - - +
97F GLU* 1.3 58.5 + - - +
98F ASP* 3.1 18.6 - - - +
99F GLY* 2.9 23.2 + - - -
100F GLY* 2.8 26.0 + - - +
102F LEU* 4.9 3.8 - - + -
126F PHE* 3.7 28.5 - + - -
132F VAL* 4.8 0.4 - - + -
140F TRP* 3.3 36.6 - + - -
162F LEU* 4.6 2.2 - - + -
170F LEU* 3.8 31.0 - - + -
171F ILE 3.7 2.7 - - - +
172F CYS* 3.7 14.4 - - + -
----------------------------------------------------------
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