Contacts of the strand formed by residues 98 - 104 (chain F) in PDB entry 1RBO
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 98 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F TYR* 3.6 36.1 - + - -
44F PHE* 3.2 4.7 - - - +
45F GLU 2.8 39.5 + - - +
46F THR 5.4 6.1 - - - -
49F GLY* 3.9 26.5 - - - -
50F PHE* 4.3 9.4 - + - -
67F TRP* 3.5 23.6 - + + -
96F ASN 5.4 0.7 - - - -
97F ALA* 1.3 73.8 - - - +
99F ILE* 1.3 61.4 + - - +
116F ILE* 4.2 4.9 - - + -
118F TYR 3.5 4.0 - - - -
119F LYS* 4.1 8.7 - - + -
120F PRO* 3.6 23.3 - - + -
123F TYR* 3.7 40.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 4.5 9.9 - - + -
43F GLU 3.4 11.4 - - - +
44F PHE* 4.1 4.7 - - + -
87F LEU* 3.9 18.2 - - + -
90F CYS* 3.7 34.3 - - + +
91F LYS* 3.7 26.5 - - + +
94F TYR 4.4 4.9 - - - +
97F ALA* 4.1 3.8 - - + +
98F PHE* 1.3 81.0 - - - +
100F ARG* 1.3 63.0 + - - +
116F ILE* 3.6 4.2 - - - +
117F ALA* 2.7 30.1 + - + -
118F TYR* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E ASN* 4.1 19.0 + - - +
42F LEU* 3.4 6.4 - - - +
43F GLU* 2.9 61.1 + - + +
64F GLY 5.6 0.4 + - - -
65F ARG 3.1 24.0 + - - -
66F TYR* 4.8 0.2 - - - +
67F TRP* 3.4 59.2 - - + +
99F ILE* 1.3 76.5 - - - +
101F ILE* 1.3 64.2 + - - +
102F ILE* 4.1 11.6 + - + +
111F GLN* 6.0 0.8 - - - +
114F SER* 4.1 16.3 + - - -
115F PHE 3.3 19.3 - - - +
116F ILE* 4.0 6.1 - - + -
117F ALA 4.0 0.7 - - - +
183H LYS* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 4.6 3.4 - - + -
30F VAL* 4.3 11.4 - - + -
33F LEU* 4.2 17.3 - - + -
40F PRO* 5.2 0.2 - - + -
41F CYS 3.6 8.3 - - - +
42F LEU* 4.4 13.5 - - + -
83F VAL* 4.3 26.2 - - + -
84F LEU* 5.2 1.1 - - + -
87F LEU* 4.4 15.5 - - + -
100F ARG* 1.3 78.1 - - - +
102F ILE* 1.3 69.9 + - - +
113F ILE* 4.3 0.6 - - - +
114F SER* 3.2 3.8 + - - -
115F PHE* 2.9 59.4 + - + +
117F ALA* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 3.8 6.9 - - - +
40F PRO* 3.4 3.8 - - - +
41F CYS* 2.9 49.9 + - + +
43F GLU* 3.6 39.9 - - + +
100F ARG* 4.1 10.5 - - + +
101F ILE* 1.3 81.6 - - - +
103F GLY* 1.3 58.5 + - - +
104F PHE* 3.7 29.4 - - + -
111F GLN* 3.8 24.2 - - - +
113F ILE 3.3 9.9 - - - +
114F SER* 3.8 17.5 - - - +
187H ARG* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 3.8 21.3 - - - -
38F TRP* 4.2 4.7 - - - -
39F VAL 3.2 8.1 - - - -
102F ILE* 1.3 75.1 - - - +
104F PHE* 1.3 62.6 + - - -
111F GLN* 3.4 4.6 - - - -
112F CYS* 2.9 28.9 + - - +
113F ILE* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LYS 4.6 0.2 - - - +
38F TRP* 3.2 9.2 - - - -
39F VAL* 2.8 54.5 + - + +
41F CYS* 3.8 26.0 - - + -
69F MET* 5.3 0.4 - - + -
73F PRO* 4.1 18.6 - - + -
75F PHE* 6.1 1.1 - + - -
102F ILE* 3.7 16.2 - - + -
103F GLY* 1.3 72.8 - - - -
105F ASP* 1.3 64.1 + - - +
106F SER* 3.7 6.0 + - - +
109F GLU* 6.1 2.2 - - + -
110F VAL 3.9 4.9 - - - -
111F GLN* 3.8 21.8 - - + -
184H ASN* 4.0 13.9 - - - -
187H ARG* 3.5 38.4 - - - -
----------------------------------------------------------
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