Contacts of the strand formed by residues 84 - 95 (chain B) in PDB entry 3RBH
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 TRP 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLN* 3.5 6.8 - - - +
81B TRP* 3.0 66.5 + + + +
83B ASP* 1.3 83.6 - - + +
85B SER* 1.3 63.4 + - - +
133B VAL* 3.6 28.5 - - + -
134B ASP 3.2 18.6 - - - -
135B TYR* 3.4 42.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.9 19.9 - - - -
79B GLY 3.1 15.7 - - - -
80B GLN* 4.2 7.9 - - - -
81B TRP* 3.6 5.4 - - - -
84B TRP* 1.3 76.5 - - - +
86B ALA* 1.3 60.3 + - - +
132B TRP* 4.0 5.3 - - - -
133B VAL* 3.3 7.6 - - - +
134B ASP* 2.7 55.6 + - - +
147B ARG* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA 4.5 0.7 - - - -
78B PHE* 3.4 6.4 - - - -
79B GLY* 3.0 29.6 + - - +
81B TRP* 3.9 15.5 - - + -
85B SER* 1.3 75.6 - - - +
87B TYR* 1.3 64.1 - - - +
132B TRP* 3.2 14.8 - - - +
133B VAL* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.7 32.1 - + + +
77B ALA 3.3 13.7 - - - -
78B PHE* 3.8 15.9 - + + -
86B ALA* 1.3 78.9 - - - +
88B PHE* 1.3 68.1 + - - +
89B MSE 3.7 23.7 - - + +
130B GLU* 3.9 31.9 + - + -
131B PHE* 3.0 5.4 - - - +
132B TRP* 2.9 75.6 + + + -
447B MSE 3.8 26.5 - - - +
448B SER* 5.1 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 4.7 4.5 - - + -
76B TRP* 3.2 7.8 - - - +
77B ALA* 2.9 40.7 + - + +
87B TYR* 1.3 79.5 - - - +
89B MSE 1.3 61.2 + - - +
90B GLY* 3.3 25.6 - - - -
127B ALA 5.1 0.2 - - - -
128B ALA* 4.0 28.5 - - + -
130B GLU 3.3 13.0 - - - -
131B PHE* 3.9 15.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.7 22.9 - - - +
74B ARG* 4.1 19.3 - - + -
75B PRO 3.5 8.5 - - - +
76B TRP* 3.8 20.4 - - + -
87B TYR* 3.7 28.5 - - + +
88B PHE* 1.3 79.5 - - - +
90B GLY* 1.3 71.2 + - - +
128B ALA* 3.7 1.7 - - - -
129B ARG* 2.8 52.7 + - - -
130B GLU* 2.8 28.7 + - + +
448B SER* 5.9 0.2 - - - -
449B GLN* 5.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.2 23.0 - - - +
75B PRO* 3.0 22.2 + - - -
88B PHE* 3.3 18.1 - - - -
89B MSE 1.3 78.5 - - - +
91B GLN* 1.3 63.5 + - - +
127B ALA 3.3 11.7 - - - -
129B ARG* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 2.6 33.6 + - - +
73B LEU 3.2 6.1 - - - -
74B ARG* 3.3 13.5 - - + +
75B PRO* 4.3 2.5 - - - +
90B GLY* 1.3 76.0 - - - +
92B ALA* 1.3 63.9 + - - +
93B VAL* 3.7 19.0 - - + +
101B THR* 3.9 4.6 + - - -
102B ASP* 5.7 0.2 - - - +
125B TYR* 3.8 15.4 + - + +
126B LEU* 3.2 8.4 - - - +
127B ALA* 2.9 45.7 + - + +
129B ARG* 3.0 39.8 + - + +
191B ARG* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.7 1.4 - - - +
72B ASP* 3.4 2.3 - - - -
73B LEU* 2.7 58.5 + - + +
75B PRO* 5.9 2.2 - - + -
91B GLN* 1.3 75.5 - - - +
93B VAL* 1.3 63.5 + - - +
125B TYR 3.6 3.8 - - - -
126B LEU* 3.8 17.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
71B ILE 3.4 7.2 - - - +
72B ASP* 3.6 26.7 - - + +
91B GLN* 3.7 18.2 - - + +
92B ALA* 1.3 80.1 - - - +
94B ALA* 1.3 70.1 + - - +
95B ALA* 4.6 5.6 - - + +
101B THR* 4.1 16.8 - - + +
123B LYS 4.4 6.1 - - - +
124B SER* 3.0 26.7 - - - -
125B TYR* 3.1 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLY* 3.3 0.9 - - - -
71B ILE* 2.8 46.4 + - + +
93B VAL* 1.3 74.6 - - - +
95B ALA* 1.3 60.1 + - - +
123B LYS 3.6 0.7 - - - -
124B SER* 3.4 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE 3.1 13.7 - - - +
70B GLY* 3.5 9.6 - - - -
93B VAL* 4.7 8.1 - - + -
94B ALA* 1.3 75.0 - - - +
96B THR* 1.3 65.1 + - - +
97B ASP 3.1 21.2 + - - +
99B ILE* 4.0 12.3 - - + -
123B LYS* 3.0 29.5 + - - +
124B SER* 4.5 0.7 + - - -
----------------------------------------------------------
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