Contacts of the helix formed by residues 89 - 99 (chain B) in PDB entry 2RS9
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 ASP 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.2 10.1 - - - +
70B GLU 4.3 2.5 - - - +
71B PRO* 3.6 39.4 - - + +
72B VAL 5.5 0.2 - - - +
87B PRO 5.6 0.2 - - - -
88B MET* 1.3 80.8 - - - +
90B PHE* 1.3 58.1 + - - +
91B PHE* 3.4 10.4 + - - +
92B THR* 2.7 45.2 + - - -
93B MET* 3.0 28.4 + - - +
115B ILE* 3.7 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.8 20.4 - - + +
59B LEU* 3.5 50.0 - - + -
60B GLN* 3.3 36.6 + - + +
63B ASP* 5.0 3.8 - - + -
68B PHE* 3.4 48.0 + - + +
69B SER* 4.1 6.7 - - - +
89B ASP* 1.3 71.1 - - - +
91B PHE* 1.3 60.0 + - - +
93B MET* 3.5 9.9 - - + +
94B LYS* 3.1 26.7 + - - +
112B PHE* 4.0 17.9 - + - -
115B ILE* 4.9 10.1 - - + -
136B LEU* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER 4.4 10.7 + - - +
71B PRO* 4.9 14.4 - - + -
89B ASP* 3.3 11.4 + - - +
90B PHE* 1.3 76.0 - - - +
92B THR* 1.3 62.4 + - - +
94B LYS* 3.4 10.1 + - + +
95B GLN* 2.9 70.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO 5.7 0.4 - - - +
88B MET* 3.5 29.9 - - - -
89B ASP* 2.7 34.2 + - - -
91B PHE* 1.3 75.8 - - - +
93B MET* 1.3 58.1 + - - +
95B GLN* 3.8 6.2 - - + +
96B ASN* 2.9 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.9 20.9 - - + -
59B LEU* 6.1 1.3 - - + -
88B MET* 4.3 3.5 - - + +
89B ASP 3.0 17.2 + - - +
90B PHE* 3.5 12.8 - - + +
92B THR* 1.3 75.7 - - - +
94B LYS* 1.3 57.1 + - - +
96B ASN 3.4 0.2 + - - -
97B LEU* 3.0 29.5 + - - +
102B TYR* 3.6 20.0 - - - -
108B PHE* 3.7 45.1 - - + +
111B ASP* 3.6 34.5 - - - -
112B PHE* 4.3 16.6 - - + +
115B ILE* 3.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 5.5 2.4 + - - -
53B ARG* 5.1 20.8 + - - +
56B LEU* 3.6 23.6 - - + +
57B GLU* 5.5 9.1 - - - +
90B PHE 3.1 14.7 + - - +
91B PHE* 3.4 11.6 + - + +
93B MET* 1.3 78.7 - - - +
95B GLN* 1.3 56.8 + - + +
97B LEU* 3.2 7.7 + - + +
98B GLU* 2.9 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 2.9 61.1 + - + +
92B THR* 3.8 7.6 - - + +
93B MET 3.4 0.2 - - - -
94B LYS* 1.3 71.8 - - + +
96B ASN* 1.3 65.5 + - - +
98B GLU* 3.4 22.2 + - - +
99B ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 4.0 14.8 - - - +
92B THR* 2.9 29.6 + - - +
93B MET 3.7 0.2 - - - +
95B GLN* 1.3 76.2 - - - +
97B LEU* 1.3 61.0 + - - +
99B ALA* 3.2 5.6 + - - -
101B ARG* 3.1 49.4 + - + +
102B TYR* 3.2 35.4 + - + +
111B ASP* 5.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 4.6 11.5 - - - +
44B GLY 6.1 0.2 - - - +
49B LEU* 4.6 4.4 - - + +
52B LEU* 3.5 43.7 - - + +
53B ARG* 3.8 28.7 - - + +
56B LEU* 4.1 12.6 - - + -
93B MET 3.0 17.2 + - - +
94B LYS* 3.2 11.4 + - - +
96B ASN* 1.3 75.1 - - - +
98B GLU* 1.3 62.9 + - + +
99B ALA 3.2 0.2 - - - -
100B TYR* 3.2 17.2 + - - +
101B ARG 5.0 0.9 - - - +
102B TYR* 3.9 13.9 - - + +
108B PHE* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY* 3.7 26.3 - - - -
42B SER* 4.1 12.6 + - - +
43B SER* 4.3 21.3 - - - +
94B LYS* 2.9 49.0 + - + +
95B GLN* 3.4 25.9 + - - +
97B LEU* 1.3 75.7 - - + +
99B ALA* 1.3 54.9 + - - +
100B TYR* 3.5 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLN 3.0 18.0 + - - +
96B ASN* 3.2 3.8 + - - +
97B LEU 3.2 0.4 - - - -
98B GLU* 1.3 74.8 - - - +
100B TYR* 1.3 69.7 + - - +
101B ARG* 3.0 44.4 + - + +
----------------------------------------------------------
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