Contacts of the helix formed by residues 84 - 93 (chain C) in PDB entry 1RLI
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 SER 84 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 4.2 0.4 - - - -
8C GLY 2.7 29.6 + - - -
36C LYS* 6.0 0.2 - - - -
76C THR* 2.9 15.7 + - - -
77C PRO* 3.7 3.7 + - - -
79C TYR* 3.7 25.8 - - - -
83C MET* 1.3 78.2 - - - +
85C GLY* 1.3 64.9 + - - +
86C THR* 3.0 12.3 + - - -
87C LEU* 3.1 13.7 + - - +
88C LYS* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 4.5 2.7 - - - -
89B LEU* 4.3 15.5 - - - -
92B ASP* 3.7 21.5 + - - -
54C PRO* 4.5 5.6 - - - -
79C TYR* 4.2 3.6 - - - -
84C SER* 1.3 72.7 - - - +
86C THR* 1.3 62.7 + - - +
88C LYS* 3.4 5.9 + - - +
89C LEU* 3.0 31.2 + - - +
604C PT 4.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 3.1 19.6 + - - -
34C LEU* 3.6 22.4 + - - +
35C GLN 3.7 13.2 - - - +
36C LYS* 3.8 27.1 - - + -
54C PRO* 3.6 30.4 - - + +
56C GLN* 4.9 1.0 + - - -
84C SER* 3.0 14.4 + - - -
85C GLY* 1.3 76.7 - - - +
87C LEU* 1.3 60.4 + - - +
89C LEU* 3.9 1.7 - - - +
90C PHE* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.2 8.5 - - + +
8C GLY* 4.6 3.6 - - - -
34C LEU* 3.6 19.3 - - + -
74C PHE* 4.0 30.1 - - + -
75C ALA 4.8 3.6 - - - +
76C THR* 3.9 24.2 - - + +
83C MET* 3.7 13.5 - - + -
84C SER* 3.1 14.9 + - - +
86C THR* 1.3 82.1 + - - +
88C LYS* 1.3 57.3 + - - +
90C PHE* 3.2 13.6 + - + +
91C ILE* 2.9 33.9 + - + +
136C PHE* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR 2.9 22.0 + - - -
80B TRP* 4.4 5.3 + - - +
82B GLY* 4.1 7.4 - - - -
83B MET 2.8 34.8 + - - +
84B SER 4.3 3.6 - - - -
85B GLY* 4.5 5.4 - - - -
88B LYS* 3.8 26.0 - - + -
603B PT 4.7 5.8 - - - -
83C MET* 3.6 26.7 - - + +
84C SER 3.0 19.4 + - - +
85C GLY 3.7 4.0 - - - +
87C LEU* 1.3 77.3 - - - +
89C LEU* 1.3 58.4 + - + +
91C ILE* 3.5 2.5 + - + +
92C ASP* 2.9 58.5 + - - +
135C GLN* 5.6 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY* 4.0 26.5 - - - +
89B LEU* 4.1 26.7 - - + -
53C ARG* 6.3 0.4 - - + -
54C PRO* 3.2 31.2 - - + +
56C GLN* 3.2 25.3 + - + +
85C GLY* 3.0 20.7 + - - +
86C THR 4.0 2.9 - - - +
88C LYS* 1.3 81.4 - - + +
90C PHE* 1.3 61.2 - - - +
92C ASP* 3.7 6.4 + - + +
93C ARG* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.3 17.3 - - + -
34C LEU* 3.9 23.1 - - + -
56C GLN* 3.5 9.1 - - + +
59C TYR* 3.6 32.6 - + - -
62C ILE* 3.6 34.5 - - + -
63C ILE* 4.0 10.3 - - + -
66C ILE* 4.4 8.3 - - + -
74C PHE* 4.7 4.0 - + - -
86C THR 3.0 18.2 + - - +
87C LEU* 3.4 19.5 - - + +
88C LYS 3.2 0.2 - - - -
89C LEU* 1.3 74.0 - - - +
91C ILE* 1.3 70.6 + - + +
93C ARG* 3.2 15.9 + - - +
94C TRP* 3.6 38.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 3.6 32.8 + - + -
74C PHE* 4.7 7.6 - - + -
83C MET* 3.8 26.5 - - + -
87C LEU* 2.9 29.3 + - + +
88C LYS* 4.1 4.0 - - + +
90C PHE* 1.3 78.3 - - + +
92C ASP* 1.3 65.0 + - - +
94C TRP* 2.9 53.1 + - + +
136C PHE* 3.9 21.1 - - + -
139C ILE* 4.2 13.5 - - + -
140C PHE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 3.7 15.7 - - + +
80B TRP* 3.5 22.8 + - + +
85B GLY* 3.4 29.8 + - - -
88C LYS* 2.9 52.3 + - - +
89C LEU* 3.9 7.9 - - + +
90C PHE 3.3 0.2 - - - -
91C ILE* 1.3 77.6 - - - +
93C ARG* 1.3 60.7 + - - +
94C TRP 3.2 1.0 + - - -
95C SER* 3.3 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN* 3.0 49.6 + - - +
59C TYR* 3.3 49.5 - - + +
60C ASP* 4.9 8.7 + - - -
89C LEU 3.3 10.1 + - - +
90C PHE 3.2 11.6 + - - +
91C ILE 3.1 1.0 - - - -
92C ASP* 1.3 74.7 - - - +
94C TRP* 1.3 65.0 + - - +
95C SER 3.0 2.9 - - - -
96C GLN* 2.9 50.5 + - + +
97C THR* 3.1 8.5 + - - -
----------------------------------------------------------
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