Contacts of the helix formed by residues 116 - 134 (chain A) in PDB entry 2RIO
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 ASN 116 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 1.3 80.9 + - - +
117A PRO* 1.3 70.2 - - - +
118A ILE* 3.3 22.1 - - - +
119A SER* 3.4 31.5 + - - -
120A LEU* 3.4 14.7 + - - +
164A ASN* 5.3 2.8 - - - +
263A LEU* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR* 3.5 27.5 - - + +
116A ASN* 1.3 90.0 - - - +
118A ILE* 1.3 65.3 + - - +
120A LEU* 3.1 12.2 + - + +
121A LEU* 3.0 25.5 + - - +
232A ILE* 3.8 21.1 - - + -
233A LEU* 3.9 18.2 - - + -
262A CYS* 4.3 20.2 - - + +
263A LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 3.3 14.5 - - - +
117A PRO* 1.3 77.4 - - - +
119A SER* 1.3 56.9 + - - +
121A LEU* 3.1 7.6 + - - +
122A ARG* 2.9 24.8 + - + +
233A LEU* 4.6 7.6 - - + -
263A LEU* 4.1 20.4 - - + -
268A LEU* 4.0 28.9 - - + -
298A LEU* 3.9 39.3 - - + +
299A PHE* 3.5 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 3.4 29.7 + - - -
118A ILE* 1.3 78.3 - - - +
120A LEU* 1.4 58.8 + - - +
122A ARG* 3.2 11.5 + - - +
123A GLN* 3.0 39.3 + - - +
163A GLU* 2.5 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.7 4.9 - - + -
98A LEU* 3.7 23.6 - - + -
115A TYR* 3.5 34.1 - - + +
116A ASN 3.4 6.4 + - - +
117A PRO* 3.1 11.1 + - + +
119A SER* 1.4 79.2 + - - +
121A LEU* 1.3 62.6 + - - +
123A GLN* 3.3 13.4 + - - +
124A ILE* 3.1 29.6 + - - +
148A VAL* 6.0 0.4 - - + -
165A LEU* 3.9 30.5 - - + +
167A ILE* 4.1 21.4 - - + +
232A ILE* 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO 3.0 21.6 + - - +
118A ILE* 3.1 12.5 + - - +
120A LEU* 1.3 71.2 - - - +
122A ARG* 1.3 66.5 + - - +
123A GLN 3.3 0.2 + - - -
124A ILE* 3.4 3.4 + - - -
125A ALA* 3.1 18.9 + - - +
229A PHE* 3.4 56.7 - - + +
232A ILE* 4.0 30.3 - - + -
233A LEU* 3.9 25.4 - - + -
276A ILE* 5.4 0.4 - - + -
298A LEU* 3.6 29.2 - - + -
299A PHE* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 4.9 3.4 - - - +
118A ILE* 2.9 12.6 + - + +
119A SER* 3.2 11.5 + - - +
121A LEU* 1.3 76.7 - - - +
123A GLN* 1.3 84.0 + - - +
125A ALA* 3.5 5.0 + - - +
126A SER* 3.0 42.8 + - - -
163A GLU* 3.6 23.8 + - - +
294A LEU* 4.0 14.9 - - + +
299A PHE* 3.5 30.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 3.0 38.8 + - - +
119A SER* 3.0 34.1 + - - +
120A LEU* 3.7 11.2 - - - +
121A LEU 3.2 0.4 - - - -
122A ARG* 1.3 97.9 - - - +
124A ILE* 1.3 65.9 + - - +
126A SER* 3.2 1.8 + - - -
127A GLY 3.1 19.2 + - - -
163A GLU* 4.3 8.8 + - - +
165A LEU 2.9 21.2 + - - -
166A ARG* 3.1 13.1 - - - -
167A ILE* 3.0 33.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.4 0.7 - - + -
120A LEU 3.1 16.9 + - - +
121A LEU 3.4 6.7 + - - +
123A GLN* 1.3 76.9 - - - +
125A ALA* 1.3 56.9 + - - +
127A GLY 3.4 0.5 + - - -
128A VAL* 3.0 30.9 + - + +
141A LEU* 5.9 1.3 - - + -
146A ILE* 4.3 20.6 - - + -
167A ILE* 3.7 32.7 - - + +
169A ILE* 3.5 7.5 - - + +
225A MET* 3.5 30.1 - - + -
228A VAL* 3.7 17.9 - - + -
229A PHE* 4.1 6.1 - - + -
232A ILE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU 3.1 17.0 + - - +
122A ARG* 3.6 6.3 - - - +
124A ILE* 1.3 75.9 - - - +
126A SER* 1.3 57.8 + - - +
128A VAL* 4.0 0.5 - - - +
129A ALA* 2.7 32.2 + - - +
225A MET* 3.7 14.1 - - - -
229A PHE* 4.0 4.3 - - + -
290A ALA* 4.7 3.3 - - - +
293A VAL* 3.7 30.5 - - + -
294A LEU* 3.8 16.6 - - + +
299A PHE* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 2.9 19.6 + - - -
70A ASN* 3.8 7.4 + - - -
122A ARG* 3.0 30.6 + - - -
123A GLN 3.6 5.4 - - - -
124A ILE 3.2 0.2 - - - -
125A ALA* 1.3 75.2 - - - +
127A GLY* 1.3 58.6 + - - +
130A HIS* 3.0 15.1 + - - +
294A LEU* 4.2 6.3 - - - +
159B GLN* 2.7 47.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 3.6 18.6 + - - -
70A ASN* 3.9 5.4 - - - -
71A VAL* 4.0 5.2 - - - -
123A GLN 3.1 10.3 + - - -
124A ILE 3.7 2.9 - - - -
126A SER* 1.3 73.7 - - - +
128A VAL* 1.3 63.6 + - - +
130A HIS* 3.2 5.9 + - - +
131A LEU* 3.1 24.7 + - - +
169A ILE* 3.7 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.0 13.3 + - + +
125A ALA 4.0 1.6 - - - +
127A GLY* 1.3 74.3 - - - +
129A ALA* 1.3 65.1 + - - +
131A LEU* 3.1 12.0 + - + +
132A HIS* 3.0 52.8 + - + +
141A LEU* 3.9 17.7 - - + -
169A ILE* 3.7 13.0 - - + -
221A ASP* 4.0 8.7 - - - +
222A ILE* 4.7 4.0 - - + -
225A MET* 2.4 44.2 - - + -
290A ALA* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 2.7 22.8 + - - +
126A SER 3.7 3.1 - - - +
128A VAL* 1.3 73.5 - - - +
130A HIS* 1.3 61.7 + - - +
132A HIS* 3.3 3.4 + - - +
133A SER* 3.0 25.6 + - - -
290A ALA* 3.5 22.5 - - + +
291A MET* 4.0 15.1 - - + +
294A LEU* 3.6 23.8 - - + -
157B ASP* 4.4 1.7 - - - +
159B GLN* 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 4.6 0.2 - - - -
65A SER* 3.1 32.5 + - - -
67A ASP* 5.0 0.4 - - - +
68A HIS* 3.3 33.7 + - + +
71A VAL* 4.1 3.4 - - - +
126A SER 3.0 14.8 + - - +
127A GLY 3.2 10.8 - - - +
128A VAL 3.2 0.2 - - - -
129A ALA* 1.3 73.8 - - - +
131A LEU* 1.3 66.6 + - - +
133A SER* 3.2 17.2 - - - -
134A LEU* 3.4 32.6 - - + +
153B ARG 3.9 19.2 + - - -
157B ASP* 3.0 40.5 - - + +
159B GLN* 3.6 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER* 3.8 21.3 - - - -
71A VAL* 3.7 27.6 - - + -
127A GLY 3.1 9.4 + - - +
128A VAL* 3.1 18.8 + - + +
130A HIS* 1.3 78.1 - - - +
132A HIS* 1.3 58.7 + - - +
134A LEU* 3.2 11.6 + - - +
136A ILE* 2.7 52.7 + - + +
138A HIS* 4.0 30.3 - - + +
169A ILE* 4.7 8.5 - - + -
172A PHE* 3.9 22.7 - - + -
221A ASP* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 3.0 27.7 + - + +
129A ALA* 3.7 7.6 - - - +
131A LEU* 1.3 74.4 - - + +
133A SER* 1.3 61.3 + - - +
134A LEU 3.3 0.2 - - - -
135A LYS 3.2 4.9 + - - +
136A ILE 3.2 13.8 + - - +
137A ILE* 4.6 0.7 - - - -
218A ARG* 2.9 72.9 + - + +
221A ASP* 2.5 45.4 + - - -
222A ILE* 4.2 7.9 - - + +
290A ALA* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.0 13.4 + - - -
130A HIS 3.2 13.7 - - - -
132A HIS* 1.3 76.1 - - - +
134A LEU* 1.3 59.2 - - - -
135A LYS* 3.1 13.3 + - - +
218A ARG* 5.2 1.1 + - - +
156B ALA* 3.6 17.0 + - - +
157B ASP* 3.5 36.7 + - - -
158B GLN 4.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 3.4 39.5 - - + +
65A SER* 3.9 14.4 - - - +
130A HIS* 3.4 37.0 - - + +
131A LEU* 3.2 8.4 + - - +
133A SER* 1.3 77.4 - - - +
135A LYS* 1.3 67.7 + - - +
136A ILE* 3.3 10.6 + - + +
177A LYS* 3.0 28.1 - - - -
152B SER* 3.4 15.9 - - - +
153B ARG* 4.8 2.0 - - - +
156B ALA* 3.3 31.2 - - + -
157B ASP 5.0 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