Contacts of the helix formed by residues 122 - 135 (chain G) in PDB entry 2I2R
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 THR 122 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLY* 1.3 74.5 - - - +
123G VAL* 1.3 66.2 + - - +
124G HIS* 3.2 18.8 + - + +
125G GLU* 2.9 38.5 + - + +
126G LYS* 2.8 20.8 + - - +
207N ARG* 6.0 5.6 - - + -
210N GLN* 3.5 31.8 + - - -
211N LEU* 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLY 3.8 0.8 + - - -
122G THR* 1.3 70.9 + - - +
124G HIS* 1.3 54.8 + - - +
126G LYS* 3.2 7.4 + - - +
127G LEU* 2.7 47.2 + - + +
200G GLN* 4.3 11.9 - - - +
206G MET* 3.8 18.8 - - + -
209G LEU* 3.7 23.8 - - + -
210G GLN* 4.0 33.2 - - + +
123N VAL* 5.4 2.0 - - + -
206N MET* 6.5 0.2 - - - -
210N GLN* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G THR* 3.2 13.8 + - + +
123G VAL* 1.3 80.6 - - - +
125G GLU* 1.3 53.3 + - + +
127G LEU* 3.6 5.9 - - - +
128G ARG* 2.7 72.4 + - + +
192G LEU* 5.8 1.6 - - + -
196G LEU* 3.5 35.3 - - + +
200G GLN* 5.2 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ASN* 5.5 0.5 - - - +
117G ILE* 3.5 28.8 - - + +
121G GLY* 3.6 17.0 - - - -
122G THR* 2.9 36.6 + - + +
124G HIS* 1.3 73.5 - - - +
126G LYS* 1.3 60.7 + - - +
128G ARG* 3.5 21.5 + - - +
129G TRP* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 4.0 20.6 - - - +
118G LEU* 4.5 15.3 - - + +
121G GLY 5.0 2.2 - - - +
122G THR 2.8 12.4 + - - +
123G VAL* 3.6 10.1 - - - +
125G GLU* 1.3 75.6 - - - +
127G LEU* 1.3 62.5 + - - +
129G TRP* 3.4 5.4 + - - +
130G THR* 3.1 22.5 + - - -
209G LEU* 4.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ILE* 5.5 5.6 - - + -
123G VAL* 2.7 31.0 + - + +
124G HIS 3.6 4.0 - - - +
126G LYS* 1.3 71.0 - - - +
128G ARG* 1.3 64.3 + - - +
130G THR* 3.1 9.3 + - - +
131G PHE* 2.9 22.4 + - - +
195G PHE* 3.7 25.2 - - + -
196G LEU* 3.7 19.7 - - + +
199G CYS* 4.0 28.5 - - + -
200G GLN* 3.5 28.5 - - - +
205G ILE 5.7 0.4 - - - +
206G MET* 4.6 1.1 - - + -
209G LEU* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G HIS* 2.7 55.8 + - + +
125G GLU* 3.9 21.4 + - - +
127G LEU* 1.3 72.6 - - - +
129G TRP* 1.3 63.3 + - - +
131G PHE* 3.2 6.2 + - - +
132G ASN* 3.0 40.3 + - - +
192G LEU* 3.7 36.0 - - + +
196G LEU* 4.5 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.1 21.3 - + + -
14C ALA* 4.2 9.9 - - + -
94G LEU* 4.0 23.3 - - + -
97G ALA* 4.8 16.3 + - + -
98G PHE* 4.5 12.7 - + - -
114G ALA* 4.3 20.7 - - + +
117G ILE* 4.2 23.5 - - + +
118G LEU* 3.5 36.1 - - + -
125G GLU 3.0 14.7 + - - +
126G LYS 3.4 10.1 - - - +
127G LEU 3.1 0.2 - - - -
128G ARG* 1.3 77.5 - - - +
130G THR* 1.3 67.3 + - - +
132G ASN* 3.3 8.7 + - + +
133G LEU* 3.3 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 2.8 36.1 + - - +
15C ALA* 5.1 0.7 - - - -
17C ILE* 4.1 8.5 - - + +
126G LYS 3.1 12.3 + - - -
127G LEU* 3.1 11.5 + - - -
129G TRP* 1.3 79.7 - - - +
131G PHE* 1.3 64.6 + - - +
133G LEU* 3.0 16.6 + - - +
134G TYR* 3.0 47.2 + - + +
195G PHE* 3.9 13.7 - - + -
209G LEU* 5.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G LEU 2.9 12.8 + - - +
128G ARG 3.2 8.5 + - - +
130G THR* 1.3 77.5 - - - +
132G ASN* 1.3 68.6 + - - +
134G TYR* 3.2 7.1 + - - +
135G ASP* 2.8 33.1 + - + +
140G GLY* 3.2 43.3 - - - -
141G TYR 4.4 0.2 - - - -
142G ILE* 3.4 30.7 - - + -
190G VAL 3.9 4.5 - - - -
191G THR 3.6 7.9 - - - -
192G LEU* 3.4 51.4 - - + -
195G PHE* 3.7 25.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ALA* 5.0 6.4 - - + +
128G ARG* 3.0 43.8 + - - +
129G TRP* 3.8 8.1 - - + +
130G THR 3.2 0.2 - - - -
131G PHE* 1.3 86.4 - - - +
133G LEU* 1.3 60.9 + - - +
135G ASP* 3.3 16.2 - - - +
138G LYS* 2.8 43.5 + - - +
192G LEU* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE 4.7 1.6 - - - +
14C ALA 5.4 0.4 - - - -
15C ALA* 3.7 33.2 - - + +
90G TYR* 4.4 14.6 - - + +
93G TYR* 3.4 39.5 - - + +
94G LEU* 4.1 5.8 - - + +
97G ALA* 3.7 15.0 - - + +
129G TRP* 3.3 35.8 + - + +
130G THR* 3.0 11.8 + - - +
132G ASN* 1.3 78.3 - - - +
134G TYR* 1.3 66.5 + - + +
135G ASP 4.4 0.2 - - - -
136G ILE* 4.3 7.6 + - - +
150G ILE* 3.7 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 2.5 40.9 + - + -
17C ILE 2.9 24.1 + - - -
19C TRP* 2.9 12.0 + - - -
130G THR* 3.0 36.0 + - + +
131G PHE* 3.2 2.4 + - - +
133G LEU* 1.3 80.2 - - + +
135G ASP* 1.3 57.4 + - - +
136G ILE* 2.8 19.8 + - - +
142G ILE* 3.5 29.8 - - + +
146G GLU* 3.7 13.0 - - - +
147G MET* 3.5 34.1 - - + -
150G ILE* 3.7 22.1 - - + +
178G PHE* 4.5 7.2 - + - -
195G PHE* 4.2 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G PHE* 2.8 28.2 + - + +
132G ASN* 3.3 21.0 + - - +
133G LEU 3.4 0.6 - - - -
134G TYR* 1.3 68.4 - - - +
136G ILE* 1.4 65.7 + - - +
138G LYS* 3.1 19.3 + - - +
139G ASP* 2.7 30.4 + - - +
140G GLY* 2.8 16.4 + - - -
141G TYR 3.7 5.6 - - - +
142G ILE* 4.1 7.8 - - + +
146G GLU* 4.0 4.7 - - - -
504G CA 2.4 31.2 - - - -
----------------------------------------------------------
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