Contacts of the helix formed by residues 123 - 144 (chain B) in PDB entry 2ONL
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 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LYS* 4.6 6.1 - - - +
122B LEU* 1.3 75.4 - - - +
124B ASP* 1.3 64.4 + - - +
125B ASP* 3.1 20.4 + - - +
126B HIS* 2.9 41.4 + - + +
127B VAL* 3.1 16.4 + - - +
374D LYS* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 1.3 73.2 - - - +
125B ASP* 1.3 58.0 + - - +
127B VAL* 3.4 6.0 + - - +
128B GLN* 2.9 39.5 + - - +
217B LEU* 3.6 19.5 - - + +
278B ASN* 2.9 39.7 + - - +
307B TYR* 3.2 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 3.0 12.3 + - - +
124B ASP* 1.3 76.8 - - - +
126B HIS* 1.3 66.1 + - - +
128B GLN* 3.2 22.8 + - - +
129B PHE 3.1 13.2 + - - -
310B GLN* 5.7 1.7 - - - +
311B TYR* 3.9 4.2 + - - -
375D ILE* 3.0 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLN* 4.1 21.3 - - - -
121B LYS 5.5 0.2 - - - -
122B LEU* 3.5 28.2 - - + +
123B THR* 2.9 44.1 + - + +
125B ASP* 1.3 78.8 - - - +
127B VAL* 1.3 53.6 + - - +
129B PHE* 3.1 4.5 + - - +
130B LEU* 2.7 40.8 + - + +
162B CYS* 3.5 26.0 - - - -
372D ILE* 3.5 5.3 - - + +
373D LYS 2.9 24.0 + - - -
374D LYS* 3.9 12.1 - - + -
375D ILE* 3.7 16.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.6 11.2 - - + +
123B THR 3.1 17.9 + - - +
124B ASP* 3.7 8.3 - - - +
126B HIS* 1.3 74.0 - - - +
128B GLN* 1.3 64.3 + - - +
130B LEU* 4.2 8.7 - - - -
131B ILE* 2.9 33.9 + - + +
213B MET* 4.6 7.2 - - + -
216B LEU* 3.9 41.7 - - + +
217B LEU* 4.4 20.9 - - + -
307B TYR* 3.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 2.9 31.9 + - - +
125B ASP* 3.2 25.7 + - - +
127B VAL* 1.3 78.4 - - - +
129B PHE* 1.3 61.1 + - - +
132B TYR* 3.1 22.7 + - - +
278B ASN* 4.1 8.7 - - - +
307B TYR* 3.4 47.1 + - + +
308B PHE* 3.5 7.4 - - - -
310B GLN* 3.6 24.7 + - - +
311B TYR* 3.9 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP 3.1 0.8 + - - -
126B HIS 3.1 3.4 + - - +
128B GLN* 1.3 77.1 - - - +
130B LEU* 1.3 70.2 + - - +
132B TYR* 3.3 5.6 + + - +
133B GLN* 2.9 51.7 + - + -
162B CYS* 3.6 26.0 - - + -
311B TYR* 3.3 44.9 - + - +
375D ILE* 3.4 15.0 - - + -
380D ASN* 3.9 9.9 - - - -
382D LEU* 3.5 30.3 - - + -
383D LEU* 3.0 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.0 17.7 - - + -
122B LEU* 3.8 31.9 - - + -
126B HIS* 2.7 27.7 + - + +
127B VAL* 3.7 6.5 - - - +
129B PHE* 1.3 71.5 - - - +
131B ILE* 1.3 70.7 + - + +
133B GLN* 3.0 19.5 + - - +
134B ILE* 3.1 9.3 + - + +
158B VAL* 3.7 37.9 - - + -
162B CYS* 4.3 18.2 - - - +
164B LEU* 3.8 20.1 - - + +
216B LEU* 4.9 7.6 - - + -
372D ILE* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 2.9 37.7 + - + +
130B LEU* 1.3 70.9 - - + +
132B TYR* 1.3 66.6 + - - +
134B ILE* 3.0 26.2 + - + +
135B LEU* 3.0 29.8 + - + +
209B VAL* 4.3 13.9 - - + +
212B ILE* 4.0 9.4 - - + -
213B MET* 4.1 29.2 - - + +
216B LEU* 3.9 20.9 - - + -
284B LEU* 5.5 0.2 - - + -
288B MET* 5.7 0.7 - - + -
307B TYR* 5.4 0.4 - - + -
308B PHE* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN 3.1 20.6 + - - +
129B PHE* 3.5 10.1 - + - +
130B LEU 3.2 0.2 - - - -
131B ILE* 1.3 76.7 - - - +
133B GLN* 1.3 68.3 + - + +
135B LEU* 3.1 13.8 + - - +
136B ARG* 2.8 47.1 + - - +
303B LEU* 3.5 25.8 - - + -
308B PHE* 3.8 22.6 - + + -
311B TYR* 3.4 31.4 - - + -
312B HIS* 3.9 9.2 - - + -
317B GLU* 3.2 23.3 + - - +
382D LEU* 4.2 9.2 - - + -
386D ARG* 2.7 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASN* 3.3 40.6 + - - +
129B PHE* 2.9 57.9 + - + +
130B LEU* 3.0 11.1 + - - +
132B TYR* 1.3 77.0 - - + +
134B ILE* 1.3 64.1 + - - +
137B GLY 3.0 17.8 + - - -
162B CYS 3.1 10.7 + - - -
163B GLU* 3.6 8.5 - - - +
164B LEU* 3.0 32.8 + - + +
382D LEU* 3.6 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 5.6 1.3 - - + -
130B LEU* 3.1 2.7 + - + +
131B ILE* 3.0 38.9 + - + +
133B GLN* 1.3 75.2 - - - +
135B LEU* 1.3 57.6 + - - +
137B GLY 3.2 1.4 + - - -
138B LEU* 2.9 31.2 + - + +
151B LEU* 4.8 6.3 - - + -
156B LEU* 3.0 37.5 - - + -
164B LEU* 3.6 18.8 - - + -
166B ILE* 3.4 19.9 - - + +
209B VAL* 4.2 27.8 - - + -
212B ILE* 4.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.0 23.3 + - + +
132B TYR* 3.4 7.9 - - - +
134B ILE* 1.3 74.5 - - - +
136B ARG* 1.3 65.7 + - - +
138B LEU* 3.0 7.6 + - + +
139B LYS* 2.9 25.3 + - - +
206B ILE* 4.8 9.6 - - + -
209B VAL* 4.5 18.6 - - + -
284B LEU* 5.3 0.4 - - + -
288B MET* 4.9 4.7 - - - -
299B ALA* 4.2 12.4 - - + +
302B ALA* 3.5 26.5 - - + -
303B LEU* 3.8 17.1 - - + +
308B PHE* 3.2 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS* 3.4 23.2 + - + +
81B GLU* 2.7 38.4 + - - +
82B ASN* 3.4 25.4 + - - +
132B TYR* 2.8 43.3 + - + +
133B GLN 3.7 0.4 - - - +
135B LEU* 1.3 72.9 - - - +
137B GLY* 1.3 60.9 + - - +
139B LYS* 3.8 4.2 + - - +
140B TYR 3.6 10.2 + - - -
303B LEU* 3.5 15.8 - - + +
316B ASP* 2.8 47.0 + - - -
317B GLU* 4.0 15.8 - - + +
318B PRO* 3.9 11.3 - - - +
382D LEU* 3.9 14.4 - - - +
385D LYS* 3.8 2.6 - - - +
386D ARG* 4.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS* 3.9 15.4 + - - -
82B ASN* 3.9 11.2 - - - -
83B VAL* 4.2 4.1 - - - +
133B GLN 3.0 14.1 + - - -
134B ILE 3.6 3.4 - - - -
136B ARG* 1.3 75.7 - - - +
138B LEU* 1.3 65.2 + - - +
140B TYR* 3.3 5.5 + - - +
141B ILE* 3.1 24.6 + - - +
166B ILE* 4.1 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 2.9 18.8 + - + +
135B LEU* 3.0 10.5 + - + +
137B GLY* 1.3 74.3 - - - +
139B LYS* 1.3 58.4 + - - +
141B ILE* 3.0 15.9 + - + +
142B HIS* 2.8 65.2 + - + +
148B HIS* 5.1 2.7 - - + -
151B LEU* 3.9 19.5 - - + -
166B ILE* 4.2 12.3 - - + -
205B ASP* 3.6 19.1 - - + +
206B ILE* 4.5 6.7 - - + +
209B VAL* 3.9 23.8 - - + -
299B ALA* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 2.9 15.1 + - - +
136B ARG 3.9 5.4 - - - +
138B LEU* 1.3 76.1 - - - +
140B TYR* 1.3 65.4 + - - +
142B HIS* 3.9 2.9 - - - +
143B SER* 2.9 26.6 + - - -
299B ALA* 3.7 13.1 - - + +
300B ALA* 3.8 32.9 - - + +
303B LEU* 3.9 15.2 - - + +
314B PRO* 5.4 2.4 + - - +
317B GLU* 2.9 39.2 + - + +
318B PRO 4.5 7.6 - - - +
319B VAL* 3.9 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS* 3.5 10.9 + - - -
78B MET* 4.2 17.0 - - + -
79B LYS* 3.1 47.5 + - - +
80B HIS* 3.3 44.0 - - + +
83B VAL* 5.0 1.8 - - + -
136B ARG 3.6 1.8 + - - -
137B GLY 3.3 9.2 + - - +
138B LEU 3.2 0.2 - - - -
139B LYS* 1.3 80.3 - - - +
141B ILE* 1.3 71.6 + - + +
143B SER* 2.6 25.5 + - - -
144B ALA* 3.5 2.2 + - + -
318B PRO* 3.8 16.8 - - + +
319B VAL 3.8 3.8 - - - -
320B ALA* 3.0 41.3 - - + +
321B ASP* 5.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MET* 4.9 5.2 - - - -
83B VAL* 4.2 14.4 - - + -
137B GLY 3.1 13.6 + - - +
138B LEU* 3.0 18.9 + - + +
140B TYR* 1.3 85.1 - - + +
142B HIS* 1.3 63.4 + - + +
144B ALA* 2.7 35.6 + - - +
145B ASP 3.4 2.4 + - - -
146B ILE* 3.2 37.7 + - + +
147B ILE* 4.4 2.2 - - - +
148B HIS* 4.7 8.1 - - + +
166B ILE* 4.5 8.3 - - + -
169B PHE* 3.0 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 2.8 46.8 + - + +
139B LYS* 4.2 3.4 - - - +
141B ILE* 1.3 79.8 - - + +
143B SER* 1.3 55.4 + - - +
145B ASP* 2.8 17.9 + - - +
146B ILE 3.1 23.1 - - - -
147B ILE* 4.6 0.2 - - - -
202B GLN* 3.2 62.6 + - + +
205B ASP* 2.7 26.5 + - + +
206B ILE* 4.8 6.3 - - + +
299B ALA* 4.2 16.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS* 2.9 21.3 + - - -
140B TYR 2.6 14.8 + - - -
141B ILE 2.8 0.6 + - - -
142B HIS* 1.3 78.3 - - - +
144B ALA* 1.3 56.3 + - - +
145B ASP* 3.1 5.1 + - - +
319B VAL* 3.9 22.0 - - - -
320B ALA* 2.7 27.6 + - - +
322B PRO* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS* 3.9 7.2 - - + -
140B TYR* 4.3 0.7 - - + +
141B ILE* 2.7 15.3 + - - +
143B SER* 1.3 74.9 + - - +
145B ASP* 1.3 69.9 + - - +
146B ILE* 3.3 20.5 + - + +
320B ALA* 4.3 7.9 - - + -
321B ASP 3.6 22.4 - - - +
322B PRO* 5.2 1.3 - - - -
323B TYR* 3.5 29.8 + - + +
325B GLN* 4.4 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