Contacts of the helix formed by residues 142 - 156 (chain O) in PDB entry 2I2X
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 LYS 142 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93O ASN* 4.7 8.1 - - - +
129O ILE* 3.8 33.2 + - + +
130O ARG* 4.6 11.4 - - - -
131O GLU 4.0 20.4 + - - +
132O ASN* 4.9 4.9 - - - +
137O GLN* 4.4 25.5 + - + +
140O GLY 3.3 1.0 - - - -
141O ASP* 1.3 90.6 - - + +
143O TYR* 1.3 65.3 + - - +
144O SER 3.4 1.1 - - - -
145O VAL* 3.1 16.1 + - + +
146O PHE* 2.9 21.1 + - - +
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Residues in contact with TYR 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O ARG* 3.9 19.5 - - - +
137O GLN 5.4 0.6 + - - -
138O LEU 3.3 19.7 - - - -
139O ARG* 4.5 9.0 - - - +
140O GLY 3.3 17.9 + - - +
141O ASP 3.2 0.8 - - - -
142O LYS* 1.3 76.5 - - - +
144O SER* 1.3 61.3 + - - +
146O PHE* 2.8 34.0 + + - +
147O LEU* 3.1 31.6 + - + +
198O LEU* 3.4 38.8 + - + +
199O ILE* 3.9 10.8 - - + -
202O ASP* 2.5 34.6 + - - +
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Residues in contact with SER 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140O GLY 4.8 0.2 + - - -
141O ASP 3.6 13.4 + - - -
143O TYR* 1.3 85.8 - - - +
145O VAL* 1.3 61.9 + - - +
147O LEU* 3.5 8.8 + - - +
148O GLU* 2.9 33.9 + - - +
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Residues in contact with VAL 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O SER 3.8 11.4 - - - +
93O ASN* 3.7 24.2 - - - +
95O PRO* 3.9 12.3 - - + -
129O ILE* 4.0 10.8 - - + -
141O ASP 4.5 2.9 - - - +
142O LYS* 3.1 23.2 + - + +
144O SER* 1.3 78.6 + - - +
146O PHE* 1.3 59.8 + - - +
148O GLU* 3.1 14.5 + - - +
149O ALA* 2.9 29.1 + - - +
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Residues in contact with PHE 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O ILE* 4.2 4.7 - - + -
127O GLY 3.6 24.9 - - - -
128O ASP* 3.7 15.9 - - - -
129O ILE* 4.0 15.0 - - + +
130O ARG* 4.0 22.4 - - + -
142O LYS 2.9 11.1 + - - +
143O TYR* 2.8 22.4 + + - +
145O VAL* 1.3 74.5 - - - +
147O LEU* 1.3 71.8 + - + +
149O ALA* 3.2 18.2 + - - +
150O PHE* 3.3 40.0 - + - -
163O VAL* 3.9 22.9 - - + -
199O ILE* 4.1 30.3 - - + -
203O ILE* 4.7 1.3 - - + -
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Residues in contact with LEU 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143O TYR* 3.1 38.5 + - + +
144O SER* 3.8 9.2 - - - +
146O PHE* 1.3 95.3 - - + +
148O GLU* 1.3 63.7 + - - +
150O PHE* 3.2 12.7 + - + +
151O GLU* 3.0 21.8 + - - +
199O ILE* 5.2 0.4 - - - +
202O ASP* 4.0 33.7 - - + +
203O ILE* 5.0 2.9 - - + -
206O ILE* 3.7 24.8 - - + +
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Residues in contact with GLU 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O PRO* 3.6 20.1 - - + +
144O SER* 2.9 21.1 + - - +
145O VAL* 3.1 22.2 + - - +
147O LEU* 1.3 75.1 - - - +
149O ALA* 1.3 63.9 + - - +
151O GLU* 4.0 11.3 - - + +
152O GLN* 2.9 37.8 + - + +
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Residues in contact with ALA 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O HIS* 5.0 4.3 - - + -
92O SER* 4.0 22.0 - - - +
95O PRO* 4.0 13.4 - - + +
126O ILE* 3.7 26.7 - - + -
145O VAL 2.9 12.4 + - - +
146O PHE* 3.2 11.2 + - - +
148O GLU* 1.3 76.3 - - - +
150O PHE* 1.3 64.1 + - - +
152O GLN* 3.8 1.0 - - - +
153O CYS* 3.0 28.7 + - - -
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Residues in contact with PHE 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O ILE* 3.7 27.3 - - + +
146O PHE* 3.3 52.2 + + - -
147O LEU* 3.2 13.9 + - + +
149O ALA* 1.3 78.6 - - - +
151O GLU* 1.3 59.4 + - - +
153O CYS* 3.8 2.1 - - - +
154O ALA* 3.0 28.6 + - - +
161O LEU* 4.0 20.3 - - + +
162O SER 3.3 32.8 - - - -
163O VAL* 3.9 10.3 - - + -
203O ILE* 3.5 40.6 - - + -
206O ILE* 4.1 15.7 - - + -
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Residues in contact with GLU 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147O LEU* 3.0 16.9 + - - +
148O GLU* 4.5 12.4 - - + +
150O PHE* 1.3 72.9 - - - +
152O GLN* 1.3 74.8 + - - +
154O ALA* 3.5 3.1 + - - +
155O GLU* 3.0 39.5 + - - +
206O ILE* 3.3 31.7 - - + +
209O LYS* 2.7 40.4 + - - +
210O THR* 4.5 4.2 - - + +
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Residues in contact with GLN 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O PRO* 3.7 23.8 - - + +
96O SER* 4.7 7.2 - - - +
99O ALA* 3.7 21.2 - - + +
148O GLU* 2.9 30.9 + - + +
149O ALA 3.8 2.9 - - - +
151O GLU* 1.3 82.9 - - - +
153O CYS* 1.3 63.3 + - - +
155O GLU* 3.3 19.0 + - - +
156O ASN* 2.9 33.6 + - - +
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Residues in contact with CYS 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O HIS* 3.5 35.2 - - - -
95O PRO 4.9 1.3 - - - -
98O GLY* 3.6 22.2 - - - -
99O ALA* 3.8 6.7 - - - +
102O ALA* 4.3 2.1 - - + +
124O HIS* 3.6 11.7 - - + -
126O ILE* 4.8 1.8 - - + -
149O ALA 3.0 20.8 + - - +
150O PHE* 3.8 4.9 - - - +
152O GLN* 1.3 73.6 - - - +
154O ALA* 1.3 58.0 + - - +
156O ASN 2.8 21.8 + - - -
157O GLY 3.3 1.2 + - - -
158O ALA* 3.2 32.1 + - + +
161O LEU* 5.0 2.7 - - + -
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Residues in contact with ALA 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O PHE 3.0 17.7 + - - +
151O GLU* 3.8 5.6 - - - +
153O CYS* 1.3 75.9 - - - +
155O GLU* 1.3 61.5 + - - +
156O ASN 3.5 0.2 + - - -
157O GLY* 4.1 3.3 + - - -
158O ALA* 3.8 15.9 - - - +
161O LEU* 4.2 12.9 - - + +
206O ILE* 4.8 0.2 - - + -
210O THR* 3.3 30.8 - - + +
212O THR* 3.6 26.2 - - - +
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Residues in contact with GLU 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151O GLU* 3.0 37.4 + - - +
152O GLN* 3.8 21.5 + - - +
153O CYS 3.1 0.2 - - - -
154O ALA* 1.3 76.2 - - - +
156O ASN* 1.3 68.0 + - - +
157O GLY 3.7 0.8 + - - -
209O LYS* 4.6 6.2 - - - -
210O THR* 4.0 19.7 - - + +
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Residues in contact with ASN 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99O ALA* 3.4 31.2 - - - +
102O ALA* 3.3 1.1 - - - -
103O HIS* 2.9 54.9 + - + +
152O GLN* 2.9 27.7 + - - +
153O CYS 2.8 8.9 + - - +
155O GLU* 1.3 87.4 + - - +
157O GLY* 1.3 54.8 + - - +
158O ALA 3.7 0.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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