Contacts of the helix formed by residues 137 - 150 (chain D) 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 ASP 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C ASP* 5.4 0.8 - - + +
130D VAL* 4.6 4.9 - - - -
135D VAL* 2.9 13.6 + - - +
136D HIS* 1.3 72.9 - - - +
138D ILE* 1.3 68.1 + - + +
139D GLY 3.4 1.1 - - - -
140D LYS* 3.0 30.4 + - - +
141D ASN* 2.9 34.9 + - - +
159D ARG* 3.4 32.3 + - - +
500D B13 2.9 20.2 + - - +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASP* 4.5 8.5 - - + +
176C VAL* 5.7 1.3 - - + -
177C LEU* 4.4 20.0 - - + -
225C THR* 3.5 32.3 - - + -
229C ILE* 3.8 15.5 - - + -
136D HIS 3.6 1.0 - - - -
137D ASP* 1.3 77.5 - - + +
139D GLY* 1.3 59.3 + - - +
141D ASN* 3.0 11.1 + - - +
142D ILE* 2.9 52.5 + - + +
500D B13 2.9 62.7 + - + +
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Residues in contact with GLY 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D HIS 5.1 1.4 + - - -
137D ASP 3.4 0.2 - - - -
138D ILE* 1.3 79.5 - - - +
140D LYS* 1.3 56.1 + - - +
142D ILE* 3.5 3.5 + - - -
143D VAL* 3.0 31.9 + - - +
181D THR* 5.0 0.7 - - - -
500D B13 3.4 55.2 + - - +
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D CYS* 4.4 13.9 - - + -
129D HIS* 4.4 12.3 - - - +
130D VAL* 3.7 29.3 - - + +
137D ASP* 3.0 28.2 + - - +
139D GLY* 1.3 73.3 - - - +
141D ASN* 1.3 81.4 + - - +
143D VAL* 2.8 8.7 + - + +
144D THR* 2.6 42.3 + - - +
156D ASP* 3.2 37.5 + - - +
158D GLY* 4.0 18.8 - - - +
179D THR* 5.7 0.4 - - - +
181D THR* 4.1 16.2 + - - +
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Residues in contact with ASN 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASP* 6.4 0.2 - - - +
177C LEU* 4.5 21.7 - - + +
99D MET* 5.0 5.7 - - + +
137D ASP* 2.9 33.4 + - - +
138D ILE* 3.4 10.8 - - - +
140D LYS* 1.3 101.8 + - - +
142D ILE* 1.3 58.3 + - - +
144D THR* 3.4 8.5 - - - +
145D ALA* 2.8 31.5 + - - +
156D ASP* 4.2 3.6 - - - +
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 5.0 6.3 - - + -
229C ILE* 5.7 2.5 - - + -
237C ASN* 5.5 3.6 - - - +
88D TYR* 5.0 4.3 - - - +
95D LEU* 3.4 41.1 - - + -
99D MET* 5.3 2.5 - - - -
138D ILE* 2.9 41.6 + - + +
139D GLY 3.9 4.3 - - - +
141D ASN* 1.3 77.7 - - + +
143D VAL* 1.3 60.9 + - - +
145D ALA* 4.5 4.5 - - - +
146D LEU* 3.2 38.2 + - + +
231D ALA* 3.6 21.2 - - + +
500D B13 4.1 22.4 - - + -
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D CYS* 4.6 2.2 - - - -
139D GLY 3.0 18.5 + - - +
140D LYS* 2.8 12.1 + - + +
142D ILE* 1.3 76.1 - - - +
144D THR* 1.3 63.3 + - - +
146D LEU* 3.6 2.8 + - - +
147D LEU* 3.1 36.7 + - + +
179D THR* 4.2 20.9 - - + +
231D ALA* 4.0 15.3 - - + -
234D ALA* 3.4 23.3 - - + -
500D B13 3.5 36.8 - - + -
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D CYS* 4.4 5.7 - - - +
140D LYS* 2.6 28.4 + - - +
141D ASN* 3.4 13.7 - - - +
143D VAL* 1.3 73.7 - - - +
145D ALA* 1.3 63.4 + - + +
147D LEU* 3.7 2.8 - - - +
148D ARG* 3.2 64.4 + - - +
154D VAL* 4.0 16.0 - - + +
156D ASP* 3.8 22.5 + - - +
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D VAL* 5.8 2.5 - - + -
99D MET* 3.7 32.3 - - + -
102D ALA* 4.8 13.5 - - + +
141D ASN 2.8 20.5 + - - +
142D ILE* 4.3 2.9 - - - +
144D THR* 1.3 76.5 - - + +
146D LEU* 1.3 63.7 + - + +
148D ARG* 3.8 7.0 - - - +
149D ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ILE* 5.9 6.7 - - + -
88D TYR* 4.1 28.7 - - + -
89D ASP* 6.5 0.2 - - - -
95D LEU* 4.7 5.6 - - + -
98D VAL* 4.5 16.8 - - + -
142D ILE* 3.2 39.0 + - + +
143D VAL 4.0 2.5 - - - +
145D ALA* 1.3 81.9 - - + +
147D LEU* 1.3 57.7 + - - +
149D ALA* 3.3 3.8 + - - -
150D ASN* 2.6 44.7 + - - +
231D ALA 4.2 13.2 - - - +
232D ALA* 3.9 23.1 - - + +
235D PRO* 3.9 16.2 - - + -
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 3.7 36.3 - - + -
128D CYS* 3.8 10.5 - - - -
143D VAL* 3.1 37.2 + - + +
146D LEU* 1.3 74.1 - - - +
148D ARG* 1.3 58.7 + - - +
150D ASN 2.9 15.8 + - - -
151D GLY 3.1 9.0 + - - -
152D TYR* 3.2 21.1 + - + -
154D VAL* 3.7 15.3 - - + -
177D MET* 6.0 0.7 - - - -
179D THR* 4.6 2.2 - - + -
234D ALA* 3.5 13.9 - - + +
235D PRO* 3.4 37.7 - - + -
238D ALA* 4.6 7.6 - - + -
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 4.4 3.5 - - - +
102D ALA* 6.0 2.2 - - + -
105D MET* 4.3 18.9 - - + +
106D LEU* 4.6 30.4 - - + +
144D THR* 3.2 41.1 + - - +
145D ALA* 3.8 6.2 - - - +
147D LEU* 1.3 76.8 - - - +
149D ALA* 1.3 58.5 + - - +
151D GLY* 3.0 20.3 + - - -
152D TYR 3.4 14.7 + - - +
153D ASN* 5.5 0.2 - - - -
154D VAL* 3.4 40.3 + - + +
156D ASP* 4.3 11.7 + - - +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 4.0 4.9 - - - +
81D MET* 3.3 43.9 - - + +
85D ILE* 2.7 28.2 - - + +
98D VAL* 4.9 5.2 - - + -
102D ALA* 4.7 6.7 - - + +
105D MET* 4.7 5.8 - - - +
145D ALA 2.9 20.0 + - - +
146D LEU* 3.6 6.7 - - - +
148D ARG* 1.3 75.9 - - - +
150D ASN* 1.3 59.7 + - - +
151D GLY 3.4 0.2 - - - -
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Residues in contact with ASN 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 3.4 11.1 - - - +
85D ILE* 3.5 33.2 - - - +
123D LYS* 3.0 22.0 + - - -
146D LEU* 2.6 37.4 + - - +
147D LEU 2.9 5.8 + - - +
149D ALA* 1.3 80.5 - - - +
151D GLY* 1.3 59.9 + - - +
152D TYR* 4.2 8.5 - - + -
235D PRO* 3.5 30.1 - - + +
239D ASP* 5.2 5.2 - - - +
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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