Contacts of the helix formed by residues 137 - 149 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169M LYS* 5.9 0.2 + - - -
173M ASP* 5.0 4.3 - - + +
130N VAL* 5.2 0.7 - - - -
135N VAL* 2.9 19.3 + - - +
136N HIS* 1.3 72.5 - - - +
138N ILE* 1.3 55.2 + - - +
139N GLY 3.4 0.9 - - - -
140N LYS* 3.0 27.2 + - - +
141N ASN* 2.7 47.8 + - - +
159N ARG* 3.0 38.0 + - - +
500N B13 3.0 17.1 + - - +
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Residues in contact with ILE 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP* 4.8 6.5 - - + +
176M VAL* 5.8 1.3 - - + -
177M LEU* 4.0 27.8 - - + -
225M THR* 3.4 33.4 - - + -
229M ILE* 3.9 17.0 - - + -
137N ASP* 1.3 74.0 - - + +
139N GLY* 1.3 55.4 + - - +
141N ASN* 3.0 11.2 + - - +
142N ILE* 2.7 57.5 + - + +
500N B13 3.2 48.9 + - + +
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Residues in contact with GLY 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N HIS 4.8 2.0 + - - -
137N ASP 3.4 0.6 - - - -
138N ILE* 1.3 77.4 - - - +
140N LYS* 1.3 62.0 + - - +
142N ILE* 3.3 6.2 + - - +
143N VAL* 3.1 27.6 + - - +
181N THR* 4.6 4.9 - - - -
183N LEU* 5.5 0.2 - - - +
500N B13 3.3 48.6 + - - +
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Residues in contact with LYS 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N CYS* 4.8 9.6 - - + -
129N HIS* 4.5 10.1 - - - +
130N VAL* 3.5 26.5 - - + -
136N HIS 4.7 0.2 + - - -
137N ASP* 3.0 25.8 + - - +
139N GLY* 1.3 73.5 - - - +
141N ASN* 1.3 82.6 + - - +
143N VAL* 3.1 9.0 + - + +
144N THR* 2.7 38.9 + - - +
156N ASP* 3.3 35.9 + - - +
158N GLY* 3.6 27.3 + - - +
179N THR* 5.8 1.1 - - - +
181N THR* 4.0 16.8 + - - +
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Residues in contact with ASN 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP* 5.9 4.2 - - - +
177M LEU* 4.5 20.6 - - + +
99N MET* 5.1 3.7 - - + +
137N ASP* 2.7 39.8 + - - +
138N ILE* 3.3 12.8 - - - +
140N LYS* 1.3 95.2 + - - +
142N ILE* 1.3 58.2 + - - +
144N THR* 3.4 10.5 + - - +
145N ALA* 2.8 30.2 + - - +
156N ASP* 4.7 1.2 - - - +
500N B13 5.2 0.2 + - - -
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Residues in contact with ILE 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M LEU* 5.3 2.5 - - + -
229M ILE* 5.8 3.6 - - + -
237M ASN* 5.3 6.1 - - - +
88N TYR* 5.4 3.8 - - - +
95N LEU* 3.9 43.3 - - + -
99N MET* 5.6 1.1 - - - -
138N ILE* 2.7 44.3 + - + +
139N GLY* 3.7 4.7 - - - +
141N ASN* 1.3 73.4 - - + +
143N VAL* 1.3 57.7 + - - +
145N ALA* 3.4 6.5 + - - +
146N LEU* 3.0 34.9 + - + +
231N ALA* 3.5 18.6 - - + -
500N B13 3.8 30.5 - - + +
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Residues in contact with VAL 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N CYS* 4.4 3.4 - - - -
139N GLY 3.1 14.1 + - - +
140N LYS* 3.1 11.1 + - + +
142N ILE* 1.3 75.2 - - - +
144N THR* 1.3 64.1 + - - +
146N LEU* 3.5 0.9 + - - -
147N LEU* 3.1 36.7 + - + +
179N THR* 4.2 20.6 - - + +
181N THR* 5.5 0.2 - - - +
231N ALA* 3.7 23.8 - - + -
234N ALA* 3.7 20.9 - - + -
500N B13 3.6 33.2 - - + +
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Residues in contact with THR 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N CYS* 4.4 7.6 - - - +
140N LYS* 2.7 21.0 + - - -
141N ASN* 3.4 14.4 - - - +
143N VAL* 1.3 71.5 - - - +
145N ALA* 1.3 64.4 + - - +
147N LEU* 3.1 4.2 + - - +
148N ARG* 3.1 67.8 + - - +
154N VAL* 3.8 20.2 - - + +
156N ASP* 4.0 18.9 + - - +
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Residues in contact with ALA 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N VAL* 5.5 1.5 - - + +
99N MET* 3.3 38.4 - - + -
102N ALA* 4.9 5.0 - - - +
141N ASN 2.8 20.7 + - - +
142N ILE* 3.5 7.4 - - - +
144N THR* 1.3 77.1 - - - +
146N LEU* 1.3 62.1 + - + +
148N ARG* 3.7 5.6 + - - +
149N ALA* 3.1 28.1 + - - +
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Residues in contact with LEU 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N ILE* 4.5 15.9 - - + -
88N TYR* 4.8 20.4 - - + -
95N LEU* 4.3 15.0 - - + -
98N VAL* 4.4 20.4 - - + -
142N ILE* 3.0 34.3 + - + +
143N VAL 4.2 1.8 - - - +
145N ALA* 1.3 78.7 - - + +
147N LEU* 1.3 65.4 + - - +
149N ALA* 3.8 6.2 - - + +
150N ASN* 2.7 44.1 + - - +
231N ALA 3.9 21.8 - - - +
232N ALA* 4.9 6.1 - - + -
235N PRO* 3.6 8.0 - - + +
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Residues in contact with LEU 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N VAL* 3.6 35.4 - - + -
128N CYS* 4.0 16.8 - - - -
143N VAL* 3.1 25.2 + - + +
146N LEU* 1.3 76.7 - - + +
148N ARG* 1.3 60.7 + - - +
150N ASN* 3.1 17.5 + - - +
151N GLY 3.4 0.2 + - - -
152N TYR* 3.1 37.3 + - + +
154N VAL* 3.3 16.4 - - + -
177N MET* 6.4 0.2 - - - -
179N THR* 4.7 2.9 - - + -
234N ALA* 3.6 28.0 - - + +
235N PRO* 3.6 22.2 - - + -
238N ALA* 5.6 1.6 - - + -
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Residues in contact with ARG 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N MET* 5.6 0.9 - - - +
102N ALA* 6.1 2.0 - - + -
105N MET* 3.4 20.5 - - + +
106N LEU* 3.8 41.2 - - + +
109N ILE* 5.6 1.9 - - - +
144N THR* 3.1 42.0 + - - +
145N ALA* 4.1 5.8 - - - +
147N LEU* 1.3 74.6 - - - +
149N ALA* 1.3 58.2 + - - +
150N ASN 3.3 0.4 + - - -
151N GLY* 4.2 5.9 + - - -
152N TYR 3.8 11.7 - - - +
154N VAL* 3.7 36.0 + - + +
156N ASP* 4.1 19.0 + - - +
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Residues in contact with ALA 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N MET* 4.4 5.6 - - - +
81N MET* 3.4 40.9 - - + +
85N ILE* 3.0 29.9 - - + +
98N VAL* 4.8 7.4 - - + -
102N ALA* 4.9 3.3 - - + +
105N MET* 4.8 3.6 - - - -
145N ALA 3.1 19.0 + - - +
146N LEU* 4.0 11.0 - - + +
147N LEU 3.2 0.6 - - - -
148N ARG* 1.3 76.7 - - - +
150N ASN* 1.3 57.7 + - - +
151N GLY 3.6 0.7 - - - -
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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