Contacts of the helix formed by residues 150 - 160 (chain A) in PDB entry 2I6W
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ASN* 4.6 3.8 - - - -
147A GLY 5.1 0.2 - - - +
148A THR 4.9 2.0 - - - +
149A MET* 1.3 83.6 - - - +
151A GLN* 1.3 64.0 + - - +
152A GLU* 2.8 18.9 + - - +
153A ASP* 2.9 27.9 + - - +
154A ILE* 2.6 44.4 + - - +
285A PRO* 4.9 3.1 - - - -
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 1.3 76.6 + - - +
152A GLU* 1.3 85.2 + - - +
154A ILE* 4.6 5.6 - - - -
155A SER* 3.1 40.6 + - - -
178A PHE 4.5 2.4 - - - +
179A GLY* 3.9 7.9 - - - -
180A SER 4.8 0.8 - - - +
277A ILE 3.8 16.0 + - - -
278A ILE* 3.6 22.1 - - + +
279A ALA 3.5 23.3 + - - +
285A PRO* 4.1 19.5 - - + +
286A ALA 3.5 14.8 - - - +
287A SER* 5.2 0.2 - - - -
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 2.8 10.0 + - + +
151A GLN* 1.3 118.0 + - - +
153A ASP* 1.3 66.6 + - - +
155A SER* 4.2 2.1 - - - -
156A ASP* 3.6 10.2 + - - +
180A SER 4.6 2.8 - - - +
182A TYR* 3.6 28.8 - - + +
270A LEU 5.8 0.4 - - - +
271A GLY* 5.4 2.0 - - - -
272A GLY* 4.9 8.3 - - - +
275A TYR* 4.1 32.5 - - + +
278A ILE* 4.8 3.7 - - - +
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Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR 4.4 7.4 - - - +
149A MET* 4.1 17.5 - - + +
150A THR* 2.9 37.0 + - - +
152A GLU* 1.3 75.4 - - - +
154A ILE* 1.3 68.4 + - - +
155A SER 3.1 1.8 - - - -
156A ASP* 2.8 17.7 + - - +
157A TYR* 2.9 11.4 + - - -
182A TYR* 2.7 28.3 + - + -
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 3.4 43.1 - - + +
144A ASN* 3.9 23.3 - - - +
149A MET* 3.5 22.8 - - + +
150A THR 2.6 30.9 + - - +
151A GLN* 4.5 0.9 - - - +
153A ASP* 1.3 70.2 - - - +
155A SER* 1.3 68.2 + - - +
157A TYR* 3.1 9.5 + - - +
158A VAL* 3.0 21.8 + - - +
285A PRO 3.7 24.0 - - - +
286A ALA* 3.9 8.3 - - - -
287A SER* 3.8 8.7 - - - -
321A LEU* 4.2 6.5 - - + -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 3.1 22.5 + - - -
152A GLU* 4.2 1.8 - - - -
153A ASP 2.9 4.0 + - - -
154A ILE* 1.3 73.8 - - - +
156A ASP* 1.3 55.1 + - - -
158A VAL* 2.5 27.9 + - - +
159A ALA* 2.8 16.1 + - - -
177A LEU* 4.7 2.2 - - - -
178A PHE 3.4 1.0 + - - -
179A GLY* 3.4 14.8 - - - -
180A SER 3.7 24.7 - - - -
287A SER* 2.9 29.8 + - - -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU 3.6 4.8 + - - +
153A ASP 2.8 12.5 + - - +
155A SER* 1.3 76.7 - - - +
157A TYR* 1.3 65.7 + - - +
158A VAL 3.1 0.2 + - - -
159A ALA* 4.2 8.5 - - - -
160A ALA* 3.1 21.8 + - - +
180A SER 3.9 1.8 + - - +
181A GLN* 3.8 4.0 - - - +
182A TYR* 2.9 57.4 + - + +
765A ARG* 4.0 8.7 + - - -
769A LYS* 2.8 31.7 + - - -
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A MET* 5.1 6.5 - - + -
153A ASP 2.9 15.4 + - - +
154A ILE* 3.6 9.4 - - - +
156A ASP* 1.3 78.5 + - - +
158A VAL* 1.3 65.0 + - - +
161A ASN* 3.2 51.2 + - + +
162A MET* 4.0 8.5 - - + -
313A MET 4.8 1.4 + - - -
316A PHE* 3.7 15.1 + - - +
317A PHE* 3.1 41.3 - + - -
318A PRO* 3.9 22.9 - - + -
321A LEU* 3.2 26.5 - - + -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 3.5 19.7 - - + -
154A ILE 3.0 16.7 + - - +
155A SER* 2.5 15.5 + - - +
157A TYR* 1.3 69.0 - - + +
159A ALA* 1.3 57.5 + - - +
160A ALA 2.6 3.6 + - - -
161A ASN 2.5 28.6 + - - -
162A MET* 2.7 49.8 + - + -
163A LYS* 3.6 2.1 + - + +
177A LEU* 3.5 22.9 - - + -
287A SER* 4.6 4.0 - - - -
288A GLY 4.6 1.3 - - - +
289A LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER 2.8 14.7 + - - +
156A ASP 4.1 0.9 - - - +
158A VAL* 1.3 77.0 - - - +
160A ALA* 1.3 59.1 + - - +
161A ASN 3.8 0.2 + - - -
163A LYS* 4.2 20.8 - - + +
164A ASP* 4.2 5.4 + - - +
177A LEU* 4.3 13.4 - - + +
181A GLN* 3.3 44.8 + - + +
767A ARG* 3.5 15.8 + - - -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP* 3.1 15.9 + - - +
158A VAL 2.6 5.3 + - - -
159A ALA* 1.3 75.0 - - - +
161A ASN* 1.3 70.1 + - - +
164A ASP* 5.5 3.8 - - - +
181A GLN* 3.9 18.2 - - + +
767A ARG* 3.9 24.7 + - + +
769A LYS* 4.1 18.6 - - - +
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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