Contacts of the strand formed by residues 125 - 131 (chain F) 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 THR 125 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122F THR* 4.8 1.9 + - - -
124F GLY* 1.3 73.0 - - - -
126F VAL* 1.3 72.5 + - - +
153F ASN* 3.4 31.5 + - - +
155F VAL* 4.2 14.8 - - + -
173F GLU* 4.1 33.6 + - + +
174F LYS 4.9 1.5 + - - -
175F PRO* 3.2 7.5 - - + +
176F ILE* 2.8 34.8 + - - +
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Residues in contact with VAL 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F THR* 1.3 81.2 - - - +
127F VAL* 1.3 70.4 + - - +
128F CYS* 4.2 1.1 - - - -
147F LEU* 3.8 31.2 - - + -
152F TYR* 3.9 30.7 - - + -
153F ASN 2.9 10.3 + - - +
154F VAL* 3.5 5.5 - - + +
155F VAL* 3.2 27.2 + - - +
175F PRO* 4.1 0.2 - - - -
176F ILE* 4.5 4.0 - - + -
177F MET* 3.2 43.1 - - + +
179F THR* 4.4 5.4 - - + -
238F ALA* 5.0 3.6 - - + -
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Residues in contact with VAL 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F VAL* 1.3 77.3 - - - +
128F CYS* 1.3 60.4 + - - +
155F VAL* 3.6 20.2 - - + -
157F LEU* 3.5 32.5 - - + -
166F VAL* 5.0 5.2 - - + -
169F ALA* 4.2 18.8 - - + +
170F VAL* 5.0 2.9 - - + -
173F GLU* 4.6 1.8 - - + -
175F PRO* 3.6 27.4 - - + -
177F MET 3.0 7.2 + - - +
178F LEU* 3.2 22.6 - - + +
179F THR 2.7 31.9 + - - -
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Residues in contact with CYS 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F VAL* 4.5 2.2 - - - -
127F VAL* 1.3 78.7 - - - +
129F HIS* 1.3 61.6 + - - +
140F LYS* 4.5 18.8 - - + -
143F VAL* 4.8 7.0 - - + -
144F THR* 5.0 5.6 - - - +
147F LEU* 4.1 19.7 - - - -
154F VAL* 3.8 27.4 - - + -
155F VAL 3.5 5.0 + - - +
156F ASP* 4.2 4.0 - - - +
157F LEU* 2.8 30.6 + - - +
179F THR* 3.1 24.7 - - - +
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Residues in contact with HIS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F CYS* 1.3 74.6 - - - +
130F VAL* 1.3 83.4 + - - +
131F ALA* 4.0 9.8 + - - -
140F LYS* 5.0 3.8 - - - +
157F LEU* 3.8 16.6 - - + -
158F GLY 4.1 2.9 - - - -
161F VAL* 4.2 8.3 - - + -
166F VAL* 3.7 27.1 - - + -
178F LEU* 3.7 12.2 - - + +
179F THR 2.8 26.2 + - - +
180F GLY* 3.6 22.3 - - - -
181F THR* 3.1 23.6 + - - -
190F ALA 4.8 0.6 + - - -
191F PHE* 4.6 5.4 - + - -
194F VAL* 3.9 21.0 - - + +
207F PHE* 3.7 24.1 - + - -
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Residues in contact with VAL 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F HIS* 1.3 85.1 - - - +
131F ALA* 1.3 65.2 + - - +
132F GLU 3.6 0.9 + - - -
134F ASP* 3.3 37.5 - - + +
136F HIS* 3.9 23.3 - - + +
137F ASP* 4.7 0.7 - - - -
140F LYS* 3.8 30.7 - - + +
158F GLY 3.2 15.3 + - - +
159F ARG* 2.8 29.6 - - - +
161F VAL* 3.6 5.7 + - - +
181F THR* 3.4 17.5 - - + +
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Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F HIS* 4.0 12.0 + - - -
130F VAL* 1.3 75.9 - - - +
132F GLU* 1.3 60.1 + - - +
134F ASP* 3.1 25.2 + - - +
159F ARG 3.7 1.6 - - - +
181F THR 3.0 17.2 + - - +
182F ALA* 4.1 3.1 - - + -
187F THR* 3.5 31.2 - - + +
190F ALA* 3.6 11.4 - - + -
191F PHE* 4.0 15.5 - - + -
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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