Contacts of the strand formed by residues 125 - 130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B THR* 5.1 0.9 + - - -
124B GLY* 1.3 74.6 + - - -
126B VAL* 1.3 72.2 + - - +
153B ASN* 3.5 24.1 + - - +
155B VAL* 4.2 8.1 - - + -
173B GLU* 4.0 31.0 + - + +
174B LYS 4.7 1.7 + - - -
175B PRO* 3.1 22.7 - - + +
176B ILE* 2.7 39.7 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B THR* 1.3 79.2 - - - +
127B VAL* 1.3 71.4 + - - +
128B CYS* 4.0 2.0 - - - -
147B LEU* 3.9 22.9 - - + -
152B TYR* 4.2 26.0 - - + -
153B ASN 2.9 7.1 + - - +
154B VAL* 3.3 17.4 - - + +
155B VAL* 3.3 24.4 + - - +
176B ILE* 4.5 2.5 - - + -
177B MET* 3.1 41.5 - - + +
179B THR* 3.8 13.9 - - + -
238B ALA* 4.9 2.2 - - + -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 1.3 75.3 - - - +
128B CYS* 1.3 65.4 + - - +
129B HIS* 5.5 0.9 - - + -
155B VAL* 3.7 21.5 - - + -
157B LEU* 3.5 30.5 - - + -
166B VAL* 5.1 3.1 - - + -
169B ALA* 4.3 21.1 - - + +
170B VAL* 4.6 3.4 - - + -
173B GLU* 4.6 1.3 - - + -
175B PRO* 3.6 28.7 - - + +
177B MET 3.1 5.5 + - - -
178B LEU* 3.5 23.6 - - + +
179B THR 2.8 25.6 + - - -
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Residues in contact with CYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 4.0 3.1 - - - -
127B VAL* 1.3 80.4 - - - +
129B HIS* 1.3 60.7 + - - +
140B LYS* 4.5 11.9 - - + -
143B VAL* 4.4 5.2 - - - -
144B THR* 4.4 12.6 - - - +
147B LEU* 3.8 23.8 - - - -
154B VAL* 3.8 26.2 - - + -
155B VAL 3.3 7.4 + - - +
156B ASP* 3.9 4.1 - - - +
157B LEU* 2.9 30.1 + - - +
179B THR* 3.0 22.2 - - - +
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 5.5 0.9 - - + -
128B CYS* 1.3 77.1 - - - +
130B VAL* 1.3 85.3 + - - +
131B ALA* 4.1 8.0 + - - -
140B LYS* 4.3 5.1 - - - +
157B LEU* 4.0 15.5 - - + -
158B GLY 4.0 5.8 - - - -
161B VAL* 4.1 13.9 - - + -
166B VAL* 3.9 26.7 - - + -
178B LEU* 4.4 6.6 - - + +
179B THR* 2.8 32.5 + - - -
180B GLY* 3.4 18.0 - - - -
181B THR* 3.2 23.7 + - - -
190B ALA 5.4 0.2 + - - -
191B PHE* 4.9 3.6 - + - -
194B VAL* 3.9 19.5 - - + +
207B PHE* 3.7 21.2 - + - -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B HIS* 1.3 84.5 - - - +
131B ALA* 1.3 65.3 + - - +
134B ASP* 3.5 33.7 - - + +
136B HIS 3.7 27.8 - - - +
137B ASP* 4.7 1.6 - - - -
140B LYS* 3.4 35.4 - - + +
158B GLY 3.3 8.8 + - - +
159B ARG* 2.7 30.5 - - - +
161B VAL* 3.5 5.0 + - - +
181B THR* 3.4 15.9 - - - +
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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