Contacts of the strand formed by residues 177 - 181 (chain L) 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 MET 177 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125L THR 3.7 0.6 + - - -
126L VAL* 3.3 29.8 - - + -
127L VAL 3.2 21.5 + - - -
147L LEU* 6.1 0.9 - - - -
175L PRO* 3.3 7.5 + - - +
176L ILE* 1.3 84.3 - - + +
178L LEU* 1.3 69.6 + - - +
179L THR* 4.4 4.0 - - + -
205L ILE* 3.8 6.5 - - - +
206L PRO* 3.8 21.3 - - + +
208L ALA* 4.3 9.4 - - + -
234L ALA 4.3 2.9 - - - +
237L ILE* 3.7 51.1 - - + +
238L ALA* 3.8 22.2 - - + -
241L ILE* 4.0 14.6 - - + -
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Residues in contact with LEU 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L VAL* 3.4 39.7 - - + +
129L HIS* 3.9 10.3 - - - +
166L VAL* 3.9 11.7 - - + -
170L VAL* 4.6 8.1 - - + -
177L MET* 1.3 78.5 - - - +
179L THR* 1.3 66.4 + - - +
194L VAL* 3.8 13.7 - - + -
198L LEU* 3.7 27.8 - - + -
205L ILE* 3.7 14.3 - - + +
206L PRO 3.1 7.0 + - - +
207L PHE* 3.2 28.3 - - + -
208L ALA 2.8 30.8 + - - -
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Residues in contact with THR 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L VAL* 3.8 21.5 - - + -
127L VAL 2.9 6.1 + - - -
128L CYS* 3.4 25.9 - - - +
129L HIS* 3.0 26.3 + - - -
140L LYS* 5.7 1.4 - - - +
143L VAL* 4.1 10.1 - - + +
147L LEU* 4.2 9.0 - - + -
177L MET* 4.4 5.4 - - + -
178L LEU* 1.3 79.8 - - - +
180L GLY* 1.3 59.3 + - - +
181L THR* 5.3 1.0 + - - -
207L PHE* 4.0 2.9 - - - -
208L ALA* 3.1 12.3 - - + -
234L ALA* 5.3 3.8 - - + -
500L B13 3.4 25.4 - - - +
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Residues in contact with GLY 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L HIS* 3.2 23.1 - - - -
179L THR* 1.3 75.7 - - - +
181L THR* 1.3 62.6 + - - -
191L PHE* 3.4 14.0 - - - -
207L PHE* 3.8 4.1 - - - -
208L ALA 2.9 8.2 + - - +
210L GLY 3.0 25.3 + - - -
500L B13 3.5 6.0 - - - -
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Residues in contact with THR 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L HIS 3.1 6.9 + - - -
130L VAL* 3.2 22.5 - - - +
131L ALA 3.1 21.1 + - - -
136L HIS 4.6 5.6 - - - +
139L GLY* 4.6 0.2 - - - -
140L LYS* 3.9 22.1 - - - +
179L THR* 5.3 1.4 + - - -
180L GLY* 1.3 73.6 - - - -
182L ALA* 1.3 64.3 + - - +
183L LEU* 3.6 25.6 - - + -
191L PHE* 3.6 3.6 - - - -
210L GLY 3.3 2.9 - - - -
211L GLY* 4.0 2.5 - - - -
500L B13 2.6 40.6 + - + +
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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