Contacts of the helix formed by residues 163 - 174 (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 ALA 163 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132L GLU* 3.8 13.4 + - - +
161L VAL 3.3 8.3 + - - -
162L PRO* 1.3 69.3 - - - +
164L GLU* 1.3 65.1 + - - +
165L GLU 3.0 3.8 - - - -
166L VAL* 2.7 36.9 + - - +
167L LEU 2.9 11.1 + - - -
190L ALA* 5.5 0.4 - - + +
193L GLU* 4.2 21.3 - - + -
194L VAL* 4.3 10.4 - - + +
197L MET* 3.1 18.5 - - + +
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Residues in contact with GLU 164 (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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162L PRO 2.6 13.7 + - - +
163L ALA* 1.3 83.5 - - - +
165L GLU* 1.3 55.6 + - - +
167L LEU* 4.0 4.2 - - + +
168L ALA* 3.1 29.3 + - - +
197L MET* 3.8 22.5 - - - +
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Residues in contact with GLU 165 (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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133K ARG* 2.7 32.7 + - - -
157L LEU* 3.6 25.5 - - + +
161L VAL* 4.4 2.4 - - + +
162L PRO* 3.7 31.1 + - + +
163L ALA 3.0 0.2 - - - -
164L GLU* 1.3 75.9 - - - +
166L VAL* 1.3 61.9 - - - +
168L ALA* 4.0 7.3 - - + +
169L ALA* 3.3 23.2 + - - +
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Residues in contact with VAL 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L VAL* 5.1 3.0 - - + +
129L HIS* 4.0 20.0 - - + +
157L LEU* 4.8 3.6 - - + -
161L VAL* 3.5 27.1 - - + -
163L ALA* 2.7 26.0 + - - +
165L GLU* 1.3 74.9 - - - +
167L LEU* 1.3 59.3 + - - +
169L ALA* 3.1 6.6 + - - +
170L VAL* 3.0 33.8 + - + +
178L LEU* 3.9 38.8 - - + -
194L VAL* 4.1 15.5 - - + -
197L MET* 5.5 0.4 - - + -
198L LEU* 5.7 1.1 - - + -
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Residues in contact with LEU 167 (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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163L ALA 2.9 5.1 + - - +
164L GLU* 4.0 6.1 - - + +
166L VAL* 1.3 72.8 - - - +
168L ALA* 1.3 56.0 + - + +
169L ALA 2.8 14.6 + - - -
170L VAL* 3.0 15.0 + - - -
171L GLN* 3.3 44.8 + - - +
197L MET* 3.6 40.3 - - + +
198L LEU* 4.3 10.8 - - + -
201L ASN* 4.1 16.4 - - + +
203L ILE* 3.8 25.4 - - + -
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Residues in contact with ALA 168 (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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164L GLU 3.1 18.4 + - - +
165L GLU* 4.0 8.5 - - + +
166L VAL 3.4 0.2 - - - -
167L LEU* 1.3 78.4 - - + +
169L ALA* 1.3 56.9 + - - +
171L GLN* 3.9 12.8 - - - -
172L LYS* 3.0 35.5 - - - +
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Residues in contact with ALA 169 (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* 4.5 8.6 - - + +
155L VAL* 5.7 2.2 - - + -
157L LEU* 4.1 24.9 - - + -
165L GLU 3.3 17.4 + - - +
166L VAL* 3.1 5.5 + - - +
167L LEU 2.8 2.8 + - - -
168L ALA* 1.3 78.4 - - - +
170L VAL* 1.3 62.5 + - - +
171L GLN 3.2 1.8 - - - -
172L LYS* 3.4 5.7 + - - +
173L GLU* 3.3 31.4 + - + +
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Residues in contact with VAL 170 (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* 4.6 10.1 - - + -
166L VAL* 3.0 27.9 + - + +
167L LEU* 3.0 4.7 + - - +
169L ALA* 1.3 75.9 - - - +
171L GLN* 1.3 58.3 + - - +
174L LYS* 2.9 27.4 + - - +
175L PRO* 3.1 29.6 - - + +
178L LEU* 4.6 10.5 - - + -
198L LEU* 4.0 19.7 - - + -
203L ILE* 4.3 31.0 - - + -
205L ILE* 4.3 8.5 - - + -
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Residues in contact with GLN 171 (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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167L LEU* 3.3 38.0 + - + +
168L ALA* 3.9 10.9 - - - +
169L ALA 3.2 0.2 - - - -
170L VAL* 1.3 76.4 - - - +
172L LYS* 1.3 70.6 + - + +
174L LYS* 3.7 21.7 - - - +
201L ASN* 3.3 28.9 - - - +
203L ILE* 4.8 8.7 - - + +
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Residues in contact with LYS 172 (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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168L ALA* 3.0 32.1 - - - +
169L ALA* 3.4 6.7 + - - +
170L VAL 3.4 0.4 - - - -
171L GLN* 1.3 88.4 + - + +
173L GLU* 1.3 74.2 + - - +
174L LYS* 3.7 6.1 + - - +
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Residues in contact with GLU 173 (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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125L THR* 4.0 28.4 + - + +
127L VAL* 4.8 0.2 - - + -
153L ASN* 5.0 4.2 - - - +
155L VAL* 4.0 31.9 - - + +
169L ALA* 3.3 18.5 + - + +
172L LYS* 1.3 87.7 - - + +
174L LYS* 1.3 70.9 + - - +
175L PRO* 3.1 8.9 - - + +
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Residues in contact with LYS 174 (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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125L THR* 5.5 0.2 - - - -
170L VAL* 2.9 12.7 + - - +
171L GLN* 3.7 20.4 - - - +
172L LYS 4.5 4.7 - - - +
173L GLU* 1.3 76.8 - - - +
175L PRO* 1.4 68.5 - - - +
176L ILE* 5.4 1.7 - - - +
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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