Contacts of the helix formed by residues 163 - 174 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132N GLU* 4.3 3.4 - - + +
161N VAL* 3.2 9.6 + - - +
162N PRO* 1.3 80.5 - - - +
164N GLU* 1.3 52.4 + - - +
165N GLU 3.1 2.8 - - - +
166N VAL* 2.9 20.1 + - - +
167N LEU 2.7 29.3 + - - -
190N ALA 4.9 1.6 - - - +
193N GLU* 4.2 18.6 - - + -
194N VAL* 3.8 23.1 - - + +
197N MET* 3.2 20.1 - - + +
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Residues in contact with GLU 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N GLU* 5.0 0.5 - - - +
162N PRO* 2.9 31.8 + - + +
163N ALA* 1.3 77.7 - - - +
165N GLU* 1.3 57.8 + - - +
167N LEU* 3.5 4.4 - - - +
168N ALA* 2.9 29.1 + - - +
193N GLU* 4.9 10.6 - - - +
197N MET* 3.5 32.3 - - - +
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Residues in contact with GLU 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ARG* 3.1 30.0 + - - -
157N LEU* 3.8 24.5 - - + +
161N VAL* 4.2 3.4 - - + -
162N PRO* 3.7 29.2 - - + +
163N ALA 4.1 0.8 - - - +
164N GLU* 1.3 78.5 - - - +
166N VAL* 1.3 62.0 + - - +
167N LEU 3.3 0.2 - - - -
168N ALA* 3.6 6.9 - - + +
169N ALA* 3.2 26.0 + - + +
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Residues in contact with VAL 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N VAL* 5.9 0.7 - - - -
129N HIS* 3.6 37.9 - - + +
157N LEU* 5.0 5.6 - - + -
161N VAL* 3.7 15.9 - - + -
163N ALA* 2.9 20.5 + - - +
165N GLU* 1.3 78.0 - - - +
167N LEU* 1.3 56.6 + - - +
169N ALA* 3.4 3.1 + - - +
170N VAL* 2.9 41.6 + - + +
178N LEU* 3.7 32.5 - - + -
194N VAL* 3.9 13.2 - - + +
197N MET* 6.1 0.2 - - + -
198N LEU* 5.5 3.6 - - + -
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Residues in contact with LEU 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N ALA 2.7 14.8 + - - +
164N GLU* 3.5 9.2 - - - +
166N VAL* 1.3 70.6 - - + +
168N ALA* 1.3 55.1 + - + +
169N ALA 3.0 10.2 + - - -
170N VAL* 3.4 11.1 + - + +
171N GLN* 2.8 59.3 + - - +
197N MET* 3.6 51.1 - - + +
198N LEU* 4.3 17.5 - - + +
201N ASN* 3.8 17.7 - - + +
203N ILE* 4.5 4.3 - - + -
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Residues in contact with ALA 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N GLU 2.9 18.5 + - - +
165N GLU* 3.6 8.2 - - + +
166N VAL 3.4 0.2 - - - -
167N LEU* 1.3 74.3 - - + +
169N ALA* 1.3 58.6 + - - +
171N GLN* 4.1 4.7 - - - -
172N LYS* 3.1 34.4 - - - +
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Residues in contact with ALA 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127N VAL* 4.4 5.4 - - + +
155N VAL* 5.5 4.3 - - + -
157N LEU* 4.1 27.4 - - + -
165N GLU* 3.2 18.5 + - + +
166N VAL 4.1 2.0 - - - +
167N LEU 3.0 1.6 + - - -
168N ALA* 1.3 76.9 - - - +
170N VAL* 1.3 67.8 + - - +
171N GLN 3.2 1.1 - - - -
172N LYS* 3.8 9.6 - - + -
173N GLU* 3.3 31.9 + - + +
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Residues in contact with VAL 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127N VAL* 4.7 5.6 - - + -
166N VAL* 2.9 40.4 + - + +
167N LEU* 3.4 4.2 + - - +
169N ALA* 1.3 76.9 - - - +
171N GLN* 1.3 57.1 + - - +
173N GLU 4.1 0.2 - - - -
174N LYS* 3.2 9.5 + - - +
175N PRO* 3.1 43.3 - - + +
178N LEU* 4.5 20.2 - - + -
198N LEU* 4.2 24.0 - - + -
203N ILE* 4.4 15.0 - - + -
205N ILE* 4.4 8.1 - - + -
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Residues in contact with GLN 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N LEU* 2.8 39.4 + - - +
168N ALA* 4.1 4.7 - - - -
169N ALA 3.2 0.4 - - - -
170N VAL* 1.3 78.1 - - - +
172N LYS* 1.3 74.2 + - - +
173N GLU 3.2 2.4 + - - -
174N LYS* 4.1 15.2 + - - +
201N ASN* 3.2 39.2 + - - +
203N ILE* 4.3 12.7 - - + +
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Residues in contact with LYS 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N ALA* 3.1 42.5 - - - +
169N ALA* 3.6 9.4 + - + +
170N VAL 3.5 0.2 - - - -
171N GLN* 1.3 84.3 + - - +
173N GLU* 1.3 73.2 + - + +
174N LYS* 3.9 0.4 - - - -
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Residues in contact with GLU 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N THR* 3.9 30.5 + - + +
127N VAL* 4.6 5.8 - - + -
153N ASN* 5.0 4.0 - - - +
155N VAL* 4.0 31.0 - - + +
169N ALA* 3.3 21.6 + - + +
171N GLN 3.2 0.4 - - - -
172N LYS* 1.3 94.0 - - + +
174N LYS* 1.3 68.5 + - - +
175N PRO* 3.2 5.0 - - + +
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Residues in contact with LYS 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N THR* 5.0 1.6 - - - -
170N VAL 3.2 10.7 + - - +
171N GLN* 4.4 12.8 - - - +
172N LYS 5.8 0.2 - - - -
173N GLU* 1.3 75.2 - - - +
175N PRO* 1.3 68.6 - - - +
176N ILE* 4.1 2.4 + - - +
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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