Contacts of the helix formed by residues 163 - 174 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132H GLU* 4.2 5.9 + - - +
161H VAL 3.1 9.5 + - - -
162H PRO* 1.3 71.0 - - - +
164H GLU* 1.3 63.6 + - - +
165H GLU 3.0 4.9 - - - +
166H VAL* 2.7 30.0 + - - +
167H LEU 3.1 9.7 + - - -
193H GLU* 4.2 19.5 - - + +
194H VAL* 4.1 21.2 - - + +
197H MET* 3.3 22.4 - - + +
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Residues in contact with GLU 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H PRO* 2.7 23.7 + - + +
163H ALA* 1.3 80.0 - - - +
165H GLU* 1.3 54.8 + - - +
167H LEU* 3.7 7.0 - - + +
168H ALA* 3.0 31.7 + - - +
197H MET* 4.0 19.3 - - - +
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Residues in contact with GLU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ARG* 2.9 32.0 + - - -
157H LEU* 4.2 14.8 - - + +
161H VAL* 3.8 18.2 - - + +
162H PRO* 3.7 23.5 + - + +
163H ALA 3.0 0.2 - - - -
164H GLU* 1.3 77.2 - - - +
166H VAL* 1.3 60.3 + - - +
168H ALA* 3.8 6.2 - - - +
169H ALA* 3.3 25.5 + - - +
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Residues in contact with VAL 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H VAL* 5.0 2.4 - - + +
129H HIS* 3.7 35.4 - - + +
157H LEU* 5.1 5.8 - - + -
161H VAL* 3.8 16.8 - - + -
163H ALA* 2.7 23.0 + - - +
165H GLU* 1.3 69.6 - - - +
167H LEU* 1.3 65.5 + - - +
169H ALA* 3.1 5.2 + - - +
170H VAL* 3.0 30.3 + - + +
178H LEU* 3.7 31.4 - - + -
194H VAL* 3.8 23.6 - - + -
197H MET* 5.4 0.2 - - + -
198H LEU* 5.2 1.3 - - + -
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Residues in contact with LEU 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H ALA 3.1 4.2 + - - -
164H GLU* 3.7 11.4 - - + +
166H VAL* 1.3 77.2 - - - +
168H ALA* 1.3 56.8 + - + +
169H ALA 2.7 12.3 + - - -
170H VAL* 3.2 9.4 + - - +
171H GLN* 3.2 43.1 + - + +
197H MET* 3.6 49.2 - - + +
198H LEU* 3.8 22.9 - - + +
201H ASN* 3.5 30.5 - - + +
203H ILE* 5.1 1.3 - - + -
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Residues in contact with ALA 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H GLU 3.0 19.8 + - - +
165H GLU* 3.8 6.8 - - - +
167H LEU* 1.3 75.4 - - + +
169H ALA* 1.3 58.8 + - - +
171H GLN* 3.3 17.7 - - - +
172H LYS* 3.3 25.2 - - - +
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Residues in contact with ALA 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H VAL* 4.1 7.3 - - + +
155H VAL* 6.0 1.6 - - + -
157H LEU* 4.6 20.6 - - + -
165H GLU 3.3 19.1 - - - +
166H VAL* 3.6 4.7 - - - +
167H LEU 2.7 3.2 + - - -
168H ALA* 1.3 74.1 - - - +
170H VAL* 1.3 64.8 + - - +
171H GLN 3.2 1.5 - - - +
172H LYS* 3.5 10.8 - - + -
173H GLU* 3.0 34.9 + - + +
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Residues in contact with VAL 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H VAL* 4.4 4.3 - - + -
166H VAL* 3.0 33.0 + - + +
167H LEU 3.2 3.8 + - - +
169H ALA* 1.3 73.9 - - - +
171H GLN* 1.3 59.6 + - - +
174H LYS* 3.1 26.2 + - - +
175H PRO* 3.2 27.4 - - + +
178H LEU* 4.3 19.5 - - + -
198H LEU* 4.5 12.3 - - + -
203H ILE* 4.1 26.4 - - + +
205H ILE* 3.9 17.0 - - + -
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Residues in contact with GLN 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167H LEU* 3.2 28.5 + - + +
168H ALA* 3.3 22.0 - - - +
169H ALA 4.7 0.9 - - - +
170H VAL* 1.3 78.8 - - - +
172H LYS* 1.3 71.5 + - - +
174H LYS* 3.8 19.1 - - - +
201H ASN* 3.1 29.3 - - - +
203H ILE* 4.5 16.8 - - + -
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Residues in contact with LYS 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H ALA* 3.3 29.4 - - - +
169H ALA* 3.4 9.5 + - + +
170H VAL 3.3 0.6 - - - -
171H GLN* 1.3 90.3 - - - +
173H GLU* 1.3 76.2 + - - +
174H LYS* 5.2 1.3 - - - +
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Residues in contact with GLU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H THR* 4.3 27.0 + - + +
127H VAL* 4.6 7.9 - - + -
153H ASN* 5.7 0.5 - - - +
155H VAL* 4.1 28.0 - - + +
169H ALA* 3.0 21.0 + - + +
172H LYS* 1.3 93.4 - - + +
174H LYS* 1.3 72.0 + - - +
175H PRO* 3.2 2.9 - - + +
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Residues in contact with LYS 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H THR* 5.3 1.4 + - - -
170H VAL 3.1 12.3 + - - +
171H GLN* 3.8 17.3 - - - +
172H LYS 5.2 1.3 - - - +
173H GLU* 1.3 78.2 - - - +
175H PRO* 1.3 67.7 - - - +
176H ILE* 5.3 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