Contacts of the helix formed by residues 163 - 174 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D GLU* 4.2 8.4 + - - +
161D VAL 3.3 7.7 + - - -
162D PRO* 1.3 68.4 - - - +
164D GLU* 1.3 65.7 + - - +
165D GLU 3.0 1.1 - - - -
166D VAL* 2.6 28.3 + - - +
167D LEU 2.8 12.3 + - - -
190D ALA 5.4 0.7 - - - +
193D GLU* 4.0 26.9 - - + +
194D VAL* 4.0 20.1 - - + +
197D MET* 3.1 19.1 - - + +
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Residues in contact with GLU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU* 5.5 1.0 - - - +
162D PRO* 2.5 22.4 + - - +
163D ALA* 1.3 78.0 - - - +
165D GLU* 1.3 56.1 + - - +
167D LEU* 3.5 6.3 + - - +
168D ALA* 3.1 29.5 + - - +
197D MET* 3.7 24.5 - - - +
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 2.8 32.5 + - - -
157D LEU* 3.9 28.6 - - + +
161D VAL* 4.3 3.8 - - + +
162D PRO* 3.6 26.7 + - + +
163D ALA 3.0 0.2 - - - -
164D GLU* 1.3 77.2 - - - +
166D VAL* 1.3 62.8 + - - +
168D ALA* 4.0 7.5 - - - +
169D ALA* 3.5 21.3 + - - +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D VAL* 5.4 1.5 - - + +
129D HIS* 3.9 23.8 - - + -
157D LEU* 5.2 4.7 - - + -
161D VAL* 3.6 26.5 - - + -
163D ALA* 2.6 25.5 + - - +
165D GLU* 1.3 70.2 - - - +
167D LEU* 1.3 67.5 + - - +
169D ALA* 3.0 14.7 + - - +
170D VAL* 3.1 21.5 + - + +
178D LEU* 3.9 37.2 - - + -
194D VAL* 4.1 16.2 - - + -
197D MET* 6.0 0.2 - - + -
198D LEU* 5.1 1.8 - - + -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ALA 2.8 7.7 + - - -
164D GLU* 3.5 9.2 - - - +
166D VAL* 1.3 74.1 - - - +
168D ALA* 1.3 64.3 + - + +
169D ALA 3.1 0.3 + - - -
170D VAL* 3.1 12.1 + - - +
171D GLN* 3.2 48.9 + - - +
197D MET* 3.3 55.6 - - + +
198D LEU* 4.2 10.1 - - + -
201D ASN* 4.0 11.9 - - + +
203D ILE* 3.9 18.6 - - + -
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLU 3.1 14.8 + - - +
165D GLU* 4.0 8.1 - - - +
166D VAL 3.3 0.2 - - - -
167D LEU* 1.3 80.4 - - + +
169D ALA* 1.3 56.2 + - - +
171D GLN* 3.5 15.6 - - - +
172D LYS* 3.0 44.8 + - - +
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 4.1 9.5 - - + +
155D VAL* 5.5 1.3 - - + -
157D LEU* 3.8 27.8 - - + -
165D GLU 3.5 15.1 + - - +
166D VAL 3.0 6.8 + - - +
168D ALA* 1.3 74.8 - - - +
170D VAL* 1.3 64.9 + - - +
171D GLN 3.1 2.0 - - - -
172D LYS* 3.8 7.4 - - + +
173D GLU* 3.2 33.4 + - + +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 4.8 2.5 - - + -
166D VAL* 3.1 27.1 + - + +
167D LEU 3.1 5.8 + - - +
169D ALA* 1.3 76.2 - - - +
171D GLN* 1.3 60.4 + - - +
174D LYS* 3.1 23.7 + - - +
175D PRO* 3.3 24.8 - - + +
178D LEU* 4.5 16.6 - - + -
198D LEU* 4.2 17.5 - - + -
203D ILE* 4.1 24.2 - - + -
205D ILE* 3.9 18.8 - - + -
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Residues in contact with GLN 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D LEU* 3.2 36.0 + - + +
168D ALA* 3.5 18.6 - - - +
170D VAL* 1.3 78.3 - - - +
172D LYS* 1.3 75.0 + - + +
173D GLU 2.9 3.3 + - - -
174D LYS* 3.5 21.3 + - - +
201D ASN* 3.2 29.5 - - - +
203D ILE* 5.1 7.2 - - + +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA* 3.0 36.4 + - - +
169D ALA* 3.6 3.8 + - + +
171D GLN* 1.3 83.5 + - - +
173D GLU* 1.3 77.6 + - + +
174D LYS* 5.3 0.7 - - - +
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Residues in contact with GLU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 4.1 29.0 + - + +
127D VAL* 4.6 4.0 - - + -
153D ASN* 5.4 2.6 - - - +
155D VAL* 4.0 30.0 - - + +
169D ALA* 3.2 22.3 + - + +
171D GLN 3.1 0.6 - - - -
172D LYS* 1.3 93.3 - - + +
174D LYS* 1.3 72.1 + - - +
175D PRO* 3.3 2.5 - - + +
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 5.2 1.0 + - - -
170D VAL 3.1 11.9 + - - +
171D GLN* 3.6 16.4 - - - +
172D LYS 5.3 0.9 - - - -
173D GLU* 1.3 78.9 - - - +
175D PRO* 1.3 68.7 - - - +
176D ILE* 4.1 1.9 + - - +
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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