Contacts of the helix formed by residues 161 - 171 (chain D) in PDB entry 1JIQ
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 ASP 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386C ASN* 5.9 1.0 - - - -
154D ASN* 4.4 5.0 + - - +
156D GLY* 3.5 20.3 - - - +
157D ILE 4.2 2.9 - - - -
158D GLY 3.0 6.8 + - - +
159D GLY 3.1 0.6 - - - -
160D SER* 1.3 81.7 - - - +
162D LEU* 1.3 83.2 + - - +
163D GLY 3.4 2.0 - - - -
164D PRO* 3.4 5.6 - - - +
165D LEU* 3.0 37.5 + - - +
183D TYR* 3.7 25.8 - - - +
184D VAL 4.8 0.9 + - - +
185D SER* 3.6 27.4 + - - -
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Residues in contact with LEU 162 (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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386C ASN* 5.8 9.4 - - + +
390C ALA* 4.0 15.5 - - + -
158D GLY* 3.0 13.9 + - - +
159D GLY* 4.5 1.1 - - - -
161D ASP* 1.3 96.9 - - - +
163D GLY* 1.3 57.7 + - - +
165D LEU* 3.8 7.5 - - + +
166D MET* 2.9 32.1 + - - +
347D ARG* 5.6 5.2 - - - +
350D ALA* 4.0 21.1 - - + +
351D TYR* 3.9 21.7 - - + +
354D GLN* 3.6 37.2 - - + +
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Residues in contact with GLY 163 (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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159D GLY* 4.6 5.3 + - - -
162D LEU* 1.3 74.2 - - - +
164D PRO* 1.3 67.7 - - - +
166D MET* 3.2 1.8 + - - +
167D VAL* 2.9 34.7 + - - +
276D LEU* 3.9 16.2 - - - -
351D TYR* 3.3 27.7 - - - -
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Residues in contact with PRO 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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154D ASN* 5.0 1.3 - - - +
159D GLY 4.2 9.6 - - - +
160D SER 4.2 7.0 - - - +
161D ASP 3.4 11.9 - - - +
162D LEU 4.2 0.2 - - - +
163D GLY* 1.3 89.5 - - - +
165D LEU* 1.3 57.9 + - - +
168D THR* 2.8 32.6 + - - +
183D TYR* 3.6 11.7 - - + -
276D LEU* 4.3 7.6 - - + -
280D ILE* 3.6 32.1 - - + +
283D SER* 3.5 22.7 - - - +
284D ILE* 3.8 18.2 - - + -
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Residues in contact with LEU 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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161D ASP* 3.0 31.5 + - - +
162D LEU* 3.8 7.6 - - + +
164D PRO* 1.3 75.7 - - - +
166D MET* 1.3 65.3 + - - +
168D THR* 3.2 7.0 + - - -
169D GLU* 2.9 39.1 + - + +
183D TYR* 3.7 36.5 - - + -
191D HIS* 6.5 0.9 - - + -
347D ARG* 3.8 33.0 - - + +
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Residues in contact with MET 166 (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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162D LEU 2.9 19.7 + - - +
163D GLY 3.7 0.4 - - - +
165D LEU* 1.3 83.6 - - - +
167D VAL* 1.3 77.2 + - + +
169D GLU* 3.5 3.0 + - - +
170D ALA* 2.9 27.2 + - - +
276D LEU* 4.9 0.7 - - + -
344D TYR 4.6 0.7 - - - +
345D LEU* 4.8 2.2 - - + -
347D ARG* 3.4 39.4 + - + +
348D PHE* 3.8 21.5 - - + +
351D TYR* 3.9 31.6 - - + -
487D LEU* 4.4 10.3 - - - -
491D VAL* 3.9 24.0 - - + -
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Residues in contact with VAL 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 GLY 2.9 20.2 + - - +
166D MET* 1.3 93.8 - - + +
168D THR* 1.3 61.7 + - - +
170D ALA* 3.2 0.7 + - - -
171D LEU* 2.8 47.6 + - + +
276D LEU* 4.0 22.7 - - + -
284D ILE* 3.7 34.8 - - + -
296D LEU* 4.1 9.2 - - + -
487D LEU* 3.9 16.4 - - + -
491D VAL* 5.5 1.3 - - + -
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Residues in contact with THR 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 PRO 2.8 23.9 + - - +
165D LEU 3.2 7.3 + - - -
167D VAL* 1.3 75.7 - - - +
169D GLU* 1.3 62.5 + - - +
171D LEU* 3.8 3.4 - - - +
172D LYS* 3.3 31.0 + - - -
181D VAL* 4.0 5.0 - - + +
183D TYR* 3.2 29.7 + - - +
283D SER 4.2 2.5 - - - +
284D ILE* 3.7 31.6 - - + +
287D HIS* 3.8 26.3 - - + -
288D VAL* 5.5 1.8 - - + -
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Residues in contact with GLU 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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194C LYS* 5.6 3.5 + - - -
165D LEU* 2.9 39.1 + - + +
166D MET* 3.6 6.7 - - - +
168D THR* 1.3 80.1 + - - +
170D ALA* 1.3 62.1 + - - +
171D LEU 3.5 0.5 + - - -
172D LYS* 3.5 26.3 + - - +
183D TYR* 6.0 2.0 - - + -
344D TYR* 3.3 30.4 - - - +
346D HIS* 2.7 39.1 + - + +
347D ARG* 5.0 1.6 - - + -
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Residues in contact with ALA 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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166D MET* 2.9 19.2 + - - +
167D VAL 3.7 4.0 - - - +
169D GLU* 1.3 76.7 - - - +
171D LEU* 1.3 63.8 + - - +
172D LYS 3.4 1.4 + - - -
173D PRO* 4.1 3.3 - - - +
174D TYR* 5.5 0.5 - - - -
344D TYR* 3.2 31.4 + - - +
345D LEU* 3.9 25.1 - - + -
413D GLN* 6.0 0.5 - - - +
482D LEU* 4.1 11.8 - - + +
487D LEU* 3.9 16.8 - - + -
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Residues in contact with LEU 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 VAL* 2.8 36.3 + - + +
168D THR 3.8 2.9 - - - -
170D ALA* 1.3 82.8 - - + +
172D LYS* 1.3 64.8 + - - +
173D PRO* 3.2 5.8 - - - -
174D TYR* 2.8 28.9 + - + +
284D ILE* 5.1 1.3 - - + -
288D VAL* 3.7 28.5 - - + +
292D ASN 6.0 0.2 - - - -
296D LEU* 4.7 6.3 - - + -
482D LEU* 4.4 6.7 - - + +
483D THR 4.0 6.5 - - - +
484D PRO* 3.8 49.4 - - + -
487D LEU* 3.8 17.3 - - + -
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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