Contacts of the helix formed by residues 165 - 175 (chain D) in PDB entry 2JG1
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 SER 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D CYS* 1.3 79.7 - - - +
166D GLY* 1.3 67.8 + - - +
168D THR* 3.4 19.6 + - - -
169D LEU* 3.9 9.6 - - - -
188D GLU* 3.8 36.8 + - - -
191D GLN* 6.0 1.1 - - - -
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Residues in contact with GLY 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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165D SER* 1.3 77.0 - - - +
167D ALA* 1.3 63.5 + - - -
168D THR 3.2 0.3 + - - -
169D LEU* 3.2 2.6 + - - +
170D GLN* 3.0 19.0 + - - +
188D GLU 5.6 1.2 + - - -
191D GLN* 6.3 1.1 - - - -
192D LEU* 3.5 24.3 - - - +
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Residues in contact with ALA 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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143D GLN* 5.6 4.7 - - - +
165D SER 3.7 0.2 + - - -
166D GLY* 1.3 71.7 - - - -
168D THR* 1.3 53.1 + - - +
170D GLN* 3.6 10.9 - - + +
171D THR* 2.7 39.2 + - - +
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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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135D GLY 4.7 2.5 - - - +
136D SER* 4.6 15.3 - - - -
137D LEU* 4.6 15.4 + - + +
146D TYR* 3.8 35.0 - - + -
164D CYS* 3.9 10.8 - - + -
165D SER 3.4 11.5 + - - -
166D GLY 3.1 0.4 - - - -
167D ALA* 1.3 76.3 + - - +
169D LEU* 1.3 64.9 + - - +
171D THR* 3.4 6.7 + - - -
172D VAL* 3.4 22.9 + - - +
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Residues in contact with LEU 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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162D LEU* 4.0 24.5 - - + +
164D CYS* 3.5 33.1 - - - +
165D SER* 3.4 9.3 + - - -
166D GLY 3.2 7.6 + - - +
168D THR* 1.3 74.5 - - - +
170D GLN* 1.3 67.1 + - - +
172D VAL* 3.3 3.1 + - - +
173D LEU* 3.0 51.7 + - + +
182D ILE* 4.3 21.1 - - + -
184D PRO* 4.9 14.8 - - + -
188D GLU* 5.6 2.7 - - + +
192D LEU* 3.8 24.5 - - + -
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Residues in contact with GLN 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 GLY 3.0 16.7 + - - +
167D ALA* 3.6 11.7 - - - +
169D LEU* 1.3 76.5 - - - +
171D THR* 1.3 61.3 + - - +
173D LEU* 3.3 6.6 + - - +
174D GLU* 2.9 57.4 + - - +
192D LEU* 3.7 30.4 - - + +
212D LEU* 3.4 31.4 - - - +
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Residues in contact with THR 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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143D GLN* 3.5 43.8 + - + +
144D ASP* 4.5 7.9 - - + -
147D ALA* 5.3 4.2 - - + +
167D ALA* 2.7 23.0 + - - +
168D THR* 3.7 6.7 - - - -
169D LEU 3.3 0.4 - - - -
170D GLN* 1.3 75.9 - - - +
172D VAL* 1.3 65.0 + - + +
174D GLU* 3.4 19.8 + - - +
175D ASN* 3.4 13.5 + - - +
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Residues in contact with VAL 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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146D TYR* 3.7 32.1 - - + -
147D ALA* 4.4 7.2 - - + +
150D ILE* 3.7 25.1 - - + -
162D LEU* 3.8 22.2 - - + -
164D CYS* 5.2 0.2 - - - -
168D THR 3.4 11.6 + - - +
169D LEU* 3.3 8.3 + - - +
171D THR* 1.3 76.9 - - + +
173D LEU* 1.3 65.4 + - + +
175D ASN* 2.8 35.1 + - - +
177D TYR 4.5 0.5 - - - +
178D LYS* 4.4 1.9 + - - +
179D PRO* 3.8 17.5 - - + -
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Residues in contact with LEU 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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169D LEU* 3.0 40.1 + - + +
170D GLN* 3.3 5.1 + - - +
172D VAL* 1.3 80.3 - - + +
174D GLU* 1.3 55.4 + - - +
178D LYS* 2.7 27.8 + - - +
179D PRO* 5.2 1.8 - - + -
182D ILE* 4.5 8.5 - - + -
192D LEU* 3.8 15.5 - - + -
212D LEU* 3.5 39.3 - - + +
213D PHE* 3.7 27.4 - - + -
216D ILE* 3.3 33.7 - - + -
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Residues in contact with GLU 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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170D GLN* 2.9 48.6 + - - +
171D THR* 3.8 14.1 + - - +
172D VAL 3.1 0.6 - - - -
173D LEU* 1.3 76.3 - - - +
175D ASN* 1.3 60.1 + - - +
176D PRO* 4.6 1.4 - - - +
178D LYS* 4.4 0.8 + - - -
212D LEU* 4.2 7.0 - - + -
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Residues in contact with ASN 175 (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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147D ALA* 3.7 28.0 - - + +
171D THR 3.4 9.8 + - - +
172D VAL* 2.8 33.4 + - - +
174D GLU* 1.3 78.9 - - - +
176D PRO* 1.3 68.6 - - + +
177D TYR* 2.9 50.3 + - - +
178D LYS* 2.7 31.5 + - - +
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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