Contacts of the helix formed by residues 176 - 189 (chain N) in PDB entry 2D2C
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 GLY 176 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62N VAL* 4.7 8.9 - - - -
140N TRP* 3.5 31.2 - - - -
175N VAL* 1.3 80.7 - - - +
177N GLN* 1.3 66.9 + - - +
178N ALA 3.4 1.0 + - - +
179N THR* 3.4 6.0 + - - -
180N LEU* 3.8 9.5 + - - +
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Residues in contact with GLN 177 (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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59A LYS* 3.9 36.5 - - - +
64A GLU* 3.3 13.3 - - - +
60N PRO 4.8 0.8 + - - -
61N THR* 3.0 25.6 + - - +
62N VAL* 2.6 51.1 - - + +
176N GLY* 1.3 74.5 - - - +
178N ALA* 1.3 60.7 + - - +
180N LEU* 3.9 2.0 - - - +
181N THR* 3.0 30.3 + - - -
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Residues in contact with ALA 178 (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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56A PHE 5.7 2.0 - - - +
57A TYR* 6.4 1.1 - - + -
170N ARG 3.1 13.5 - - - +
171N GLY* 3.9 12.8 - - - -
176N GLY 3.4 0.4 - - - +
177N GLN* 1.3 75.4 - - - +
179N THR* 1.3 56.8 + - - +
180N LEU 2.5 18.5 + - - -
181N THR* 2.8 17.2 + - - -
182N ARG* 3.0 21.7 + - + +
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Residues in contact with THR 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N TRP* 5.9 0.9 - - - -
148N VAL* 4.7 9.9 - - + +
152N SER* 5.4 0.2 - - - -
169N LEU 3.9 0.6 - - - +
170N ARG* 2.5 50.6 + - + +
174N SER 3.7 0.2 + - - -
175N VAL* 3.1 50.3 - - + -
176N GLY 3.4 2.8 + - - -
177N GLN 3.8 0.2 - - - -
178N ALA* 1.3 72.2 - - - +
180N LEU* 1.3 57.0 + - - +
182N ARG 4.2 0.2 - - - -
183N TYR* 2.7 49.3 + - + +
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Residues in contact with LEU 180 (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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58N TYR* 3.8 19.3 - - - +
60N PRO* 3.3 14.6 - - + +
61N THR* 3.1 46.0 - - - +
62N VAL 4.2 1.3 - - - +
137N SER* 5.3 1.1 - - - +
138N LEU* 4.1 16.2 - - + -
140N TRP* 3.2 31.5 - - + +
176N GLY 3.8 14.1 + - - +
177N GLN* 3.9 6.5 - - - +
178N ALA 2.5 5.1 + - - -
179N THR* 1.3 71.3 - - - +
181N THR* 1.3 59.4 + - - +
182N ARG 3.0 1.3 - - - -
183N TYR* 2.6 30.2 + - - +
184N TYR* 2.8 13.2 + - + -
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Residues in contact with THR 181 (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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55A THR 3.3 18.8 - - - +
56A PHE 3.5 18.2 - - - +
57A TYR* 4.4 2.5 - - - +
58A TYR 4.0 17.5 - - - +
59A LYS* 5.2 7.3 - - + +
60N PRO* 5.1 3.8 + - - -
177N GLN* 3.0 22.8 + - - +
178N ALA* 2.8 10.0 + - - -
180N LEU* 1.3 78.8 - - - +
182N ARG* 1.3 61.1 + - - +
184N TYR* 3.9 8.3 - - + -
185N SER* 3.1 24.1 + - - -
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Residues in contact with ARG 182 (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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56A PHE* 3.3 51.9 + - + -
57A TYR* 3.4 31.1 + - - -
42D PHE* 3.4 18.9 + - - +
44D PRO* 4.6 4.4 - - - +
167N ASP 3.8 4.4 + - - -
168N LEU* 3.7 32.4 + - - +
169N LEU* 3.0 26.9 - - - +
170N ARG 4.5 1.6 - - - -
171N GLY* 4.1 22.4 + - - -
178N ALA* 3.0 24.8 + - - +
179N THR 4.0 0.2 - - - +
180N LEU 2.9 1.6 + - - -
181N THR* 1.3 73.5 - - - +
183N TYR* 1.3 68.5 + - + +
185N SER* 3.8 2.8 + - - -
186N ALA* 3.1 20.5 + - - +
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Residues in contact with TYR 183 (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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133N VAL* 4.0 13.4 - - + +
134N THR* 3.4 37.8 - - + +
137N SER* 4.0 7.6 - - - +
138N LEU* 4.5 8.5 - - + -
148N VAL* 3.0 41.2 + - + +
151N VAL* 4.6 5.0 - - - +
152N SER* 4.3 6.6 - - - -
169N LEU* 3.1 49.4 - - + +
179N THR* 2.7 26.5 - - + +
180N LEU* 2.6 15.6 + - - +
182N ARG* 1.3 71.7 - - - +
184N TYR* 1.3 68.8 + - - +
186N ALA* 2.7 14.5 + - - +
187N HIS* 2.7 14.2 + - - -
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Residues in contact with TYR 184 (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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184A TYR* 5.1 19.2 - + - -
185A SER* 5.9 0.7 - - - -
55N THR* 4.0 28.8 + - - +
58N TYR* 3.1 47.9 + + - -
60N PRO* 3.4 24.5 - - + -
138N LEU* 4.2 14.7 - - + +
180N LEU* 2.8 17.7 + - + +
181N THR* 3.9 10.1 - - + +
183N TYR* 1.3 70.5 - - - +
185N SER* 1.3 60.8 + - - +
186N ALA 2.6 12.5 + - - -
187N HIS* 2.7 4.3 + - - +
188N THR* 2.7 57.3 + - + +
301N HEM 4.6 4.0 - - + +
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Residues in contact with SER 185 (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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52A PHE* 3.9 2.6 - - - -
55A THR* 2.2 52.4 + - - -
56A PHE* 3.1 17.9 - - - -
184A TYR* 6.0 0.4 - - - -
181N THR 3.1 10.2 + - - -
182N ARG 3.8 2.0 - - - -
184N TYR* 1.3 86.5 - - - +
186N ALA* 1.3 53.5 + - - +
188N THR* 3.9 3.8 - - - -
189N PHE* 2.6 37.9 + - - +
190N VAL 2.8 2.3 + - - -
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Residues in contact with ALA 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 5.4 2.7 - - + -
134N THR* 4.1 7.0 - - + -
182N ARG 3.1 14.3 + - - +
183N TYR* 2.7 19.1 + - - +
184N TYR 2.6 4.2 + - - -
185N SER* 1.3 70.0 - - - +
187N HIS* 1.3 62.2 + - - +
190N VAL* 2.9 31.8 + - + -
191N LEU* 3.2 23.8 - - + +
192N PRO* 3.0 9.7 - - - +
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Residues in contact with HIS 187 (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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131N PHE* 2.7 51.9 + + - -
134N THR* 3.7 16.0 - - - +
135N GLY* 2.9 14.3 + - - +
138N LEU* 4.4 3.1 - - + -
183N TYR 2.7 9.9 + - - +
184N TYR* 2.7 8.4 + - - +
186N ALA* 1.3 73.3 - - - +
188N THR* 1.3 61.5 + - + +
191N LEU* 3.8 5.8 - - - +
192N PRO* 3.4 5.0 - - - +
301N HEM 2.0 89.2 + + + -
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Residues in contact with THR 188 (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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189A PHE* 3.9 19.7 - - - -
193A TRP* 4.4 1.7 - - - -
138N LEU* 5.4 1.3 - - + -
184N TYR* 2.7 64.7 + - + +
185N SER* 3.9 2.6 - - - -
187N HIS* 1.3 84.0 - - + +
189N PHE* 1.3 62.4 + - - +
192N PRO* 2.8 19.4 - - - +
193N TRP* 4.8 0.2 - - - -
301N HEM 3.5 31.6 - - + -
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Residues in contact with PHE 189 (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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48A PHE* 4.0 29.2 - + - -
52A PHE* 3.0 57.9 - + + -
55A THR* 4.3 6.1 - - + +
188A THR* 3.8 12.8 - - - -
301A HEM 3.4 33.0 - - + -
185N SER* 2.6 27.6 + - - +
188N THR* 1.3 79.2 + - - +
190N VAL* 1.3 72.1 + - + +
192N PRO* 3.1 3.7 - - - +
193N TRP* 2.8 51.5 - + - +
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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