Contacts of the helix formed by residues 189 - 200 (chain A) in PDB entry 2JFF
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 PHE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A PRO* 1.3 87.5 - - + +
190A GLY* 1.3 63.6 + - - +
192A GLN* 4.4 4.0 + - - +
193A GLN* 2.8 49.4 + - + +
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A MET* 3.9 14.8 - - - -
187A TYR* 2.9 18.6 + - - +
188A PRO 3.3 2.4 - - - -
189A PHE* 1.3 78.5 - - - +
191A LEU* 1.3 66.0 + - - -
193A GLN* 3.0 12.8 + - - +
194A TYR* 3.2 10.4 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 4.4 7.2 - - + +
180A THR* 4.2 3.6 - - - -
181A GLU* 3.8 38.1 - - + +
184A MET* 4.0 11.5 - - + -
190A GLY* 1.3 70.7 - - - -
192A GLN* 1.3 65.3 + - + +
194A TYR* 3.4 14.7 + - + +
195A ARG* 2.9 27.7 + - - +
216A LEU* 3.7 28.3 - - + -
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Residues in contact with GLN 192 (chain A).
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 4.4 3.9 + - - +
190A GLY 3.3 0.8 + - - -
191A LEU* 1.3 86.7 - - + +
193A GLN* 1.3 57.4 + - - +
195A ARG* 3.2 36.7 + - - +
196A ALA* 2.8 29.5 + - - +
216A LEU* 3.9 26.2 - - - +
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 6.3 0.8 - - - +
164A GLU* 6.0 0.2 + - - -
186A ARG 5.0 1.0 + - - -
187A TYR* 3.2 30.8 - - + -
188A PRO* 3.3 6.8 - - - +
189A PHE* 2.8 62.2 + - + +
190A GLY 3.0 9.0 + - - +
192A GLN* 1.3 75.6 - - - +
194A TYR* 1.3 63.8 + - - +
196A ALA* 3.3 8.3 + - + +
197A ALA* 3.2 20.3 + - - +
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Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 2.8 20.3 + - - -
160A SER* 3.5 13.0 - - - -
179A VAL* 4.0 19.1 - - + -
180A THR 3.2 22.4 - - - -
182A ASP* 3.6 27.9 - - + +
183A HIS* 3.7 8.5 - + - -
184A MET* 3.8 11.2 - - + -
187A TYR* 3.4 38.5 - + + -
190A GLY 3.2 1.8 + - - -
191A LEU* 3.4 16.6 + - + +
193A GLN* 1.3 75.1 - - - +
195A ARG* 1.3 64.0 + - - +
197A ALA* 3.1 14.6 + - - +
198A KCX 2.5 51.3 + - - +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 5.9 0.2 - - + -
179A VAL* 4.2 19.7 - - + -
191A LEU 2.9 17.6 + - - +
192A GLN* 3.2 31.1 + - - +
194A TYR* 1.3 76.2 - - - +
196A ALA* 1.3 62.8 + - - +
198A KCX 3.1 9.0 + - - +
199A LEU* 2.9 36.6 + - + +
215A ALA 3.7 11.3 + - - -
216A LEU* 2.8 48.5 + - + +
218A MET* 2.7 28.1 + - - +
219A PRO 4.5 1.8 + - - -
220A ILE* 4.1 20.5 - - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN 2.8 20.8 + - - +
193A GLN* 3.5 10.5 - - + +
194A TYR 3.3 0.4 - - - -
195A ARG* 1.3 72.2 - - - +
197A ALA* 1.3 63.5 + - - +
199A LEU* 3.3 22.5 + - + +
200A ARG* 3.5 14.2 + - - +
220A ILE* 6.1 2.5 - - + -
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A SER* 3.7 7.6 - - - +
163A LEU* 3.5 12.5 - - - +
164A GLU* 3.7 20.4 - - + -
187A TYR* 3.5 24.0 - - + +
193A GLN 3.2 9.9 + - - +
194A TYR 3.1 11.4 + - - +
196A ALA* 1.3 76.8 - - - +
198A KCX 1.3 62.3 + - - +
200A ARG* 3.3 29.2 - - - +
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Residues in contact with KCX 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A THR* 3.0 23.6 + - + +
111A GLY* 3.4 28.4 + - - +
112A SER* 4.0 3.6 - - - -
115A LYS* 3.6 14.5 + - - -
159A SER* 3.3 13.5 - - - -
160A SER* 3.0 36.7 + - - -
163A LEU* 3.9 7.4 - - - +
176A ILE* 3.4 31.8 - - + +
178A ASN 4.4 2.9 - - - +
179A VAL* 4.5 7.9 - - + -
182A ASP* 4.7 1.0 - - - +
183A HIS* 3.7 13.3 + - - -
194A TYR* 2.5 56.5 + - + +
195A ARG* 3.1 8.9 + - - +
197A ALA* 1.3 75.4 + - - +
199A LEU* 1.3 63.1 + - - +
201A ILE* 3.0 29.6 + - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 3.6 18.4 - - + +
195A ARG* 2.9 40.0 + - + +
196A ALA* 3.7 12.3 - - - +
197A ALA 3.3 0.4 - - - -
198A KCX 1.3 75.7 + - - +
200A ARG* 1.3 62.3 + - - +
201A ILE 3.1 1.1 + - - -
202A TYR* 3.2 25.8 + - + +
203A GLU* 4.1 7.3 + - - +
216A LEU 4.2 4.3 - - - +
218A MET 3.5 25.1 - - - +
219A PRO* 3.8 14.8 - - + -
220A ILE* 3.6 33.2 - - + +
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 2.8 35.7 + - + +
164A GLU* 3.8 18.6 + - - +
165A THR 5.4 0.2 - - - -
166A THR 3.0 24.8 + - - +
167A SER* 4.2 11.3 - - - +
169A LEU* 5.4 2.6 - - - +
196A ALA 3.5 9.3 + - - +
197A ALA* 3.3 22.4 - - - +
199A LEU* 1.3 77.3 - - - +
201A ILE* 1.3 62.0 + - - +
203A GLU* 3.2 49.3 + - - +
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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