Contacts of the helix formed by residues 285 - 296 (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 PRO 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ALA* 3.6 27.6 - - + +
131A VAL* 5.7 0.4 - - + -
283A GLY 3.7 4.2 - - - +
284A LEU* 1.4 82.5 - - + +
286A ARG* 1.3 65.5 + - - +
287A ALA* 3.4 4.3 - - + +
288A SER* 3.1 25.6 + - - +
289A SER* 3.1 14.6 + - - -
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Residues in contact with ARG 286 (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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237A TYR* 4.5 0.2 + - - -
250A VAL* 3.9 28.1 - - - +
253A GLU* 5.0 7.1 + - - -
255A VAL* 3.5 22.4 - - - +
276A LEU* 3.8 20.1 - - - +
280A ASP* 2.8 41.9 + - - +
284A LEU 3.4 4.1 + - - -
285A PRO* 1.3 71.4 - - - +
287A ALA* 1.3 58.0 + - - +
289A SER* 3.2 6.1 + - - -
290A LEU* 2.9 52.5 + - + +
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Residues in contact with ALA 287 (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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285A PRO* 3.4 4.1 - - + +
286A ARG* 1.3 79.4 - - - +
288A SER* 1.3 57.6 + - - +
290A LEU* 3.4 13.1 + - - +
291A LYS* 3.1 25.1 + - - +
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Residues in contact with SER 288 (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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125A MET 4.4 2.0 + - - -
128A ALA* 3.4 41.0 - - - +
129A ALA* 3.6 14.4 - - - +
285A PRO* 3.1 29.4 + - - +
287A ALA* 1.3 75.5 - - - +
289A SER* 1.3 58.9 + - - +
291A LYS* 3.3 9.7 + - - +
292A ALA* 3.0 23.7 + - - +
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Residues in contact with SER 289 (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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125A MET* 3.5 39.1 + - - +
276A LEU* 3.7 21.8 - - - -
279A ALA* 3.7 12.0 - - - +
280A ASP* 5.3 0.6 + - - -
284A LEU* 3.9 8.5 + - - +
285A PRO 3.1 15.1 + - - -
286A ARG* 3.2 11.2 + - - -
288A SER* 1.3 77.8 - - - +
290A LEU* 1.3 61.9 + - - +
292A ALA 3.3 2.1 + - - -
293A LEU* 3.2 21.4 + - - +
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Residues in contact with LEU 290 (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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255A VAL* 3.6 50.0 - - + +
256A LEU* 4.2 15.8 - - + +
276A LEU* 4.2 17.0 - - + -
286A ARG* 2.9 38.2 + - + +
287A ALA* 3.7 8.3 - - - +
288A SER 3.3 0.2 - - - -
289A SER* 1.3 75.7 - - - +
291A LYS* 1.3 62.4 + - - +
293A LEU* 3.1 26.6 + - + +
294A THR* 3.4 13.9 - - - +
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Residues in contact with LYS 291 (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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128A ALA* 3.9 25.7 - - + +
287A ALA 3.1 14.8 + - - +
288A SER* 3.4 13.5 - - - +
290A LEU* 1.3 74.0 - - - +
292A ALA* 1.3 66.2 + - - +
294A THR* 2.7 30.1 + - - +
295A THR* 3.3 23.8 + - + +
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Residues in contact with ALA 292 (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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121A LEU* 4.4 3.7 - - + +
124A GLU* 3.5 16.9 - - + +
125A MET* 3.5 37.2 - - + +
128A ALA* 4.5 2.2 - - + -
288A SER 3.0 8.6 + - - +
289A SER 3.3 9.2 + - - +
291A LYS* 1.3 77.4 - - - +
293A LEU* 1.3 62.8 + - - +
295A THR* 3.2 9.2 + - - -
296A PHE* 3.1 28.2 + - - +
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Residues in contact with LEU 293 (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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121A LEU* 4.1 19.0 - - + +
125A MET* 3.6 25.8 - - + -
248A LEU* 3.8 27.4 - - + -
256A LEU* 3.8 16.6 - - + -
261A MET* 3.6 27.4 - - + +
262A LYS 4.3 2.4 + - - -
263A LEU* 5.5 0.7 + - - +
272A ALA* 3.7 29.6 - - + +
276A LEU* 4.9 5.4 - - + -
289A SER 3.2 12.7 + - - +
290A LEU* 3.1 25.3 + - + +
292A ALA* 1.3 80.6 - - - +
294A THR* 1.3 58.2 + - - +
295A THR 3.8 0.2 + - - -
296A PHE* 4.3 7.4 + - - +
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Residues in contact with THR 294 (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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256A LEU* 4.1 12.6 - - + -
260A GLU* 3.3 41.5 - - + +
261A MET* 4.4 0.2 - - - +
262A LYS* 3.6 23.5 - - - +
290A LEU 3.4 15.0 - - - +
291A LYS* 2.7 23.2 + - - +
293A LEU* 1.3 78.2 - - - +
295A THR* 1.3 66.2 + - - +
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Residues in contact with THR 295 (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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124A GLU* 5.0 8.1 + - - +
262A LYS* 3.1 25.0 + - - +
291A LYS* 3.5 31.8 + - + +
292A ALA* 3.2 16.0 + - - +
294A THR* 1.3 85.7 - - - +
296A PHE* 1.3 66.7 + - - +
297A THR* 3.3 5.2 + - - +
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Residues in contact with PHE 296 (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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117A THR* 4.2 14.6 - - + -
120A THR* 3.5 35.7 - - + -
121A LEU* 3.5 33.7 - - + -
124A GLU* 4.4 18.2 - - + -
262A LYS* 3.4 18.5 + - - +
263A LEU* 3.8 29.0 + - + +
292A ALA 3.1 10.2 + - - +
293A LEU 4.3 4.4 + - - +
294A THR 3.6 0.6 - - - -
295A THR* 1.3 77.7 + - - +
297A THR* 1.3 63.2 + - - +
298A GLY* 3.5 40.4 - - - -
299A LEU* 3.9 12.1 - - + -
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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