Contacts of the helix formed by residues 359 - 374 (chain B) in PDB entry 2COJ
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 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B PHE* 3.8 18.6 - - + -
327B GLU* 3.0 24.0 - - + +
339B PRO* 4.8 1.6 - - + -
354B THR* 3.5 17.0 - - + +
355B MET* 3.6 30.3 - - + -
357B ASN 3.3 7.6 - - - +
358B GLY* 1.3 78.9 - - - +
360B LYS* 1.3 66.4 + - - +
361B LEU 3.5 1.1 - - - -
362B ALA* 3.5 18.4 - - + -
363B SER* 2.9 27.4 + - - +
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR* 5.8 3.1 - - + -
327B GLU* 3.4 4.3 + - - +
357B ASN 2.9 24.2 + - - +
358B GLY* 3.4 4.6 - - - -
359B PRO* 1.3 71.8 - - - +
361B LEU* 1.3 58.3 + - - +
363B SER* 3.6 4.1 - - - -
364B ARG* 3.0 28.0 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B TYR* 3.6 43.3 - - + -
276B LEU* 4.0 20.2 - - + -
301B TRP* 4.1 13.0 - - + -
304B PHE* 3.9 29.2 - - + -
327B GLU* 2.8 21.0 + - - +
329B PHE* 4.5 3.4 - - + -
360B LYS* 1.3 72.6 - - - +
362B ALA* 1.3 66.4 + - - +
364B ARG* 3.6 11.7 - - - +
365B ILE* 2.8 51.6 + - + +
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Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PHE* 3.9 12.3 - - + -
327B GLU* 2.8 22.5 + - - +
329B PHE* 4.4 26.0 - - + -
337B VAL* 3.8 8.9 - - + +
339B PRO* 5.2 4.5 - - + -
354B THR* 5.7 0.4 - - + -
359B PRO* 3.5 20.4 - - + -
360B LYS 3.4 0.2 - - - -
361B LEU* 1.3 73.2 - - - +
363B SER* 1.3 58.1 + - - +
365B ILE* 3.5 6.5 + - - +
366B LEU* 3.0 28.2 + - - +
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Residues in contact with SER 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 3.7 19.8 - - - -
358B GLY 5.0 1.2 - - - -
359B PRO* 2.9 24.0 + - - +
360B LYS* 3.6 4.0 - - - -
362B ALA* 1.3 74.8 - - - +
364B ARG* 1.3 56.7 + - - +
366B LEU* 3.1 5.6 + - - +
367B SER* 2.7 38.4 + - - -
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 3.7 54.1 - - + +
303B GLU* 2.7 43.0 + - - +
304B PHE* 5.1 6.9 - - - -
360B LYS 3.0 17.2 + - - +
361B LEU* 3.2 13.4 + - + +
363B SER* 1.3 75.0 - - - +
365B ILE* 1.3 57.7 + - - +
367B SER* 3.4 6.7 + - - -
368B LYS* 2.8 30.5 + - - +
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU* 5.8 0.4 - - + -
294B ILE* 3.8 31.2 - - + -
297B LEU* 5.3 4.5 - - + -
301B TRP* 4.5 12.6 - - + -
329B PHE* 3.6 31.2 - - + -
337B VAL* 3.8 11.7 - - + -
361B LEU* 2.8 42.4 + - + +
362B ALA* 3.6 4.5 - - - +
364B ARG* 1.3 73.0 - - - +
366B LEU* 1.3 67.6 + - - +
368B LYS* 3.1 6.7 + - - +
369B LEU* 2.9 45.2 + - + +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PHE* 3.5 31.0 - - + -
335B CYS 4.6 4.3 - - - +
336B VAL* 4.0 27.8 - - + -
337B VAL* 3.7 11.0 - - + -
362B ALA 3.0 17.6 + - - +
363B SER* 3.6 4.5 - - - +
365B ILE* 1.3 77.7 - - - +
367B SER* 1.3 56.3 + - - +
370B THR* 2.7 55.4 + - + +
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Residues in contact with SER 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B SER 2.7 22.3 + - - -
364B ARG* 3.5 7.9 - - - -
366B LEU* 1.3 77.2 - - - +
368B LYS* 1.3 60.1 + - - +
370B THR* 3.3 3.8 + - - -
371B ASP* 2.7 43.0 + - - +
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Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.7 37.2 - - + -
300B GLN* 5.7 3.6 + - - -
301B TRP* 4.3 20.2 - - + +
364B ARG 2.8 18.4 + - - +
365B ILE 3.1 4.0 + - - +
367B SER* 1.3 76.8 - - - +
369B LEU* 1.3 64.0 + - - +
371B ASP* 3.1 7.3 + - + +
372B ILE* 3.0 35.6 + - + +
377B GLU* 2.9 40.1 + - - +
379B ARG* 4.6 4.7 - - - +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 4.2 19.2 - - + -
290B THR* 4.2 18.2 - - + -
293B CYS* 4.1 24.7 - - + -
294B ILE* 4.3 5.6 - - + -
297B LEU* 4.1 16.6 - - + -
336B VAL* 3.5 33.0 - - + -
365B ILE* 2.9 37.5 + - + +
366B LEU 4.1 0.2 - - - +
368B LYS* 1.3 74.4 - - - +
370B THR* 1.3 58.1 + - - +
372B ILE* 3.2 6.9 + - + +
373B GLN* 2.9 38.1 + - - +
381B TRP* 4.3 5.8 - - + -
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B THR 5.4 2.0 - - - +
336B VAL* 4.8 6.3 - - + -
366B LEU* 2.7 46.4 + - + +
367B SER* 3.3 7.1 + - - -
369B LEU* 1.3 72.7 - - - +
371B ASP* 1.3 68.2 + - - +
373B GLN* 3.3 17.9 - - - +
374B TYR* 2.9 44.5 + - + +
376B ARG* 3.8 16.1 + - - -
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Residues in contact with ASP 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B SER* 2.7 35.6 + - - +
368B LYS* 3.3 9.3 - - + +
370B THR* 1.3 77.2 + - - +
372B ILE* 1.3 58.6 + - - +
376B ARG* 2.8 67.8 + - + +
377B GLU* 3.1 20.9 + - + +
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 4.0 14.1 - - + -
368B LYS* 3.0 31.4 + - + +
369B LEU* 3.5 9.4 - - - +
370B THR 3.0 0.4 - - - -
371B ASP* 1.3 76.8 - - - +
373B GLN* 1.3 65.1 + - - +
375B GLY* 3.2 11.8 + - - -
377B GLU* 3.9 35.1 - - + +
379B ARG* 3.8 35.0 - - + +
381B TRP* 4.1 25.6 - - + -
382B THR* 3.2 26.7 + - + +
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Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 5.5 0.8 - - - +
101B PHE* 3.2 63.6 - - + +
109B ARG* 4.1 16.6 - - - +
111B PHE* 3.8 32.6 - - + -
333B THR* 5.6 2.8 + - - +
336B VAL* 4.6 16.3 - - - +
369B LEU* 2.9 24.6 + - - +
370B THR* 3.0 28.5 + - - +
372B ILE* 1.3 78.1 - - - +
374B TYR* 1.3 58.8 + - + +
375B GLY 3.2 3.2 + - - -
382B THR* 4.2 7.9 - - - +
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Residues in contact with TYR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.6 32.3 - + + -
102B ARG 3.3 23.1 - - - -
103B GLY* 3.1 11.7 - - - -
104B VAL* 3.1 25.1 + - + +
105B ASP* 5.5 0.2 - - - -
109B ARG* 3.9 0.6 + - - -
155B SER 3.5 18.4 - - - -
156B THR* 3.1 33.7 + - + -
157B SER 3.9 1.2 - - - -
158B ALA 2.6 31.1 + - - -
159B SER* 4.5 0.2 - - - -
370B THR* 2.9 45.4 + - + +
373B GLN* 1.3 75.2 - - + +
375B GLY* 1.3 63.8 + - - +
376B ARG* 3.1 27.0 + - - +
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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