Contacts of the helix formed by residues 359 - 374 (chain A) in PDB entry 2COI
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A PHE* 3.6 33.4 - - + -
327A GLU* 3.0 24.5 - - + +
339A PRO* 4.5 2.9 - - + -
354A THR* 3.7 16.8 - - + +
355A MET* 4.0 23.8 - - + -
357A ASN 3.4 6.3 - - - +
358A GLY* 1.3 78.8 - - - +
360A LYS* 1.3 57.7 + - - +
361A LEU 3.5 1.3 - - - -
362A ALA* 3.6 11.0 - - + -
363A SER* 2.6 39.7 + - - +
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Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 5.9 2.0 - - + -
327A GLU* 3.3 2.4 + - - +
357A ASN 3.1 15.3 + - - +
358A GLY* 3.3 5.3 - - - -
359A PRO* 1.3 70.1 - - - +
361A LEU* 1.3 64.7 + - - +
363A SER* 3.2 4.5 + - - -
364A ARG* 2.9 26.0 + - - +
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Residues in contact with LEU 361 (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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266A TYR* 3.3 32.0 - - + -
276A LEU* 4.4 13.0 - - + -
301A TRP* 4.3 10.3 - - + -
304A PHE* 3.9 28.5 - - + -
327A GLU* 2.8 21.1 + - - +
329A PHE* 3.6 22.4 - - + -
360A LYS* 1.3 74.4 - - - +
362A ALA* 1.3 55.2 + - - +
364A ARG* 3.2 10.8 + - - +
365A ILE* 2.9 67.0 + - + +
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Residues in contact with ALA 362 (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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199A PHE* 4.0 5.1 - - + -
327A GLU* 2.8 22.0 + - - +
329A PHE* 4.4 11.2 - - + -
337A VAL* 3.8 29.6 - - + +
339A PRO* 4.8 4.7 - - + -
354A THR* 5.7 0.7 - - + -
359A PRO* 3.6 18.6 - - + -
360A LYS 3.3 0.2 - - - -
361A LEU* 1.3 76.6 - - - +
363A SER* 1.3 62.9 + - - +
365A ILE* 3.6 4.1 + - - +
366A LEU* 3.1 22.7 + - - +
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.6 22.2 - - - -
358A GLY 4.7 1.2 - - - -
359A PRO* 2.6 33.6 + - - +
360A LYS* 3.7 4.9 - - - -
362A ALA* 1.3 69.8 - - - +
364A ARG* 1.3 67.1 + - - +
366A LEU* 3.2 5.8 + - - +
367A SER* 3.0 28.8 + - - -
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Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TRP* 3.4 56.9 - - + +
303A GLU* 2.6 45.7 + - - +
304A PHE* 5.0 4.9 - - - -
360A LYS 2.9 18.2 + - - +
361A LEU* 3.4 10.9 - - - +
363A SER* 1.3 77.5 - - - +
365A ILE* 1.3 62.0 + - - +
367A SER* 3.2 7.7 + - - -
368A LYS* 3.0 23.1 + - + +
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Residues in contact with ILE 365 (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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276A LEU* 5.1 2.2 - - + -
294A ILE* 3.8 37.7 - - + +
297A LEU* 4.9 6.1 - - + -
301A TRP* 4.3 15.0 - - + -
329A PHE* 3.7 17.5 - - + -
337A VAL* 3.8 18.4 - - + -
361A LEU* 2.9 53.4 + - + +
362A ALA 3.8 4.9 - - - +
364A ARG* 1.3 74.6 - - - +
366A LEU* 1.3 63.2 + - - +
368A LYS* 3.5 5.4 + - - +
369A LEU* 3.1 31.2 + - + +
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Residues in contact with LEU 366 (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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199A PHE* 4.0 26.5 - - + +
335A CYS 4.7 2.0 - - - +
336A VAL* 3.6 35.2 - - + -
337A VAL* 4.2 12.5 - - + +
362A ALA 3.1 14.6 + - - +
363A SER* 3.2 9.2 + - - +
365A ILE* 1.3 75.3 - - - +
367A SER* 1.3 57.2 + - - +
369A LEU* 4.0 0.2 - - - -
370A THR* 2.5 49.4 + - - +
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A SER* 3.0 15.5 + - - -
364A ARG* 3.6 8.9 - - - -
366A LEU* 1.3 77.6 - - - +
368A LYS* 1.3 55.6 + - - +
370A THR* 3.2 4.6 + - - -
371A ASP* 2.7 52.4 + - - +
376A ARG* 5.8 0.2 - - - +
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Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.4 42.2 - - + -
300A GLN* 4.9 5.9 + - - -
301A TRP* 4.2 19.5 - - + +
364A ARG* 3.0 16.6 + - + +
365A ILE* 3.7 5.8 - - - +
367A SER* 1.3 78.2 - - - +
369A LEU* 1.3 63.2 + - - +
371A ASP* 3.2 6.8 + - - +
372A ILE* 3.1 28.1 + - + +
377A GLU* 3.0 38.2 + - - +
379A ARG* 3.9 9.2 - - - +
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Residues in contact with LEU 369 (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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111A PHE* 4.0 12.3 - - + -
290A THR* 4.3 19.7 - - + -
293A CYS* 4.0 13.0 - - + -
294A ILE* 4.3 3.6 - - + -
297A LEU* 4.1 11.0 - - + -
336A VAL* 3.7 29.4 - - + -
337A VAL* 4.8 0.4 - - + -
365A ILE* 3.1 29.6 + - + +
366A LEU 4.1 1.8 - - - +
368A LYS* 1.3 78.1 - - - +
370A THR* 1.3 59.1 + - - +
372A ILE* 3.1 6.9 + - - +
373A GLN* 2.8 42.4 + - - +
381A TRP* 3.7 29.6 - - + -
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Residues in contact with THR 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 4.8 4.7 - - - +
336A VAL* 5.9 0.2 - - - +
366A LEU* 2.5 45.8 + - - +
367A SER* 3.6 4.9 - - - -
369A LEU* 1.3 73.1 - - - +
371A ASP* 1.3 62.8 + - - +
373A GLN* 3.2 12.9 + - - -
374A TYR* 3.0 46.5 + - + +
376A ARG* 3.3 19.5 + - - +
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Residues in contact with ASP 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 2.7 38.7 + - - +
368A LYS* 3.4 7.5 + - - +
370A THR* 1.3 72.6 - - - +
372A ILE* 1.3 62.8 + - - +
375A GLY 3.4 0.9 + - - -
376A ARG* 2.8 67.1 + - - +
377A GLU* 3.3 28.0 + - + +
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Residues in contact with ILE 372 (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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109A ARG* 4.9 0.3 - - - -
111A PHE* 4.1 5.6 - - + -
368A LYS* 3.1 24.5 + - + +
369A LEU* 3.5 7.6 - - - +
371A ASP* 1.3 76.8 - - - +
373A GLN* 1.3 63.0 + - - +
375A GLY* 3.7 6.9 + - - -
377A GLU* 3.5 32.1 - - - +
379A ARG* 3.5 42.4 - - + +
381A TRP* 3.7 37.5 - - + -
382A THR* 3.1 30.4 + - + +
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Residues in contact with GLN 373 (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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101A PHE* 3.1 68.0 - - + +
109A ARG* 4.2 14.6 - - - +
111A PHE* 4.0 30.8 - - + -
333A THR 5.8 1.8 + - - -
336A VAL* 4.7 18.9 - - - +
369A LEU* 2.8 35.3 + - - +
370A THR* 3.6 16.8 + - - +
372A ILE* 1.3 79.5 - - - +
374A TYR* 1.3 62.5 + - + +
375A GLY 3.3 3.2 + - - -
382A THR* 4.3 5.7 - - - +
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Residues in contact with TYR 374 (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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101A PHE* 3.3 35.5 - + + -
102A ARG 3.7 22.4 - - - -
103A GLY* 2.9 12.3 - - - -
104A VAL* 2.8 28.2 + - + +
153A PRO 6.1 0.4 - - - -
155A SER 4.5 1.3 - - - -
156A THR* 3.2 38.3 + - - +
157A SER* 3.7 2.8 - - - -
158A ALA 2.5 36.3 + - - -
159A SER* 4.2 0.2 - - - -
370A THR* 3.0 35.1 + - + +
373A GLN* 1.3 79.5 - - + +
375A GLY* 1.3 54.2 + - - +
376A ARG* 3.2 30.5 + - - +
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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