Contacts of the helix formed by residues 325 - 337 (chain A) in PDB entry 3RC3
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 ALA 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A PHE* 3.7 14.1 - - + -
293A ILE* 4.0 7.4 - - + +
294A GLN* 4.0 21.8 - - + -
322A GLU* 3.0 15.1 + - - +
324A ALA* 1.3 77.8 - - - +
326A ILE* 1.4 62.3 + - - +
327A ASP 3.4 1.6 - - - -
328A LEU* 3.6 5.9 + - - +
329A VAL* 3.1 26.4 + - + +
505A ILE* 3.8 22.7 - - + -
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Residues in contact with ILE 326 (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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204A PHE* 3.8 31.9 - - + -
206A SER* 3.8 16.8 - - - +
323A PRO* 3.0 24.2 + - + +
325A ALA* 1.4 77.1 - - - +
327A ASP* 1.3 70.0 + - - +
329A VAL* 3.1 2.9 + - - +
330A MSE 3.0 42.5 + - + +
340A VAL* 5.9 0.4 - - + -
342A VAL* 3.8 39.7 - - + -
344A ASP* 4.9 2.0 - - - +
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Residues in contact with ASP 327 (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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323A PRO 4.6 1.0 + - - -
324A ALA 4.7 1.6 + - - -
325A ALA 3.4 0.6 - - - -
326A ILE* 1.3 81.1 - - - +
328A LEU* 1.3 64.9 + - - +
330A MSE 3.1 25.6 + - - +
331A GLU* 2.9 28.3 + - + +
504A PRO* 3.6 35.3 - - + +
505A ILE 5.3 0.9 - - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.8 13.5 - - + -
325A ALA 3.6 8.1 + - - +
326A ILE 3.3 0.4 - - - -
327A ASP* 1.3 79.1 - - - +
329A VAL* 1.3 63.8 + - + +
331A GLU* 3.0 9.1 + - + +
332A LEU* 2.8 41.1 + - + +
505A ILE* 3.6 41.7 + - + +
506A ARG 3.7 20.2 - - - +
507A ALA 3.5 28.0 - - - +
508A ALA* 3.8 4.7 - - + +
545A GLN* 3.9 26.7 - - + +
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Residues in contact with VAL 329 (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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202A ILE* 4.1 9.6 - - + -
204A PHE* 3.9 16.6 - - + -
293A ILE* 4.1 13.2 - - + -
296A ILE* 5.7 4.0 - - + -
309A LEU* 4.3 9.9 - - + -
319A LEU* 3.7 34.5 - - + -
325A ALA* 3.1 17.9 + - + +
326A ILE 3.1 6.5 + - - +
328A LEU* 1.3 79.4 - - + +
330A MSE 1.3 58.1 + - - +
332A LEU* 4.6 4.7 - - + -
333A MSE 2.8 52.3 + - + +
340A VAL* 4.3 9.2 - - + -
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Residues in contact with MSE 330 (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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326A ILE* 3.0 26.9 + - + +
327A ASP* 3.1 29.8 + - - +
329A VAL* 1.3 73.8 - - - +
331A GLU* 1.3 61.7 + - + +
333A MSE 4.0 0.2 - - - +
334A TYR* 2.8 31.2 + - - +
340A VAL* 4.0 34.1 - - + +
342A VAL* 4.9 4.9 - - - -
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Residues in contact with GLU 331 (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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327A ASP* 2.9 25.5 + - + +
328A LEU* 3.5 16.4 - - + +
330A MSE 1.3 75.3 - - - +
332A LEU* 1.3 63.1 + - - +
334A TYR* 3.5 10.8 + - - +
335A THR* 3.4 22.5 + - - +
545A GLN* 4.6 18.4 + - + +
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Residues in contact with LEU 332 (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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296A ILE* 3.9 17.5 - - + -
306A THR* 5.5 1.6 - - + -
309A LEU* 3.6 26.0 - - + -
310A LEU* 4.8 10.4 - - + +
328A LEU* 2.8 33.7 + - + +
329A VAL* 3.7 3.8 - - - +
331A GLU* 1.3 72.1 - - - +
333A MSE 1.3 66.5 + - + +
335A THR* 2.6 30.6 + - - +
336A THR* 3.3 7.7 + - - +
508A ALA* 4.1 8.5 - - + -
545A GLN* 3.5 31.4 - - + +
546A TYR* 3.4 29.6 - - + +
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Residues in contact with MSE 333 (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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200A ARG* 4.6 3.8 - - - -
202A ILE* 3.6 26.5 - - + -
309A LEU* 3.9 28.9 - - + -
310A LEU* 5.3 2.5 - - + -
329A VAL* 2.8 45.5 + - + +
330A MSE 4.0 1.1 - - - +
332A LEU* 1.3 74.4 - - + +
334A TYR* 1.3 61.5 + - - +
336A THR* 3.0 7.0 + - - -
337A GLY* 2.8 24.6 + - - -
338A GLU* 3.1 44.8 + - + +
340A VAL* 3.4 28.5 - - + -
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Residues in contact with TYR 334 (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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330A MSE 2.8 19.5 + - - +
331A GLU* 3.5 13.7 - - - +
333A MSE 1.3 78.9 - - - +
335A THR* 1.3 68.9 + - + +
337A GLY* 3.3 11.6 + - - +
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Residues in contact with THR 335 (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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187A ILE* 6.6 0.2 - - - -
189A PRO* 3.9 21.0 - - - +
331A GLU 3.5 14.6 - - - +
332A LEU* 2.6 22.5 + - - -
334A TYR* 1.3 83.2 - - + +
336A THR* 1.3 59.9 + - - +
337A GLY 3.3 0.2 - - - -
545A GLN* 4.2 21.3 - - - +
546A TYR* 4.6 6.3 + - + +
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Residues in contact with THR 336 (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 PRO* 3.7 33.9 - - + -
196A ARG* 3.9 24.4 + - - +
310A LEU* 4.1 11.7 - - + -
332A LEU 3.3 7.3 + - - +
333A MSE 3.0 19.3 + - - -
335A THR* 1.3 78.3 - - - +
337A GLY* 1.3 62.8 + - - +
338A GLU* 2.8 33.1 + - - +
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Residues in contact with GLY 337 (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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333A MSE 2.8 7.4 + - - -
334A TYR* 3.3 12.3 + - - -
335A THR 3.3 0.6 - - - -
336A THR* 1.3 79.2 - - - +
338A GLU* 1.3 59.3 + - - +
339A GLU 4.1 0.7 + - - -
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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