Contacts of the helix formed by residues 322 - 331 (chain A) in PDB entry 3RI4
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 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A PRO* 3.5 23.3 - - + +
320A VAL 3.3 10.1 - - - +
321A ILE* 1.3 86.3 - - - +
323A ALA* 1.3 66.6 + - - +
324A ALA* 4.7 3.4 - - + +
325A ALA* 4.0 16.6 - - + +
326A LEU* 3.0 21.7 + - - +
343A GLU* 3.2 10.5 - - - +
304D PHE* 3.8 13.6 - - + -
308D VAL* 5.8 3.4 - - + -
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE 3.3 2.9 + - - -
322A PRO 1.3 65.3 - - - -
324A ALA* 1.3 65.1 + - - +
326A LEU* 2.9 8.5 + - - +
327A ALA 2.8 21.0 + - - -
335A ILE* 2.9 31.6 - - + +
339A GLN 4.1 6.3 - - - +
340A PHE* 4.0 13.2 - - - -
343A GLU* 2.2 41.9 + - + +
378A ARG* 3.6 10.3 - - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 4.6 3.1 - - + +
323A ALA* 1.3 77.7 - - - +
325A ALA* 1.3 61.8 + - - +
327A ALA* 3.5 4.7 + - - +
328A GLY* 3.1 17.2 + - - -
335A ILE* 3.2 9.5 - - - +
343A GLU* 4.0 1.4 + - - -
378A ARG* 4.3 8.3 - - - +
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Residues in contact with ALA 325 (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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322A PRO* 3.4 19.3 + - + +
323A ALA 3.1 0.8 - - - -
324A ALA* 1.3 75.5 - - - +
326A LEU* 1.3 57.1 + - - +
328A GLY* 2.9 4.5 + - - -
329A TYR 2.8 31.2 + - - -
304D PHE* 3.1 25.5 - - + -
307D TYR* 3.6 9.0 - - + -
308D VAL* 5.0 7.2 - - + -
317D ASP* 5.4 8.1 - - - +
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Residues in contact with LEU 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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321A ILE* 4.0 21.1 - - + -
322A PRO 3.0 13.7 + - - +
323A ALA* 2.9 10.4 + - - +
325A ALA* 1.3 74.1 - - - +
327A ALA* 1.3 58.5 + - - +
329A TYR* 3.0 4.0 + - + +
330A THR* 2.8 41.0 + - + +
338A TRP* 3.8 21.1 - - + -
339A GLN* 3.3 42.8 - - + +
342A LEU* 4.8 2.7 - - + -
421A LEU* 5.2 3.6 - - + -
422A LEU* 4.2 13.7 - - + -
304D PHE* 3.1 33.8 - - + -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ALA 2.8 4.6 + - - -
324A ALA* 3.6 7.0 - - - +
326A LEU* 1.3 77.1 - - - +
328A GLY* 1.3 57.0 + - - +
330A THR* 3.6 1.1 - - - -
331A GLY* 2.8 24.4 + - - -
332A SER* 3.0 29.9 + - - +
333A GLY 3.6 19.0 + - - +
335A ILE* 3.6 26.5 - - + +
339A GLN* 3.9 5.3 - - - +
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Residues in contact with GLY 328 (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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324A ALA 3.1 10.3 + - - -
325A ALA* 2.9 8.6 + - - -
327A ALA* 1.3 78.3 - - - +
329A TYR* 1.3 63.0 + - - +
331A GLY* 3.1 13.1 + - - -
307D TYR* 3.8 16.5 + - - -
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Residues in contact with TYR 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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325A ALA 2.8 8.9 + - - -
326A LEU* 3.0 5.6 + - + +
328A GLY* 1.3 75.1 - - - +
330A THR* 1.3 71.9 + - + +
331A GLY 3.6 0.2 + - - -
420A SER 4.9 3.1 + - - -
421A LEU* 4.4 22.2 - - + +
302D GLY 2.4 29.4 + - - -
303D THR* 3.0 28.8 - - - -
304D PHE* 3.3 40.8 - + + -
307D TYR* 3.3 37.7 - + + -
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Residues in contact with THR 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 LEU* 2.8 35.2 + - + +
327A ALA 3.3 0.5 + - - -
329A TYR* 1.3 89.5 - - + +
331A GLY* 1.3 62.8 + - - +
332A SER* 3.2 24.5 + - - -
338A TRP* 5.0 4.7 - - + -
339A GLN* 3.3 9.8 + - - +
421A LEU* 4.6 17.3 - - + -
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Residues in contact with GLY 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 ALA 2.8 12.2 + - - -
328A GLY* 3.1 11.6 + - - -
329A TYR 3.3 0.4 + - - -
330A THR* 1.3 79.6 - - - +
332A SER* 1.3 58.1 - - - -
333A GLY 3.3 3.2 + - - -
114C T 5.1 11.4 + - - +
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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