Contacts of the helix formed by residues 324 - 330 (chain A) in PDB entry 5OIV
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 PHE 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A THR 4.4 1.3 - - - -
321A ALA* 3.1 25.8 + - - +
322A ALA 3.0 1.6 - - - -
323A GLN* 1.3 77.3 - - + +
325A ALA* 1.3 64.6 + - - +
326A PRO* 3.2 4.9 - - - -
327A LEU* 2.8 26.6 + - + +
328A LEU* 3.8 1.9 + - - +
340A LEU* 3.6 32.3 - - + -
343A LEU* 3.9 9.4 - - + -
344A LEU* 3.5 57.2 - - + -
349A PHE* 3.6 48.0 - + - -
360A ILE* 4.5 4.3 - - + -
388A PHE* 3.7 22.9 - + + -
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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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253A VAL 3.6 27.1 - - - +
254A PHE* 3.9 17.3 - - - -
257A ALA* 3.4 25.0 - - + +
294A VAL* 4.2 3.4 - - + -
305A ALA* 4.1 7.0 - - + -
322A ALA 3.0 17.2 + - - +
324A PHE* 1.3 75.3 - - - +
326A PRO* 1.3 66.9 - - + +
328A LEU* 3.0 16.5 + - - +
329A CYS 3.6 1.2 + - - -
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Residues in contact with PRO 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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294A VAL* 4.0 14.4 - - + -
295A VAL* 5.2 2.5 - - + -
298A THR* 3.6 28.3 - - + -
303A GLY 3.7 9.2 - - - +
305A ALA* 3.6 6.7 - - + -
323A GLN 3.3 11.7 - - - +
324A PHE* 3.2 7.4 - - - +
325A ALA* 1.3 93.8 - - + +
327A LEU* 1.3 56.5 + - - +
329A CYS* 4.0 4.9 - - - -
330A GLY* 2.9 33.7 + - - +
332A LEU* 3.6 27.1 - - + -
337A GLU* 3.9 3.0 - - - +
340A LEU* 3.9 3.1 - - + -
395A ARG* 3.8 1.0 + - - -
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Residues in contact with LEU 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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324A PHE* 2.8 34.1 + - + +
326A PRO* 1.3 78.6 - - - +
328A LEU* 1.3 61.0 + - + +
337A GLU* 3.8 27.4 - - + +
340A LEU* 3.6 26.7 - - + -
341A LEU* 3.8 26.0 - - + -
344A LEU* 4.0 11.9 - - + -
392A PHE* 3.8 29.4 - - + -
395A ARG* 2.8 32.8 + - - +
397A TRP* 3.9 10.8 - - + -
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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
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254A PHE* 3.7 32.1 - - + -
257A ALA* 4.4 7.9 - - + -
258A ILE* 4.1 21.8 - - + +
261A VAL* 3.3 18.4 - - + +
324A PHE 4.3 4.7 - - - +
325A ALA* 3.0 12.1 + - - +
327A LEU* 1.3 79.8 - - - +
329A CYS* 1.3 59.8 + - - +
387A LEU* 4.6 7.0 - - + +
388A PHE* 3.6 37.2 - - + +
391A CYS* 3.7 39.5 - - + +
392A PHE* 4.8 1.3 - - + -
394A ARG* 4.1 6.1 + - - -
395A ARG* 3.9 10.6 - - - -
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Residues in contact with CYS 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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257A ALA* 3.8 34.3 - - - +
260A SER* 3.7 20.1 + - - +
261A VAL* 3.8 7.0 - - + -
291A ARG* 3.2 29.3 + - - -
294A VAL* 3.9 23.3 - - - -
325A ALA 3.9 5.8 - - - -
326A PRO* 4.1 1.3 - - - -
328A LEU* 1.3 78.2 - - - +
330A GLY* 1.3 75.4 + - - +
394A ARG* 5.4 3.0 + - - +
395A ARG* 4.9 2.2 - - - -
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Residues in contact with GLY 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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291A ARG* 3.3 13.2 - - - +
295A VAL* 4.0 5.5 - - - +
326A PRO* 2.9 17.1 + - - +
328A LEU 3.5 1.8 - - - -
329A CYS* 1.3 89.9 - - - +
331A GLY* 1.3 59.5 + - - -
332A LEU 3.6 3.5 + - - -
337A GLU* 4.4 0.9 - - - -
395A ARG* 3.5 28.1 - - - +
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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