Contacts of the helix formed by residues 333 - 346 (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 PRO 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A VAL* 4.8 4.3 - - + -
331A GLY 3.6 4.7 - - - +
332A LEU* 1.3 93.6 - - + +
334A HIS* 1.3 66.9 + - - +
335A ASP* 3.3 4.5 - - + +
336A ARG* 3.0 36.0 + - + +
337A GLU* 3.0 19.1 + - - +
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Residues in contact with HIS 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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332A LEU 3.6 2.5 + - - -
333A PRO* 1.3 71.4 - - - +
335A ASP* 1.3 76.7 + - - +
337A GLU* 3.3 6.5 + - - +
338A ARG* 3.1 41.1 + - + +
505A GOL 3.4 39.4 - - - -
264B GLN* 5.8 0.4 - - - -
268B GLU* 5.5 3.8 - - + -
271B GLU* 2.9 33.3 + - - -
284B TYR* 3.3 20.5 + + - -
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Residues in contact with ASP 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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333A PRO* 3.3 3.7 - - + +
334A HIS* 1.3 97.3 - - - +
336A ARG* 1.3 66.4 + - + +
338A ARG* 3.5 9.2 + - - +
339A ALA* 3.2 20.4 + - - +
271B GLU* 4.2 6.8 - - - +
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Residues in contact with ARG 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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295A VAL* 4.5 8.9 + - - +
298A THR* 2.7 34.3 + - - -
299A ASP 2.8 27.3 + - - -
300A GLN* 3.2 41.1 + - - +
301A ARG 4.9 2.0 - - - +
302A THR 3.7 2.8 - - - +
303A GLY* 3.9 7.5 - - - +
332A LEU* 3.8 21.0 - - + +
333A PRO* 3.0 32.7 + - + +
335A ASP* 1.3 78.3 - - + +
337A GLU* 1.3 60.4 + - - +
339A ALA* 3.2 8.3 + - - +
340A LEU* 2.9 27.4 + - - +
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Residues in contact with GLU 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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326A PRO 3.9 7.4 - - - +
327A LEU* 3.8 17.9 - - + +
330A GLY* 4.4 2.6 - - - -
332A LEU* 3.9 28.6 - - + +
333A PRO 3.0 14.9 + - - +
334A HIS* 3.8 6.6 - - - +
336A ARG* 1.3 75.5 - - - +
338A ARG* 1.3 60.5 + - + +
340A LEU* 3.3 2.1 + - - +
341A LEU* 2.9 37.5 + - + +
395A ARG* 2.8 44.2 + - - -
397A TRP* 3.7 11.7 - - - -
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Residues in contact with ARG 338 (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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334A HIS* 3.1 50.3 + - + +
335A ASP* 3.7 12.9 + - - +
337A GLU* 1.3 74.4 - - + +
339A ALA* 1.3 58.0 + - - +
341A LEU* 3.4 4.6 + - + -
342A LYS* 3.0 27.3 + - - +
512A GLY* 3.2 37.6 + - - +
268B GLU* 4.4 5.3 + - - +
271B GLU* 3.7 41.6 + - - +
272B ASP* 2.8 32.9 + - - +
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Residues in contact with ALA 339 (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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301A ARG 3.4 25.4 - - - +
302A THR* 3.6 8.7 - - - +
335A ASP 3.2 14.0 + - - +
336A ARG* 3.2 8.7 + - - +
338A ARG* 1.3 75.7 - - - +
340A LEU* 1.3 58.6 + - - +
342A LYS* 3.2 17.2 + - - +
343A LEU* 3.0 26.3 + - - +
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Residues in contact with LEU 340 (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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302A THR 3.1 17.6 + - - +
303A GLY 3.6 14.8 - - - +
304A ALA* 3.8 18.4 - - + -
323A GLN 4.1 2.7 - - - +
324A PHE* 3.6 24.9 - - + -
326A PRO* 3.9 17.7 - - + -
327A LEU* 3.6 28.0 - - + -
332A LEU* 3.8 12.6 - - + -
336A ARG 2.9 14.1 + - - +
337A GLU* 3.3 6.5 + - - +
339A ALA* 1.3 77.3 - - - +
341A LEU* 1.3 57.3 + - - +
343A LEU* 3.2 12.8 + - + +
344A LEU* 3.0 25.9 + - - +
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Residues in contact with LEU 341 (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 LEU* 3.8 27.6 - - + -
337A GLU* 2.9 27.5 + - + +
338A ARG* 3.8 6.1 - - + +
340A LEU* 1.3 76.9 - - - +
342A LYS* 1.3 58.6 + - - +
344A LEU* 3.2 12.8 + - + +
345A GLU* 2.9 34.5 + - - +
392A PHE* 5.0 0.4 - - + -
397A TRP* 3.9 31.4 - - + +
400A ARG* 3.9 43.1 - - - +
512A GLY* 4.0 16.6 - - - +
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Residues in contact with LYS 342 (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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338A ARG 3.0 15.2 + - - +
339A ALA* 3.4 17.9 - - - +
341A LEU* 1.3 78.4 - - - +
343A LEU* 1.3 61.2 + - - +
345A GLU* 3.9 5.2 - - - +
346A GLY* 3.0 23.4 + - - -
512A GLY 4.0 9.1 + - - +
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Residues in contact with LEU 343 (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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302A THR* 4.5 17.5 - - + -
304A ALA* 4.3 10.5 - - + -
323A GLN* 4.2 17.7 - - - +
324A PHE* 3.9 21.5 - - + -
339A ALA 3.0 12.7 + - - +
340A LEU* 3.2 20.2 + - + +
342A LYS* 1.3 80.0 - - - +
344A LEU* 1.3 62.9 + - - +
345A GLU 3.4 0.2 + - - -
346A GLY* 3.5 8.6 + - - -
348A ARG* 3.8 34.3 - - + +
349A PHE* 3.8 16.9 + - + +
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Residues in contact with LEU 344 (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* 3.5 46.3 - - + -
327A LEU* 4.0 7.4 - - + -
340A LEU 3.0 9.8 + - - +
341A LEU* 3.2 14.8 + - + +
343A LEU* 1.3 77.4 - - - +
345A GLU* 1.3 56.3 + - + +
349A PHE* 3.3 3.7 - - + +
350A CYS* 2.9 32.8 + - - +
360A ILE* 3.9 30.3 - - + -
388A PHE* 5.5 0.2 - - + -
392A PHE* 3.7 34.8 - - + -
511A GLY* 3.9 19.1 - - - +
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Residues in contact with GLU 345 (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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341A LEU* 2.9 19.8 + - - +
342A LYS* 4.3 3.0 - - - +
344A LEU* 1.3 76.9 - - + +
346A GLY* 1.3 61.1 + - - +
350A CYS* 4.1 6.1 - - - +
351A GLY* 3.2 19.7 + - - -
400A ARG* 2.8 25.1 + - - +
511A GLY* 2.7 39.9 + - - +
512A GLY 2.5 30.6 + - - -
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Residues in contact with GLY 346 (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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342A LYS 3.0 16.2 + - - -
343A LEU* 3.5 3.9 + - - -
344A LEU 3.4 2.0 - - - -
345A GLU* 1.3 77.2 - - - +
347A PRO* 1.3 69.9 - - - +
348A ARG 3.2 2.7 - - - -
349A PHE 3.1 14.8 + - - -
351A GLY* 2.9 21.9 + - - -
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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