Contacts of the helix formed by residues 329 - 344 (chain B) in PDB entry 3C6G
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 TYR 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B PHE* 3.0 47.7 + + - +
326B MET 3.5 6.1 - - - +
328B LEU* 1.3 102.7 - - + +
330B PRO* 1.3 68.1 - - - +
331B ASN* 3.0 5.5 + - + +
332B ILE* 3.0 41.6 + - + +
333B GLN 3.2 7.3 + - - -
420B PHE* 4.2 13.3 - + + +
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Residues in contact with PRO 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B MET 3.6 10.3 - - - +
327B ALA 4.1 8.5 - - - +
328B LEU 3.3 12.8 - - - +
329B TYR* 1.3 82.8 - - - +
331B ASN* 1.3 62.9 + - - +
333B GLN* 3.3 6.4 + - + +
334B GLY* 2.9 26.3 + - - -
470B HIS* 4.7 19.4 - - + -
471B LEU 5.6 1.1 - - - +
476B GLU* 5.7 4.7 - - - +
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B TYR* 3.0 2.3 + - + -
330B PRO* 1.3 79.6 - - - +
332B ILE* 1.3 67.0 + - + +
334B GLY* 3.5 1.5 + - - -
335B GLN* 3.2 33.7 + - - +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B MET* 3.8 17.0 - - + -
329B TYR* 3.0 31.7 + - + +
331B ASN* 1.3 77.8 - - + +
333B GLN* 1.3 61.9 + - - +
335B GLN* 3.6 2.5 + - - +
336B VAL* 3.3 21.8 + - - +
360B TYR* 3.6 25.5 - - - +
364B VAL* 3.7 22.9 - - + -
420B PHE* 3.8 25.6 - - + +
422B PRO* 3.9 16.2 - - + -
423B GLU* 5.5 1.8 - - - +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B MET* 3.0 47.5 + - + +
329B TYR 3.2 5.1 + - - -
330B PRO* 3.4 10.2 - - - +
331B ASN 3.2 0.2 - - - -
332B ILE* 1.3 74.1 - - - +
334B GLY* 1.3 53.7 + - - +
336B VAL* 3.1 7.0 + - - +
337B GLN* 2.9 63.3 + - - +
466B LEU* 3.8 20.3 - - + +
470B HIS* 3.3 14.5 + - - -
471B LEU* 3.0 42.4 + - - +
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B PRO 2.9 16.3 + - - -
331B ASN* 3.9 2.2 - - - -
332B ILE 3.4 0.2 - - - -
333B GLN* 1.3 75.9 - - - +
335B GLN* 1.3 54.5 + - - +
337B GLN* 3.3 13.4 + - - +
338B LYS* 2.8 31.1 + - - +
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Residues in contact with GLN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ASN* 3.2 21.4 + - - +
332B ILE* 3.7 4.1 - - - +
333B GLN 3.3 0.2 - - - -
334B GLY* 1.3 76.4 - - - +
336B VAL* 1.3 63.2 + - - +
338B LYS* 3.3 12.2 + - + +
339B GLU* 3.0 22.3 + - - +
360B TYR* 3.2 53.1 + - + +
423B GLU* 4.0 8.4 + - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B MET* 4.9 1.3 - - - -
332B ILE 3.3 12.5 + - - +
333B GLN* 3.1 9.5 + - - +
335B GLN* 1.3 77.8 - - - +
337B GLN* 1.3 51.5 + - - +
339B GLU* 3.0 5.6 + - - +
340B ILE* 2.8 46.1 + - + +
360B TYR* 3.8 17.7 - - + -
361B THR* 3.9 25.8 - - + +
364B VAL* 3.9 18.8 - - + -
462B PHE* 3.9 16.4 - - + -
466B LEU* 3.8 25.8 - - + -
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Residues in contact with GLN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B GLN* 2.9 55.1 + - - +
334B GLY* 3.6 10.8 + - - +
336B VAL* 1.3 71.2 - - - +
338B LYS* 1.3 57.1 + - - +
340B ILE* 3.7 6.4 - - - +
341B ASP* 2.8 37.7 + - - +
466B LEU* 3.1 29.4 + - + +
469B PHE 3.0 28.3 + - - -
470B HIS* 3.9 5.8 + - - +
501B ARG* 3.6 29.0 - - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLY 2.8 21.2 + - - +
335B GLN* 3.5 12.1 - - + +
336B VAL 3.2 0.2 - - - -
337B GLN* 1.3 71.2 - - - +
339B GLU* 1.3 65.8 + - - +
341B ASP* 3.8 6.2 - - - +
342B LEU* 3.1 46.0 + - + +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B GLN 3.0 11.3 + - - +
336B VAL* 3.0 8.6 + - - +
338B LYS* 1.3 79.0 - - - +
340B ILE* 1.3 61.7 + - - +
342B LEU* 5.0 2.0 - - - -
343B ILE* 3.0 37.3 + - + +
357B LYS 4.7 0.7 - - - +
358B MET* 3.1 40.7 - - + -
359B PRO* 3.7 8.4 - - - +
360B TYR* 3.2 26.3 + - - +
361B THR* 2.9 29.7 + - - +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 2.8 31.1 + - + +
337B GLN* 3.7 9.9 - - - +
339B GLU* 1.3 72.2 - - - +
341B ASP* 1.3 60.5 + - - +
344B MET* 3.0 37.5 + - - +
345B GLY 3.0 6.3 + - - +
358B MET* 3.8 20.8 - - + +
463B THR* 3.5 31.9 - - + +
466B LEU* 3.8 15.7 - - + -
467B GLN* 3.6 49.8 - - + +
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Residues in contact with ASP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B GLN 2.8 20.0 + - - +
338B LYS* 3.8 8.4 - - - +
339B GLU 3.2 0.2 - - - -
340B ILE* 1.3 81.3 - - - +
342B LEU* 1.3 61.8 + - + +
345B GLY* 3.0 28.9 - - - -
346B PRO* 3.5 25.0 - - + +
467B GLN* 5.5 0.2 - - - -
501B ARG* 2.8 39.2 + - - -
502B HIS* 3.6 15.6 + - - -
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B LYS* 3.1 43.0 + - + +
339B GLU* 4.3 2.7 - - - +
341B ASP* 1.3 81.5 - - + +
343B ILE* 1.3 72.5 + - + +
345B GLY* 4.4 1.1 - - - -
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLU* 3.0 24.6 + - + +
342B LEU* 1.3 89.4 - - + +
344B MET* 1.3 63.8 + - - +
345B GLY 3.5 0.2 - - - -
354B ASP* 4.3 16.7 - - + +
357B LYS* 3.6 39.9 - - + +
358B MET* 3.7 26.9 - - + -
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Residues in contact with MET 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B ILE* 3.0 32.8 + - + +
343B ILE* 1.3 77.6 - - - +
345B GLY* 1.3 63.9 + - - +
348B GLY* 3.3 23.5 - - - +
349B LYS 5.2 0.9 - - - +
350B PRO* 3.7 28.7 - - + -
351B SER 3.8 0.2 - - - +
354B ASP* 3.3 28.0 - - + +
358B MET* 3.6 21.1 - - - +
459B PHE* 3.6 32.5 - - + -
463B THR* 3.7 16.4 - - - +
467B GLN* 4.2 4.9 - - - +
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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