Contacts of the helix formed by residues 339 - 352 (chain F) in PDB entry 6O81
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 SER 339 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221F GLY* 6.0 3.4 - - - -
223F ASN* 5.9 2.2 - - - -
336F TYR 5.0 4.0 + - - -
337F GLY 4.3 0.4 + - - -
338F CYS* 1.3 80.9 + - - +
340F SER* 1.3 64.6 + - - +
341F LEU* 4.3 8.1 - - - -
342F VAL* 3.3 26.5 - - - +
343F SER* 3.0 24.3 + - - -
372F THR* 3.9 5.1 - - - +
404F GLY* 4.2 11.5 - - - -
406F HIS* 5.1 10.3 - - - -
442F LYS* 6.3 0.7 - - - -
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Residues in contact with SER 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F ASN* 3.9 24.2 + - - +
339F SER* 1.3 72.7 - - - +
341F LEU* 1.3 61.6 + - - +
343F SER* 3.6 5.9 + - - -
344F ARG* 2.9 31.4 + - - +
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Residues in contact with LEU 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F ASN* 4.5 7.4 - - - +
316F ALA* 3.9 37.9 - - + +
319F ILE* 4.1 13.0 - - + -
320F SER* 4.8 0.9 - - - +
339F SER* 3.3 4.6 - - - -
340F SER* 1.3 80.6 + - - +
342F VAL* 1.3 61.8 + - + +
344F ARG* 3.4 4.7 + - + +
345F ILE* 2.9 49.7 + - + +
404F GLY* 6.6 0.2 - - - -
437F CYS* 3.6 37.5 - - + +
439F GLU* 3.6 30.5 - - - +
442F LYS* 5.6 1.6 - - - +
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Residues in contact with VAL 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F VAL* 3.7 35.0 - - + -
336F TYR 5.6 3.8 - - - +
339F SER* 3.3 25.1 + - - +
340F SER 3.4 0.4 - - - -
341F LEU* 1.3 77.9 - - + +
343F SER* 1.3 59.5 + - - +
345F ILE* 3.3 6.8 + - - +
346F LEU* 3.0 34.2 + - + +
372F THR* 5.9 4.5 - - + -
402F LEU* 3.8 22.7 - - + +
403F LEU 4.0 2.2 - - - +
404F GLY* 3.8 24.0 - - - +
437F CYS* 5.0 4.0 - - + -
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Residues in contact with SER 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F SER 3.0 16.6 + - - -
340F SER* 4.0 6.0 - - - -
341F LEU 3.4 0.4 - - - -
342F VAL* 1.3 77.9 - - - +
344F ARG* 1.3 57.8 + - - +
346F LEU* 3.8 6.9 - - - +
347F GLN* 2.9 37.5 + - - +
372F THR* 3.3 22.9 - - - +
375F SER* 3.6 25.0 + - - -
376F LEU* 5.1 5.5 - - - +
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Residues in contact with ARG 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F ILE* 5.3 1.4 - - - +
313F VAL* 4.0 24.2 + - - +
316F ALA* 3.6 33.9 - - - +
317F GLN* 3.4 35.5 - - - +
320F SER* 4.4 5.4 - - - +
340F SER 2.9 19.8 + - - +
341F LEU* 3.7 6.3 - - + +
343F SER* 1.3 73.3 - - - +
345F ILE* 1.3 60.4 + - - +
347F GLN* 3.8 9.8 - - + +
348F GLU* 2.9 52.1 + - + +
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Residues in contact with ILE 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F ILE* 3.7 26.2 - - + +
320F SER* 3.6 31.9 - - - +
323F ALA* 4.0 21.5 - - + -
327F ILE* 4.6 7.4 - - + -
341F LEU* 2.9 28.9 + - + +
342F VAL* 3.6 7.4 - - - +
344F ARG* 1.3 76.2 - - - +
346F LEU* 1.3 59.4 + - + +
348F GLU* 3.8 1.4 - - - +
349F ALA* 2.9 29.9 + - + +
402F LEU* 4.1 19.5 - - + -
437F CYS* 3.7 23.1 - - - -
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F ILE* 5.1 1.3 - - + -
333F ILE* 4.0 20.4 - - + -
335F VAL* 3.8 26.5 - - + -
342F VAL* 3.0 25.0 + - + +
343F SER* 3.9 3.8 - - - +
345F ILE* 1.3 83.7 - - + +
347F GLN* 1.3 57.4 + - - +
349F ALA* 4.5 1.6 - - - -
350F TRP* 2.9 30.5 + - - +
356F PHE* 3.7 30.7 - - + -
358F VAL* 3.8 19.5 - - + -
376F LEU* 3.8 27.4 - - + -
381F VAL* 4.7 4.3 - - + +
402F LEU* 5.0 4.0 - - + -
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Residues in contact with GLN 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F SER* 2.9 21.9 + - - +
344F ARG* 3.8 9.8 - - - +
346F LEU* 1.3 77.5 - - + +
348F GLU* 1.3 57.6 + - + +
350F TRP* 3.3 4.6 + - - +
351F THR* 2.7 36.6 + - + +
375F SER* 3.3 36.7 + - - +
376F LEU* 6.0 0.7 - - + -
378F HIS* 5.8 1.6 - - - +
379F ALA* 3.8 25.9 - - + +
381F VAL* 5.6 0.7 - - + -
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Residues in contact with GLU 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F GLN* 4.5 11.1 - - - +
320F SER* 3.3 31.6 + - - +
321F ARG* 5.4 3.5 - - - +
324F TYR* 5.5 1.6 - - + -
344F ARG* 2.9 47.1 + - + +
345F ILE 4.0 2.2 - - - +
347F GLN* 1.3 76.4 - - + +
349F ALA* 1.3 57.6 + - - +
351F THR* 3.2 8.1 + - - +
352F GLU* 2.9 40.7 + - + +
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Residues in contact with ALA 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F ALA 6.1 0.2 - - - -
324F TYR* 4.5 16.4 - - + -
327F ILE* 4.3 18.2 - - + -
345F ILE* 2.9 19.4 + - + +
346F LEU* 4.5 0.4 - - - -
348F GLU* 1.3 78.2 - - - +
350F TRP* 1.3 59.9 + - - +
352F GLU 4.3 0.3 - - - -
353F GLY 3.7 2.8 + - - -
354F ARG* 3.1 35.7 + - + +
356F PHE* 3.7 23.6 - - + -
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Residues in contact with TRP 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F LEU 2.9 19.1 + - - +
347F GLN* 3.8 3.8 - - - +
349F ALA* 1.3 79.9 - - - +
351F THR* 1.3 67.3 + - + +
352F GLU 3.7 0.2 + - - -
353F GLY 3.8 0.5 + - - -
354F ARG 3.4 13.7 - - - -
355F ARG* 3.8 45.0 + - + -
356F PHE* 3.5 42.5 - + + -
379F ALA* 3.3 27.0 + - + -
380F GLY* 3.3 20.6 + - - -
381F VAL* 3.6 22.7 - - + -
382F PRO* 3.6 16.8 - - + -
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Residues in contact with THR 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F GLN* 2.7 26.7 + - + +
348F GLU* 3.2 13.9 + - - +
350F TRP* 1.3 87.5 - - + +
352F GLU* 1.3 64.4 + - - +
353F GLY* 3.3 1.1 + - - -
379F ALA* 5.6 5.2 - - + +
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Residues in contact with GLU 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F TYR* 3.3 45.5 + - + -
348F GLU* 2.9 26.9 + - + +
349F ALA 3.8 0.4 + - - +
350F TRP 3.4 0.4 - - - -
351F THR* 1.3 81.0 + - - +
353F GLY* 1.3 56.2 + - - +
354F ARG 3.9 1.1 - - - -
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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