Contacts of the helix formed by residues 311 - 326 (chain A) in PDB entry 1O86
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 THR 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A GLY 3.6 11.9 - - - +
310A TRP* 1.3 79.5 - - - +
312A PRO* 1.3 77.3 - - - +
313A ARG* 3.4 9.6 + - - +
314A ARG* 3.0 31.3 + - + +
315A MET* 3.0 19.1 + - - +
373A VAL* 4.3 1.1 - - - -
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Residues in contact with PRO 312 (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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311A THR* 1.3 88.2 - - - +
313A ARG* 1.3 62.0 + - - +
315A MET* 3.2 15.1 + - - +
316A PHE* 3.0 29.8 + - - -
341A LEU* 3.6 23.8 - - + +
342A GLU* 3.9 32.8 - - + +
371A THR* 3.6 28.7 - - + +
373A VAL* 4.0 14.4 - - + -
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Residues in contact with ARG 313 (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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311A THR* 3.1 9.3 + - - +
312A PRO* 1.3 77.0 - - - +
314A ARG* 1.3 66.0 + - - +
316A PHE* 3.2 3.0 + - - +
317A LYS* 2.9 41.4 + - + +
336A TRP* 3.1 63.8 + - + +
341A LEU* 4.5 18.6 - - + +
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Residues in contact with ARG 314 (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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308A GLN 5.2 4.0 + - - -
309A GLY 5.2 3.4 + - - +
310A TRP* 3.0 53.8 - - + +
311A THR* 3.0 29.1 + - + +
313A ARG* 1.3 78.1 - - - +
315A MET* 1.3 58.0 + - - +
317A LYS* 3.1 12.0 + - - +
318A GLU* 2.9 61.3 + - - +
430A LEU* 4.9 4.6 + - - +
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Residues in contact with MET 315 (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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305A MET* 4.0 12.3 - - + -
310A TRP* 3.9 21.5 - - + -
311A THR 3.0 19.4 + - - +
312A PRO* 3.3 17.9 - - - +
314A ARG* 1.3 78.5 - - - +
316A PHE* 1.3 66.3 + - + +
318A GLU* 3.3 4.0 + - - +
319A ALA* 3.2 19.6 + - - +
371A THR* 3.8 12.1 - - + -
372A THR 3.4 24.2 - - - +
373A VAL* 4.1 9.0 - - - -
374A ASN 3.7 7.4 - - - +
377A ASP 3.7 6.1 - - - +
378A LEU* 3.6 48.2 - - + +
381A ALA* 4.7 5.9 - - + +
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Residues in contact with PHE 316 (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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312A PRO 3.0 25.7 + - - +
313A ARG 3.2 2.0 + - - +
315A MET* 1.3 76.7 - - + +
317A LYS* 1.3 60.7 + - - +
319A ALA* 3.3 5.3 + - - +
320A ASP* 2.8 29.3 + - - +
335A PHE* 4.6 1.3 - + + -
336A TRP* 3.8 23.2 - - + -
341A LEU* 3.7 29.4 - - + -
367A ILE* 3.6 31.2 - - + -
369A GLN* 3.4 24.5 - - - -
371A THR* 3.4 23.8 - - + -
381A ALA* 3.7 26.2 - - + -
385A MET* 3.9 23.5 - - + +
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Residues in contact with LYS 317 (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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313A ARG* 2.9 37.6 + - + +
314A ARG* 3.1 17.0 + - - +
316A PHE* 1.3 76.4 - - - +
318A GLU* 1.3 61.3 + - - +
320A ASP* 3.3 5.8 + - - +
321A ASP* 2.9 28.4 + - - +
336A TRP* 3.5 50.7 - - + +
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Residues in contact with GLU 318 (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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310A TRP* 3.7 27.8 - - + -
314A ARG* 2.9 41.8 + - - +
315A MET* 3.6 7.6 - - - +
317A LYS* 1.3 78.4 - - - +
319A ALA* 1.3 62.2 + - - +
321A ASP* 3.1 17.2 + - - +
322A PHE* 3.0 21.0 + - - +
378A LEU* 5.1 4.3 - - + -
382A HIS* 4.5 4.9 + - + -
430A LEU* 3.8 25.4 - - + +
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Residues in contact with ALA 319 (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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315A MET 3.2 9.0 + - - +
316A PHE* 3.6 9.2 - - - +
318A GLU* 1.3 76.2 - - - +
320A ASP* 1.3 64.1 + - - +
322A PHE* 3.1 12.0 + - - +
323A PHE* 3.2 21.2 + - + -
381A ALA* 4.6 1.1 - - + +
382A HIS* 3.4 42.5 + - + +
385A MET* 3.9 22.7 - - + -
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Residues in contact with ASP 320 (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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316A PHE 2.8 17.2 + - - +
317A LYS* 3.5 11.4 + - - +
319A ALA* 1.3 76.2 - - - +
321A ASP* 1.3 63.5 + - - +
323A PHE* 3.3 6.8 + - - +
324A THR* 3.1 24.3 + - - +
329A LEU 4.5 1.6 - - - +
330A PRO* 3.5 17.6 - - - +
331A VAL* 2.9 44.3 + - - +
336A TRP* 4.3 9.7 + - + -
385A MET* 3.6 11.9 - - + +
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Residues in contact with ASP 321 (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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317A LYS 2.9 14.0 + - - +
318A GLU* 3.3 20.8 - - - +
319A ALA 3.1 0.2 - - - -
320A ASP* 1.3 75.2 + - - +
322A PHE* 1.3 59.2 + - - +
324A THR* 3.0 12.2 + - - -
325A SER* 2.9 28.5 + - - -
553A TYR* 2.6 33.2 + - - -
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Residues in contact with PHE 322 (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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318A GLU 3.0 12.6 + - - +
319A ALA* 3.1 11.2 + - - +
321A ASP* 1.3 75.3 + - - +
323A PHE* 1.3 62.7 + - - +
325A SER* 2.6 25.5 + - - -
326A LEU* 3.2 11.5 + - + +
382A HIS* 4.7 3.6 - - - +
417A LEU* 3.5 35.0 - - + -
420A SER* 3.6 20.4 - - - -
421A VAL* 3.5 32.5 - - + -
426A HIS* 3.7 21.1 - + - -
552A ILE* 3.9 12.1 - - + -
553A TYR* 3.6 45.5 - + + -
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Residues in contact with PHE 323 (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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319A ALA* 3.2 28.4 + - + -
320A ASP* 3.7 9.6 - - - +
322A PHE* 1.3 79.5 - - - +
324A THR* 1.3 60.6 + - - +
326A LEU* 3.0 9.3 + - - +
328A LEU* 2.9 48.2 + - + +
329A LEU 4.3 4.3 - - - +
382A HIS* 4.4 6.3 - + - -
385A MET* 3.7 29.2 - - + -
386A GLY* 3.5 23.1 - - - -
389A GLN* 3.8 37.9 - - + +
413A ILE* 4.1 13.5 - - + -
414A GLY* 4.4 9.2 - - - -
417A LEU* 3.6 29.2 - - + -
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASP* 3.1 15.5 + - - +
321A ASP* 3.0 23.4 + - - -
323A PHE* 1.3 73.8 - - - +
325A SER* 1.3 60.9 + - - +
327A GLY* 2.8 19.8 + - - -
328A LEU 3.5 15.2 - - - +
330A PRO* 3.5 38.4 - - + -
556A LYS* 4.6 2.9 - - - -
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Residues in contact with SER 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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321A ASP* 2.9 18.0 + - - -
322A PHE* 2.6 18.6 + - - -
324A THR* 1.3 77.3 + - - +
326A LEU* 1.3 55.8 + - - +
553A TYR* 3.5 26.4 - - - -
554A GLN* 2.9 41.4 + - - -
556A LYS* 2.9 27.4 + - - +
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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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322A PHE* 3.5 14.8 - - + +
323A PHE 3.0 8.4 + - - +
324A THR 3.0 0.8 - - - -
325A SER* 1.3 79.4 + - - +
327A GLY* 1.3 59.7 + - - +
328A LEU* 4.0 15.7 - - + -
417A LEU* 3.9 36.3 - - + -
552A ILE* 3.1 42.8 - - + +
554A GLN 3.9 4.3 - - - +
555A SER* 3.3 24.2 - - - +
556A LYS* 3.8 11.2 - - - +
558A ALA* 4.5 1.8 - - + -
559A GLY* 3.3 32.6 - - - +
562A LEU* 4.6 4.0 - - + -
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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