Contacts of the helix formed by residues 309 - 320 (chain B) in PDB entry 1OFD
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 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B ALA 3.7 23.3 - - - -
306B LEU* 2.9 19.1 + - + +
308B ASP* 1.3 95.7 - - + +
310B PRO* 1.3 64.8 - - - +
311B GLU* 3.1 3.1 - - - -
312B ILE* 3.1 42.1 + - + +
313B SER* 3.6 4.9 + - - -
403B TYR* 3.6 36.2 - + + +
404B GLN* 5.3 0.6 + - - -
407B GLN* 3.5 36.6 - - + +
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Residues in contact with PRO 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU 4.0 2.2 - - - +
307B LYS 4.2 7.0 - - - +
308B ASP 3.3 9.9 - - - +
309B TYR* 1.3 89.8 - - - +
311B GLU* 1.3 63.1 + - + +
313B SER* 3.3 11.3 + - - +
314B ASP* 3.0 35.0 + - - +
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Residues in contact with GLU 311 (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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309B TYR 3.1 1.2 + - - -
310B PRO* 1.3 82.9 - - + +
312B ILE* 1.3 61.3 + - + +
314B ASP* 3.4 13.4 + - - +
315B PHE* 3.0 22.3 + - - +
407B GLN* 5.4 9.3 + - + +
410B ALA* 3.3 25.5 - - + +
411B GLN* 3.2 38.5 - - + +
413B TYR 5.2 2.1 - - - +
415B TYR* 5.2 0.2 - - - -
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B MET* 5.1 2.5 - - + -
298B GLU* 4.5 5.2 - - - +
306B LEU* 3.8 18.4 - - + -
309B TYR* 3.1 38.7 + - + +
311B GLU* 1.3 74.3 - - - +
313B SER* 1.3 64.8 + - - +
315B PHE* 3.3 4.2 + - - +
316B HIS* 3.1 41.5 + - + +
403B TYR* 3.7 24.5 - - + +
406B LYS* 3.8 17.3 - - + +
407B GLN* 3.7 33.7 - - + +
410B ALA* 3.8 5.4 - - + -
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.7 25.1 + - - -
306B LEU* 4.0 23.1 + - - +
309B TYR 3.6 8.5 + - - -
310B PRO* 3.3 11.0 + - - +
312B ILE* 1.3 79.2 - - - +
314B ASP* 1.3 57.3 + - - +
316B HIS 3.4 0.3 + - - -
317B ASP* 2.8 30.8 + - - +
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Residues in contact with ASP 314 (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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310B PRO* 3.0 24.1 + - - +
311B GLU* 3.5 18.0 - - + +
312B ILE 3.3 0.2 - - - -
313B SER* 1.3 76.0 - - - +
315B PHE* 1.3 57.9 + - - +
317B ASP* 3.2 11.4 + - - +
318B TYR* 2.9 30.8 + - - +
415B TYR* 3.7 6.9 - - + +
416B GLY* 3.5 36.1 + - - +
419B ILE* 3.8 2.5 - - - +
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Residues in contact with PHE 315 (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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290B GLU* 3.9 24.9 - - + -
293B MET* 3.6 31.4 - - + -
294B ILE* 3.7 19.1 - - + -
311B GLU 3.0 15.4 + - - +
312B ILE* 3.3 9.2 + - - +
314B ASP* 1.3 76.0 - - - +
316B HIS* 1.3 83.7 + + - +
318B TYR* 3.3 2.6 + - - +
319B TYR* 3.0 64.7 + + + -
409B ALA 4.5 3.8 - - - -
410B ALA* 3.8 20.0 - - + -
415B TYR* 3.4 33.8 - + + +
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Residues in contact with HIS 316 (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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293B MET* 3.4 39.0 + - + +
297B PRO* 3.6 25.6 - - + +
298B GLU* 4.2 14.9 + - + +
300B TYR* 3.5 42.8 - + + -
312B ILE* 3.1 36.5 + - + +
315B PHE* 1.3 90.9 - + - +
317B ASP* 1.3 61.8 + - - +
318B TYR 3.1 0.4 - - - -
319B TYR* 4.4 4.8 - - - +
320B SER* 2.8 34.7 + - - -
406B LYS* 5.4 1.4 - - - +
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Residues in contact with ASP 317 (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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300B TYR* 3.4 18.3 + - + +
301B LYS* 5.2 2.3 - - - -
313B SER 2.8 19.5 + - - +
314B ASP* 3.2 13.7 + - - +
316B HIS* 1.3 76.9 - - - +
318B TYR* 1.3 58.6 + - - +
320B SER* 2.9 17.5 + - - -
321B GLY 4.1 0.2 + - - -
419B ILE* 3.7 15.3 - - + +
423B ARG* 2.8 50.1 + - - -
540B LYS* 4.1 8.3 + - - -
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Residues in contact with TYR 318 (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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314B ASP 2.9 12.4 + - - +
315B PHE 3.4 7.4 - - - +
317B ASP* 1.3 75.0 - - - +
319B TYR* 1.3 84.4 + + - +
321B GLY* 3.1 13.5 + - - -
322B LEU* 3.3 39.3 - - + +
415B TYR* 3.3 37.5 - + + -
418B TRP* 3.6 21.8 - + - -
419B ILE* 3.5 15.4 - - + +
423B ARG* 4.5 2.3 + - - +
531B PRO* 3.7 5.8 - - + +
532B LYS 2.9 36.3 + - - -
535B SER* 3.5 9.2 - - - -
536B ALA* 4.1 28.7 - - + -
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Residues in contact with TYR 319 (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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286B ARG* 2.9 31.7 + - - -
293B MET 5.9 0.2 - - - +
294B ILE* 3.9 40.6 - - + +
297B PRO* 6.5 0.7 - - + -
315B PHE* 3.0 66.3 + + + +
316B HIS* 4.5 6.5 - - - +
318B TYR* 1.3 86.0 - + - +
320B SER* 1.3 57.1 + - - +
321B GLY 3.0 5.2 - - - -
322B LEU* 2.8 21.5 + - + +
323B GLN* 2.8 35.4 + - + +
415B TYR* 2.8 31.4 + + - -
527B ASN 6.0 0.2 - - - -
528B LEU* 4.7 5.4 - - + -
531B PRO* 3.4 8.1 - - + +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.9 16.3 + - - -
316B HIS 2.8 20.3 + - - -
317B ASP* 2.9 22.7 + - - -
319B TYR* 1.3 71.6 - - - +
321B GLY* 1.3 57.8 + - - +
322B LEU 3.8 0.2 + - - -
323B GLN 4.2 11.9 + - - +
324B GLU* 5.2 0.7 + - - -
521B PHE* 3.4 28.7 - - - -
540B LYS* 5.7 0.5 + - - -
722B LEU* 5.6 10.3 - - - -
724B ALA* 5.0 9.4 - - - +
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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