Contacts of the helix formed by residues 319 - 329 (chain B) in PDB entry 6FF7
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 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B GLY* 6.2 3.6 - - - -
307B VAL 4.7 5.4 - - - -
308B CYS* 3.7 24.6 - - - +
317B CYS 4.0 0.2 - - - -
318B PHE* 1.3 79.5 - - - +
320B LEU* 1.3 55.3 + - - +
321B GLY* 3.2 5.4 - - - -
322B SER* 2.8 9.6 + - - -
323B PHE* 2.5 34.0 + - - +
429B GLY* 4.4 14.0 - - - -
432B ASP* 5.4 4.3 - - - -
433B MET* 6.0 1.1 - - - -
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Residues in contact with LEU 320 (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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302B PRO* 5.3 9.8 + - + +
319B THR* 1.3 74.4 - - - +
321B GLY* 1.3 56.5 + - - +
323B PHE* 4.2 7.4 - - - +
324B ALA* 2.9 33.1 + - - +
340B ALA* 3.3 33.7 - - + +
341B LYS* 5.3 0.9 - - - -
343B LEU* 6.0 2.7 - - + -
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Residues in contact with GLY 321 (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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193B THR* 4.9 9.7 - - - -
319B THR* 3.2 3.4 - - - -
320B LEU* 1.3 78.2 - - - +
322B SER* 1.3 59.0 + - - +
324B ALA* 4.2 2.5 - - - +
325B LYS* 4.0 13.3 + - - +
337B GLN* 6.1 3.8 - - - -
340B ALA* 4.3 7.7 - - - +
432B ASP* 4.7 16.6 - - - -
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Residues in contact with SER 322 (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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317B CYS* 4.8 4.9 - - - -
318B PHE 4.6 2.5 - - - -
319B THR* 2.8 13.9 + - - +
321B GLY* 1.3 78.4 - - - +
323B PHE* 1.3 58.6 + - - +
324B ALA 3.3 0.2 - - - -
325B LYS* 3.2 21.4 + - - +
326B ILE* 3.7 5.5 + - - +
428B THR* 3.6 20.2 - - - -
429B GLY* 3.5 34.3 - - - -
432B ASP* 4.8 1.4 - - - +
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Residues in contact with PHE 323 (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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318B PHE 3.6 12.6 - - - +
319B THR 2.5 20.6 + - - +
320B LEU* 4.4 4.3 - - - -
322B SER* 1.3 69.7 - - - +
324B ALA* 1.3 60.2 + - - +
325B LYS 3.2 1.6 - - - -
326B ILE* 3.3 7.9 + - - +
327B TYR* 2.9 24.0 + - - +
373B ILE* 5.7 9.4 - - + -
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Residues in contact with ALA 324 (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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320B LEU 2.9 20.4 + - - +
321B GLY* 4.5 4.5 - - - +
322B SER 3.3 0.2 - - - -
323B PHE* 1.3 74.8 - - - +
325B LYS* 1.3 59.1 + - - +
327B TYR* 3.3 11.9 - - + +
328B ALA* 2.9 27.9 + - - +
334B ILE* 5.0 0.8 - - + +
336B TYR* 3.7 29.1 - - + +
340B ALA* 3.8 13.5 - - + +
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Residues in contact with LYS 325 (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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193B THR* 5.1 14.8 - - - -
321B GLY 4.0 8.0 + - - +
322B SER* 3.2 15.3 + - - +
323B PHE 3.2 0.8 - - - -
324B ALA* 1.3 78.4 - - - +
326B ILE* 1.3 58.3 + - - +
328B ALA* 3.1 5.3 + - - +
329B ASP* 3.0 32.9 + - - +
428B THR* 5.7 4.7 - - - -
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Residues in contact with ILE 326 (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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322B SER 3.7 6.0 + - - +
323B PHE* 3.3 9.9 + - - +
325B LYS* 1.3 75.0 - - - +
327B TYR* 1.3 64.5 + - - +
329B ASP* 4.5 3.6 - - - +
330B THR* 4.4 14.4 + - - +
423B PHE 5.3 7.9 - - - +
424B PHE* 6.1 3.1 - - - +
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Residues in contact with TYR 327 (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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323B PHE 2.9 13.7 + - - +
324B ALA* 3.3 16.6 - - + +
325B LYS 3.2 0.2 - - - -
326B ILE* 1.3 78.1 - - - +
328B ALA* 1.3 63.4 + - - +
330B THR 3.3 9.8 - - - +
332B GLY* 3.3 23.0 - - - -
334B ILE* 4.7 11.4 - - + -
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Residues in contact with ALA 328 (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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324B ALA 2.9 17.3 + - - +
325B LYS* 3.1 7.1 + - - +
327B TYR* 1.3 78.3 - - - +
329B ASP* 1.3 63.4 + - - +
330B THR 3.3 1.2 + - - -
331B PHE 4.5 0.3 + - - -
332B GLY 4.1 2.1 + - - -
333B ASP* 3.9 19.8 + - - +
334B ILE* 4.6 14.6 - - + +
335B ASN 5.5 1.8 - - - +
336B TYR* 5.2 6.3 - - + +
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Residues in contact with ASP 329 (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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325B LYS 3.0 15.3 + - - +
326B ILE* 5.2 2.0 - - - -
327B TYR 3.6 0.2 - - - -
328B ALA* 1.3 77.7 - - + +
330B THR* 1.3 58.0 + - - +
331B PHE 4.1 1.0 + - - -
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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