Contacts of the helix formed by residues 294 - 305 (chain B) in PDB entry 5FFO
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 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ALA 5.5 1.1 - - - -
299A LEU* 3.6 44.0 - - + -
311A GLU* 3.3 13.0 + - - +
339A ARG* 4.0 3.1 - - - +
259B PHE* 4.5 4.9 - - - -
260B GLY* 3.9 14.1 - - - +
293B PRO* 1.3 76.0 - - - +
295B ILE* 1.3 60.1 + - - +
296B GLY 3.2 5.2 + - - -
297B GLN* 3.0 38.1 + - + +
298B LEU* 2.9 32.7 + - - +
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Residues in contact with ILE 295 (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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272A MET 4.3 0.7 - - - +
273A ALA* 3.7 30.5 + - + +
301A MET* 4.2 6.5 - - - -
226B PHE* 4.6 16.2 - - + -
259B PHE* 5.2 1.4 - - + +
294B THR* 1.3 75.4 - - - +
296B GLY* 1.3 56.9 + - - +
298B LEU* 3.9 7.7 - - + +
299B ILE* 2.8 56.8 + - + +
324B TYR* 3.7 37.7 - - + -
327B LEU* 3.9 29.4 - - + -
328B ILE* 4.1 11.4 - - + -
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 5.8 0.4 + - - -
301A MET* 3.6 29.0 - - - +
311A GLU* 3.8 13.2 - - - -
337A PHE* 3.9 9.0 - - - -
294B THR* 3.2 6.7 + - - -
295B ILE* 1.3 76.1 - - - +
297B GLN* 1.3 59.7 + - - +
299B ILE* 3.4 2.4 + - - +
300B ASP* 3.0 29.1 + - - +
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLU* 3.9 7.5 + - - +
337A PHE* 4.6 10.3 - - + -
339A ARG* 2.9 32.3 - - - +
230B MET* 3.7 13.2 - - + +
271B PRO* 4.8 1.0 - - - +
272B ASN* 2.7 44.7 + - - +
274B GLY 4.9 0.2 + - - -
292B TYR 4.3 2.4 + - - -
293B PRO* 3.8 5.4 - - - +
294B THR* 3.0 38.0 + - - +
296B GLY* 1.3 73.6 - - - +
298B LEU* 1.3 62.4 + - - +
300B ASP* 3.2 8.9 + - - +
301B LYS* 3.2 25.6 + - - +
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Residues in contact with LEU 298 (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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226B PHE* 3.5 63.5 - - + +
229B ILE* 4.1 20.9 - - + -
230B MET* 3.9 24.5 - - + +
293B PRO* 4.0 6.5 - - + +
294B THR 2.9 20.9 + - - +
295B ILE* 3.9 8.3 - - + +
297B GLN* 1.3 74.1 - - - +
299B ILE* 1.3 60.3 + - + +
301B LYS 3.2 0.5 + - - -
302B LEU* 2.9 47.9 + - + +
309B LEU* 6.2 1.1 - - + -
328B ILE* 5.4 9.4 - - + -
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A MET* 3.8 21.5 - - + -
308A LYS* 6.3 2.5 - - + -
309A LEU* 3.9 15.3 - - + +
295B ILE* 2.8 44.0 + - + +
296B GLY* 3.8 4.9 - - - +
298B LEU* 1.3 76.1 - - - +
300B ASP* 1.3 62.3 + - - +
301B LYS 3.4 0.7 + - - -
302B LEU* 4.7 4.3 - - - -
303B VAL* 3.3 24.8 + - + +
327B LEU 3.5 25.1 - - - +
328B ILE* 3.9 20.2 - - + -
329B PRO* 3.9 19.1 - - + -
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Residues in contact with ASP 300 (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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337A PHE* 3.3 32.6 - - + -
296B GLY 3.0 17.7 + - - +
297B GLN* 3.2 6.7 + - - +
299B ILE* 1.3 79.5 - - - +
301B LYS* 1.3 63.6 + - + +
303B VAL* 4.5 1.6 - - - +
304B GLN* 3.2 41.5 + - - +
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Residues in contact with LYS 301 (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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230B MET* 3.9 28.0 - - + -
233B ALA* 4.4 2.9 - - + +
234B VAL* 4.0 15.8 - - + +
273B ASP 4.3 6.7 + - - -
274B GLY* 3.2 25.5 + - - +
275B LEU* 4.5 9.9 - - - +
297B GLN 3.2 15.8 + - - +
298B LEU* 3.2 2.4 + - - +
300B ASP* 1.3 82.7 - - + +
302B LEU* 1.3 60.4 + - + +
303B VAL 3.2 5.6 - - - -
304B GLN* 2.9 35.0 + - + +
305B ASN* 2.6 38.3 + - - +
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Residues in contact with LEU 302 (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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229B ILE* 4.4 16.2 - - + -
233B ALA* 3.8 21.1 - - + -
249B LEU* 5.2 0.7 - - + -
298B LEU* 2.9 33.2 + - + +
299B ILE* 4.5 3.8 - - - +
301B LYS* 1.3 76.7 - - + +
303B VAL* 1.3 61.2 + - + +
306B ASN* 3.2 1.9 - - - -
307B VAL* 2.6 68.3 + - + +
309B LEU* 4.2 25.1 - - + -
328B ILE* 3.9 28.0 - - + -
329B PRO 6.1 0.4 - - - +
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Residues in contact with VAL 303 (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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308A LYS* 5.5 8.3 - - - +
299B ILE* 3.3 21.4 + - + +
300B ASP* 5.0 1.6 - - - +
301B LYS 3.2 0.2 - - - -
302B LEU* 1.3 82.9 - - + +
304B GLN* 1.3 65.0 + - - +
305B ASN 3.0 2.0 - - - -
306B ASN* 3.0 17.9 + - - +
329B PRO* 4.3 23.1 - - + +
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Residues in contact with GLN 304 (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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236B LYS* 3.4 16.6 + - - -
300B ASP* 3.2 42.7 + - - +
301B LYS* 2.9 36.7 + - - +
303B VAL* 1.3 78.1 - - + +
305B ASN* 1.3 63.7 + - - +
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA* 2.9 39.4 + - - +
234B VAL* 3.4 15.7 - - - +
236B LYS* 3.2 30.6 + - + +
241B TRP* 5.7 2.0 - - + -
247B HIS* 3.0 20.4 + - - -
301B LYS* 2.6 27.2 + - - +
304B GLN* 1.3 84.6 - - - +
306B ASN* 1.3 72.2 + - - +
307B VAL* 3.8 10.7 - - + +
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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