Contacts of the helix formed by residues 320 - 333 (chain B) in PDB entry 1FTA
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 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B ILE* 3.8 6.0 - - - +
203B LYS 3.0 24.2 + - - -
204B LYS 3.2 12.1 - - - -
205B LYS* 3.9 0.4 - - - -
206B GLY 3.7 2.4 + - - -
259B GLY* 3.6 5.4 - - - -
260B GLY 2.8 29.2 + - - -
319B GLY* 1.3 72.0 - - - +
321B PRO* 1.3 70.1 - - - +
323B ASP* 3.0 29.5 + - - +
324B VAL* 3.0 11.8 + - - +
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Residues in contact with PRO 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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202B ILE* 4.4 4.9 - - + +
203B LYS 3.9 6.5 - - - +
204B LYS* 3.4 27.6 - - + +
292B GLY 3.7 25.1 - - - +
294B MET* 3.9 23.3 - - + +
319B GLY 3.5 4.5 - - - +
320B SER* 1.3 81.8 - - - +
322B ASP* 1.3 62.0 + - - +
324B VAL 3.6 0.3 + - - -
325B LEU* 2.9 38.0 + - + +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 2.8 59.7 + - - +
205B LYS* 4.2 23.4 - - + +
321B PRO* 1.3 78.8 - - - +
323B ASP* 1.3 65.6 + - - +
325B LEU* 3.8 14.3 - - - +
326B GLU* 3.1 25.1 + - - +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 3.7 6.7 - - - +
206B GLY 3.0 23.3 + - - -
226B TYR* 3.8 5.1 + - - +
230B LYS* 4.8 0.3 + - - -
240B TYR* 2.6 38.8 + - - -
260B GLY* 3.1 21.6 - - - +
261B ILE* 3.8 26.9 - - + +
320B SER* 3.0 12.2 + - - +
322B ASP* 1.3 75.2 - - - +
324B VAL* 1.3 64.9 + - - +
326B GLU* 3.0 19.2 + - - +
327B PHE 3.0 10.7 + - - -
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Residues in contact with VAL 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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261B ILE* 4.1 14.4 - - + -
294B MET* 3.8 36.1 - - + +
296B THR* 3.8 28.5 - - + -
317B ILE* 4.3 4.3 - - + +
318B LEU* 3.6 10.3 - - - +
319B GLY* 3.4 31.0 - - - +
320B SER 3.0 12.4 + - - +
321B PRO 4.2 0.7 - - - +
323B ASP* 1.3 73.1 - - - +
325B LEU* 1.3 57.6 + - - +
327B PHE* 3.3 3.5 + - - +
328B LEU* 3.0 27.5 + - + +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B MET* 3.7 28.5 - - + -
321B PRO* 2.9 26.2 + - + +
322B ASP* 3.8 15.9 - - - +
324B VAL* 1.3 73.1 - - - +
326B GLU* 1.3 65.0 + - - +
328B LEU* 3.5 13.4 + - + +
329B LYS* 3.1 33.9 + - - +
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Residues in contact with GLU 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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205B LYS* 4.6 14.0 + - - -
226B TYR* 4.1 7.7 - - + -
229B ARG* 3.5 32.0 + - - +
230B LYS* 2.9 37.0 + - - -
240B TYR* 4.7 0.9 + - - -
322B ASP 3.1 15.2 + - - +
323B ASP* 3.0 13.6 + - - +
325B LEU* 1.3 73.2 - - - +
327B PHE* 1.3 66.5 + - - +
329B LYS* 3.1 25.0 + - + +
330B VAL* 3.3 12.8 + - - +
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Residues in contact with PHE 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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220B ASP* 5.6 1.6 - - - -
222B ALA* 4.5 2.2 - - + -
223B VAL* 3.9 34.5 - - + -
226B TYR* 3.7 35.5 - + + -
261B ILE* 4.2 9.6 - - + -
263B LEU* 4.0 16.4 - - + -
265B PRO* 5.8 1.3 - - + -
296B THR* 4.7 1.1 - - + -
298B GLY* 4.4 4.5 - - - -
317B ILE* 3.8 38.1 - - + -
323B ASP 3.0 11.9 + - - +
324B VAL 3.5 7.6 - - - +
326B GLU* 1.3 75.7 - - - +
328B LEU* 1.3 72.9 + - + +
330B VAL* 3.0 8.6 + - + +
331B TYR* 3.0 52.0 + + + +
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Residues in contact with LEU 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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294B MET* 4.0 26.5 - - + -
296B THR* 3.7 28.0 - - + +
298B GLY* 3.6 28.3 - - - +
324B VAL* 3.0 18.3 + - + +
325B LEU* 3.6 14.8 - - + +
326B GLU 3.3 0.2 - - - -
327B PHE* 1.3 77.5 - - + +
329B LYS* 1.3 57.0 + - - +
331B TYR* 3.1 6.8 + - + +
332B GLU* 2.9 45.7 + - + +
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Residues in contact with LYS 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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229B ARG* 5.2 12.1 - - - +
325B LEU* 3.1 23.7 + - - +
326B GLU* 3.1 17.7 + - + +
328B LEU* 1.3 76.8 - - - +
330B VAL* 1.3 60.1 + - + +
332B GLU* 3.7 7.6 + - - +
333B LYS* 3.2 22.2 + - - +
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Residues in contact with VAL 330 (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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222B ALA* 3.5 27.9 - - + +
225B GLU* 3.4 25.4 - - + +
226B TYR* 3.8 19.3 - - + +
229B ARG* 4.1 34.8 - - - +
326B GLU 3.3 7.1 + - - +
327B PHE* 3.0 20.1 + - + +
329B LYS* 1.3 74.4 - - + +
331B TYR* 1.3 63.0 + - - +
333B LYS* 3.4 10.7 + - + +
334B HIS* 3.0 28.1 + - - -
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Residues in contact with TYR 331 (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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220B ASP* 4.9 9.9 - - - -
222B ALA* 3.7 15.7 - - + -
297B THR 4.4 4.3 + - - -
298B GLY* 3.4 34.3 - - - -
299B LYS* 3.5 27.4 + - + +
317B ILE* 6.4 0.2 - - + -
327B PHE* 3.0 37.4 + + + +
328B LEU* 3.3 14.1 - - + +
330B VAL* 1.3 77.1 - - - +
332B GLU* 1.3 65.3 + - + +
334B HIS* 2.8 29.8 + - - +
335B SER* 3.6 12.5 + - - -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 2.9 31.3 + - + +
329B LYS* 4.2 6.5 + - - +
331B TYR* 1.3 81.4 - - + +
333B LYS* 1.3 56.7 + - - +
334B HIS 3.1 4.1 + - - -
335B SER* 3.7 20.0 + - - -
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Residues in contact with LYS 333 (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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225B GLU* 2.9 37.5 + - - +
329B LYS 3.2 18.1 + - - +
330B VAL* 3.6 7.2 - - + +
331B TYR 3.0 1.2 + - - -
332B GLU* 1.3 75.7 - - - +
334B HIS* 1.3 75.1 + - + +
335B SER 3.7 0.7 - - - -
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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